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Parent(s):
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Upload 3 files
Browse files- test.jsonl +25 -0
- train.jsonl +139 -0
- val.jsonl +21 -0
test.jsonl
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| 1 |
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{"Unnamed: 0": 135, "Gene1": "sigmaB", "Gene2": "yvyD", "Keywords": "dependent, inducible", "Direct dependency relations": "-1", "INO Type": "induction", "INO ID": "INO_0000122", "Num. Keywords": 2, "Sentence": "In addition to the typical [PROTEIN1] sigmaB [/PROTEIN1]-dependent, stress- and starvation-inducible pattern, [PROTEIN2] yvyD [/PROTEIN2] is also induced in response to amino acid depletion."}
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{"Unnamed: 0": 115, "Gene1": "sigma(X)", "Gene2": "ypuN", "Keywords": "recognize, promoter ", "Direct dependency relations": "-1", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": 2, "Sentence": "We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both sigma(A) and [PROTEIN1] sigma(X) [/PROTEIN1] holoenzymes recognize promoter elements within the sigX-[PROTEIN2] ypuN [/PROTEIN2] control region."}
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{"Unnamed: 0": 131, "Gene1": "sigmaH", "Gene2": "yvyD", "Keywords": "dependent, drives, expression, promoter", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of transcription by binding to promoter", "INO ID": "INO_0000072", "Num. Keywords": 4, "Sentence": "The sigmaB-dependent promoter drives expression of yvyD under stress conditions and after glucose starvation, whereas a [PROTEIN1] sigmaH [/PROTEIN1]-dependent promoter is responsible for [PROTEIN2] yvyD [/PROTEIN2] transcription following amino acid limitation."}
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{"Unnamed: 0": 55, "Gene1": "sigmaB", "Gene2": "ydaG", "Keywords": "dependent", "Direct dependency relations": "ONE WORD", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 1, "Sentence": "Three new [PROTEIN1] sigmaB [/PROTEIN1]-dependent genes (ydaE, [PROTEIN2] ydaG [/PROTEIN2] and yfkM) encoding proteins with still unknown functions were also described."}
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{"Unnamed: 0": 95, "Gene1": "sigma(K)", "Gene2": "cotC", "Keywords": "transcription", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": 1, "Sentence": "Transcription of the cotB, cotC, and [PROTEIN2] cotX [/PROTEIN2] genes by final [PROTEIN1] sigma(K) [/PROTEIN1] RNA polymerase is activated by a small, DNA-binding protein called GerE."}
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{"Unnamed: 0": 29, "Gene1": "RocR", "Gene2": "rocG", "Keywords": "requires, expression", "Direct dependency relations": "-1", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "The [PROTEIN2] rocG [/PROTEIN2] gene of Bacillus subtilis, encoding a catabolic glutamate dehydrogenase, is transcribed by SigL-containing RNA polymerase and requires for its expression [PROTEIN1] RocR [/PROTEIN1], a member of the NtrC/NifA family of proteins that bind to enhancer-like elements, called upstream activating sequences (UAS)."}
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{"Unnamed: 0": 157, "Gene1": "sigma W", "Gene2": "PBP4*", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein ([PROTEIN2] PBP4* [/PROTEIN2]) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
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{"Unnamed: 0": 51, "Gene1": "SpoIIE", "Gene2": "SpoIIAA-P", "Keywords": "dephosphorylation", "Direct dependency relations": "ONE WORD", "INO Type": "dephosphorylation reaction", "INO ID": "MI:0203", "Num. Keywords": 1, "Sentence": "Dephosphorylation of [PROTEIN2] SpoIIAA-P [/PROTEIN2] by [PROTEIN1] SpoIIE [/PROTEIN1] is strictly dependent on the presence of the bivalent metal ions Mn2+ or Mg2+."}
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{"Unnamed: 0": 101, "Gene1": "SpoIIID", "Gene2": "cot", "Keywords": "gene expression, action", "Direct dependency relations": "-1", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "In vitro transcription experiments suggest that the differential pattern of [PROTEIN2] cot [/PROTEIN2] gene expression results from the combined action of GerE and another transcription factor, [PROTEIN1] SpoIIID [/PROTEIN1]."}
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{"Unnamed: 0": 145, "Gene1": "SpoIIAB", "Gene2": "sigma F", "Keywords": "inhibits ", "Direct dependency relations": "ONE WORD", "INO Type": "inhibition", "INO ID": "INO_0000124", "Num. Keywords": 1, "Sentence": "The class includes AsiA form bacteriophage T4, which inhibits Escherichia coli sigma 70; FlgM, present in both gram-positive and gram-negative bacteria, which inhibits the flagella sigma factor sigma 28; [PROTEIN1] SpoIIAB [/PROTEIN1], which inhibits the sporulation-specific sigma factor,[PROTEIN2] sigma F [/PROTEIN2]and sigma G, of Bacillus subtilis; RbsW of B. subtilis, which inhibits stress response sigma factor sigma B; and DnaK, a general regulator of the heat shock response, which in bacteria inhibits the heat shock sigma factor sigma 32."}
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{"Unnamed: 0": 19, "Gene1": "sigmaB", "Gene2": "katX", "Keywords": "dependent, expression", "Direct dependency relations": "amod(expression, sigmaB-dependent)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "Therefore, the physiological role of [PROTEIN1] sigmaB [/PROTEIN1]-dependent [PROTEIN2] katX [/PROTEIN2] expression remains obscure."}
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{"Unnamed: 0": 85, "Gene1": "SigL", "Gene2": "bkd", "Keywords": "expression, induced, depended, presence", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of gene expression", "INO ID": "INO_0000038", "Num. Keywords": 4, "Sentence": "The expression of the [PROTEIN2] bkd [/PROTEIN2] operon was induced by the presence of isoleucine or valine in the growth medium and depended upon the presence of the sigma factor [PROTEIN1] SigL [/PROTEIN1], a member of the sigma 54 family."}
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{"Unnamed: 0": 15, "Gene1": "sigma(G)", "Gene2": "rsfA", "Keywords": "expression, control", "Direct dependency relations": "nsubj(control, expression)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "The expression of [PROTEIN2] rsfA [/PROTEIN2] is under the control of both sigma(F) and [PROTEIN1] sigma(G) [/PROTEIN1]."}
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{"Unnamed: 0": 66, "Gene1": "GerE", "Gene2": "cotD", "Keywords": "repressed, transcription", "Direct dependency relations": "-1", "INO Type": "negative regulation of gene transcription", "INO ID": "INO_0000042", "Num. Keywords": 2, "Sentence": "A low level of GerE activated transcription of cotD by sigmaK RNA polymerase in vitro, but a higher level of [PROTEIN1] GerE [/PROTEIN1] repressed [PROTEIN2] cotD [/PROTEIN2] transcription."}
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{"Unnamed: 0": 24, "Gene1": "SpoIIAB", "Gene2": "sigmaF", "Keywords": "controlled", "Direct dependency relations": "ONE WORD", "INO Type": "controling", "INO ID": "INO_0000057", "Num. Keywords": 1, "Sentence": "[PROTEIN2] sigmaF [/PROTEIN2] is controlled by a regulatory cascade involving an anti-sigma factor, [PROTEIN1] SpoIIAB [/PROTEIN1], an anti-anti-sigma factor, SpoIIAA, and a membrane-bound phosphatase, SpoIIE, which converts the inactive, phosphorylated form of SpoIIAA back to the active form."}
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{"Unnamed: 0": 30, "Gene1": "sigma(54)", "Gene2": "rocG", "Keywords": "dependent", "Direct dependency relations": "ONE WORD", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 1, "Sentence": "Unlike the case for other [PROTEIN1] sigma(54) [/PROTEIN1]-dependent genes, [PROTEIN2] rocG [/PROTEIN2] has no UAS; instead, its expression depends on a sequence located 1.5 kilobases downstream of the rocG promoter, beyond the end of the rocG coding region."}
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{"Unnamed: 0": 132, "Gene1": "sigmaB", "Gene2": "yvyD", "Keywords": "member of, regulons", "Direct dependency relations": "nmod:of(member, regulons)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "This indicates that the [PROTEIN2] yvyD [/PROTEIN2] gene product, being a member of both the [PROTEIN1] sigmaB [/PROTEIN1] and sigmaH regulons, might negatively regulate the activity of the sigmaL regulon."}
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{"Unnamed: 0": 105, "Gene1": "GerE", "Gene2": "cotC", "Keywords": "activate, transcription", "Direct dependency relations": "amod(transcription, activate)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": 2, "Sentence": "A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated cotB transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or [PROTEIN2] cotC [/PROTEIN2]."}
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{"Unnamed: 0": 152, "Gene1": "sigmaG", "Gene2": "sspL", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": 1, "Sentence": "The sspH and [PROTEIN2] sspL [/PROTEIN2] genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, [PROTEIN1] sigmaG [/PROTEIN1]; the sspN-tlp operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, sigmaF."}
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{"Unnamed: 0": 16, "Gene1": "sigma(K)", "Gene2": "cwlH", "Keywords": "dependent", "Direct dependency relations": "ONE WORD", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 1, "Sentence": "Expression of the [PROTEIN1] sigma(K) [PROTEIN1]-dependent [PROTEIN2] cwlH [/PROTEIN2] gene depended on gerE."}
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{"Unnamed: 0": 75, "Gene1": "ComK", "Gene2": "flgM", "Keywords": "increasing, production", "Direct dependency relations": "dobj(increasing,production)", "INO Type": "positive regulation of protein translation", "INO ID": "INO_0000053", "Num. Keywords": 2, "Sentence": "[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of hag by stimulating the transcription of comF-[PROTEIN2] flgM [/PROTEIN2], thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity."}
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{"Unnamed: 0": 18, "Gene1": "EsigmaF", "Gene2": "KatX", "Keywords": "level, depends", "Direct dependency relations": "nsubj(depends, level)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "Our results indicate that the level of [PROTEIN2] KatX [/PROTEIN2] level in outgrowing spores depends mainly on [PROTEIN1] EsigmaF [/PROTEIN1], because sigB mutants show normal KatX activity in dormant and outgrowing spores."}
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{"Unnamed: 0": 12, "Gene1": "sigma(H)", "Gene2": "spo0A", "Keywords": "dependent, expression", "Direct dependency relations": "amod(expression, dependent)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "In the shaA mutant, [PROTEIN1] sigma(H) [/PROTEIN1]-dependent expression of [PROTEIN2] spo0A [/PROTEIN2] and spoVG at an early stage of sporulation was sensitive to external NaCl."}
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{"Unnamed: 0": 9, "Gene1": "sigma(G)", "Gene2": "ywhE", "Keywords": "expression, controlled", "Direct dependency relations": "-1", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "Analysis of the expression of a translational ywhE-lacZ fusion showed that [PROTEIN2] ywhE [PROTEIN2] expression is sporulation-specific, and is controlled predominantly by the forespore-specific sigma factor sigma(F), and to a lesser extent by [PROTEIN1] sigma(G) [/PROTEIN1]."}
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{"Unnamed: 0": 31, "Gene1": "sigmaH", "Gene2": "phrC", "Keywords": "controlling, transcription", "Direct dependency relations": "amod(transcription, controlling)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": 2, "Sentence": "In addition to controlling transcription of [PROTEIN2] phrC [/PROTEIN2], [PROTEIN1] sigmaH [/PROTEIN1] appears to control expression of at least one other gene required for production of CSF."}
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train.jsonl
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{"Unnamed: 0": 0, "Gene1": "KinC", "Gene2": "Spo0A~P", "Keywords": "responsible, production", "Direct dependency relations": "nmod(responsible, production)", "INO Type": "regulation of translation", "INO ID": "INO_0000034", "Num. Keywords": "2", "Sentence": "In vivo studies of the activity of four of the kinases, KinA, [PROTEIN1] KinC [/PROTEIN1], KinD (ykvD) and KinE (ykrQ), using abrB transcription as an indicator of [PROTEIN2] Spo0A~P [/PROTEIN2] level, revealed that KinC and KinD were responsible for Spo0A~P production during the exponential phase of growth in the absence of KinA and KinB."}
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{"Unnamed: 0": 1, "Gene1": "KinD", "Gene2": "Spo0A~P", "Keywords": "responsible, production", "Direct dependency relations": "nmod(responsible, production)", "INO Type": "regulation of translation", "INO ID": "INO_0000034", "Num. Keywords": "2", "Sentence": "In vivo studies of the activity of four of the kinases, KinA, KinC, [PROTEIN1] KinD [/PROTEIN1] (ykvD) and KinE (ykrQ), using abrB transcription as an indicator of [PROTEIN2] Spo0A~P [/PROTEIN2] level, revealed that KinC and KinD were responsible for Spo0A~P production during the exponential phase of growth in the absence of KinA and KinB."}
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{"Unnamed: 0": 2, "Gene1": "sigma(A)", "Gene2": "spoIIG", "Keywords": "transcription, depends", "Direct dependency relations": "nsubj(depends, transcription)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "2", "Sentence": "In this mutant, expression of the [PROTEIN2] spoIIG [/PROTEIN2] gene, whose transcription depends on both [PROTEIN1] sigma(A) [/PROTEIN1] and the phosphorylated Spo0A protein, Spo0A~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C."}
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{"Unnamed: 0": 3, "Gene1": "Spo0A", "Gene2": "spoIIG", "Keywords": "transcription, depends", "Direct dependency relations": "nsubj(depends, transcription)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "2", "Sentence": "In this mutant, expression of the [PROTEIN2] spoIIG [/PROTEIN2] gene, whose transcription depends on both sigma(A) and the phosphorylated [PROTEIN1] Spo0A [/PROTEIN1] protein, Spo0A~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C."}
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{"Unnamed: 0": 4, "Gene1": "SigE", "Gene2": "ydhD", "Keywords": "transcription, dependent", "Direct dependency relations": "nsubj(dependent, transcription)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "2", "Sentence": "Transcription of [PROTEIN2] ydhD [/PROTEIN2] was dependent on [PROTEIN1] SigE [/PROTEIN1], and the mRNA was detectable from 2 h after the cessation of logarithmic growth (T2 of sporulation)."}
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{"Unnamed: 0": 5, "Gene1": "SigK", "Gene2": "ykuD", "Keywords": "transcribed", "Direct dependency relations": "ONE WORD", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "1", "Sentence": "[PROTEIN2] ykuD [/PROTEIN2] was transcribed by [PROTEIN1] SigK [/PROTEIN1] RNA polymerase from T4 of sporulation."}
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{"Unnamed: 0": 6, "Gene1": "SigK", "Gene2": "ykvP", "Keywords": "essential, expression", "Direct dependency relations": "nmod(essential, expression)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "Both [PROTEIN1] SigK [/PROTEIN1] and GerE were essential for [PROTEIN2] ykvP [/PROTEIN2] expression, and this gene was transcribed from T5 of sporulation."}
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{"Unnamed: 0": 7, "Gene1": "GerE", "Gene2": "ykvP", "Keywords": "essential, expression", "Direct dependency relations": "nmod(essential, expression)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "Both SigK and [PROTEIN1] GerE [/PROTEIN1] were essential for [PROTEIN2] ykvP [/PROTEIN2] expression, and this gene was transcribed from T5 of sporulation."}
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{"Unnamed: 0": 8, "Gene1": "sigma(F)", "Gene2": "ywhE", "Keywords": "expression, controlled", "Direct dependency relations": "-1", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "Analysis of the expression of a translational [PROTEIN1] ywhE [/PROTEIN1]-lacZ fusion showed that ywhE expression is sporulation-specific, and is controlled predominantly by the forespore-specific sigma factor [PROTEIN1] sigma(F) [/PROTEIN1], and to a lesser extent by sigma(G)."}
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{"Unnamed: 0": 10, "Gene1": "SpoIIE", "Gene2": "sigma(F)", "Keywords": "essential, activation", "Direct dependency relations": "nmod:for(essential, activation)", "INO Type": "regulation of gene activation", "INO ID": "INO_0000037", "Num. Keywords": "2", "Sentence": "Secondly, [PROTEIN1] SpoIIE [/PROTEIN1] is essential for the activation of the first compartment-specific transcription factor [PROTEIN2] sigma(F) [/PROTEIN2] in the prespore."}
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{"Unnamed: 0": 11, "Gene1": "FtsZ", "Gene2": "SpoIIE", "Keywords": "localization, dependent", "Direct dependency relations": "nsubj(dependent, Localization)", "INO Type": "regulation of protein location", "INO ID": "INO_0000031", "Num. Keywords": "2", "Sentence": "Localization of [PROTEIN2] SpoIIE [/PROTEIN2] was shown to be dependent on the essential cell division protein [PROTEIN1] FtsZ [/PROTEIN1]."}
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{"Unnamed: 0": 13, "Gene1": "sigma(H)", "Gene2": "spoVG", "Keywords": "dependent, expression", "Direct dependency relations": "amod(expression, dependent)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "In the shaA mutant, [PROTEIN1] sigma(H) [/PROTEIN1]-dependent expression of spo0A and [PROTEIN2] spoVG [/PROTEIN2] at an early stage of sporulation was sensitive to external NaCl."}
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{"Unnamed: 0": 14, "Gene1": "sigma(F)", "Gene2": "rsfA", "Keywords": "expression, control", "Direct dependency relations": "nsubj(control, expression)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "The expression of [PROTEIN2] rsfA [/PROTEIN2] is under the control of both [PROTEIN1] sigma(F) [/PROTEIN1] and sigma(G)."}
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{"Unnamed: 0": 17, "Gene1": "gerE", "Gene2": "cwlH", "Keywords": "expression, depended", "Direct dependency relations": "-1", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "Expression of the sigma(K)-dependent [PROTEIN2] cwlH [/PROTEIN2] gene depended on [PROTEIN1] gerE [/PROTEIN1]."}
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{"Unnamed: 0": 20, "Gene1": "sigmaB", "Gene2": "katX", "Keywords": "dependent, promoters", "Direct dependency relations": "amod(promoters, sigmaF-dependent)", "INO Type": "promoter-based regulation of transcription ", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "The -10 and -35 sequences of the [PROTEIN1] sigmaB [/PROTEIN1]- and sigmaF-dependent promoters of [PROTEIN2] katX [/PROTEIN2] overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide."}
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| 16 |
+
{"Unnamed: 0": 21, "Gene1": "sigmaF", "Gene2": "katX", "Keywords": "dependent, promoters", "Direct dependency relations": "amod(promoters, sigmaF-dependent)", "INO Type": "promoter-based regulation of transcription ", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "The -10 and -35 sequences of the sigmaB- and [PROTEIN1] sigmaF [/PROTEIN1]-dependent promoters of [PROTEIN2] katX [/PROTEIN2] overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide."}
|
| 17 |
+
{"Unnamed: 0": 22, "Gene1": "sigmaB", "Gene2": "katX", "Keywords": "dependent", "Direct dependency relations": "ONE WORD", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "1", "Sentence": "We demonstrated that [PROTEIN2] katX [/PROTEIN2] is also a [PROTEIN1] sigmaB [/PROTEIN1]-dependent general stress gene, since it is strongly induced by heat, salt and ethanol stress, as well as by energy depletion."}
|
| 18 |
+
{"Unnamed: 0": 23, "Gene1": "SpoIIE", "Gene2": "sigmaF", "Keywords": "control, activation", "Direct dependency relations": "nmod:of(control, activation)", "INO Type": "regulation of gene activation", "INO ID": "INO_0000037", "Num. Keywords": "2", "Sentence": "Taken together, the results support the idea that sequestration of [PROTEIN1] SpoIIE [/PROTEIN1] protein into the prespore plays an important role in the control of [PROTEIN2] sigmaF [/PROTEIN2] activation and in coupling this activation to septation."}
|
| 19 |
+
{"Unnamed: 0": 25, "Gene1": "SpoIIAA", "Gene2": "sigmaF", "Keywords": "controlled", "Direct dependency relations": "ONE WORD", "INO Type": "controling", "INO ID": "INO_0000057", "Num. Keywords": "1", "Sentence": "[PROTEIN2] sigmaF [/PROTEIN2] is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, [PROTEIN1] SpoIIAA [/PROTEIN1], and a membrane-bound phosphatase, SpoIIE, which converts the inactive, phosphorylated form of SpoIIAA back to the active form."}
|
| 20 |
+
{"Unnamed: 0": 26, "Gene1": "SpoIIE", "Gene2": "sigmaF", "Keywords": "controlled", "Direct dependency relations": "ONE WORD", "INO Type": "controling", "INO ID": "INO_0000057", "Num. Keywords": "1", "Sentence": "[PROTEIN2] sigmaF [/PROTEIN2] is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, SpoIIAA, and a membrane-bound phosphatase, [PROTEIN1] SpoIIE [/PROTEIN1], which converts the inactive, phosphorylated form of SpoIIAA back to the active form."}
|
| 21 |
+
{"Unnamed: 0": 27, "Gene1": "SpoIIE", "Gene2": "SpoIIAA", "Keywords": "converts, active", "Direct dependency relations": "-1", "INO Type": "regulation of gene activation", "INO ID": "INO_0000037", "Num. Keywords": "2", "Sentence": "sigmaF is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, [PROTEIN2] SpoIIAA [/PROTEIN2], and a membrane-bound phosphatase, [PROTEIN1] SpoIIE [/PROTEIN1], which converts the inactive, phosphorylated form of SpoIIAA back to the active form."}
|
| 22 |
+
{"Unnamed: 0": 28, "Gene1": "SigL", "Gene2": "rocG", "Keywords": "transcribed", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": "1", "Sentence": "The [PROTEIN2] rocG [/PROTEIN2] gene of Bacillus subtilis, encoding a catabolic glutamate dehydrogenase, is transcribed by [PROTEIN1] SigL [/PROTEIN1]-containing RNA polymerase and requires for its expression RocR, a member of the NtrC/NifA family of proteins that bind to enhancer-like elements, called upstream activating sequences (UAS)."}
|
| 23 |
+
{"Unnamed: 0": 32, "Gene1": "E sigma E", "Gene2": "yfhS", "Keywords": "transcribed", "Direct dependency relations": "ONE WORD", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "1", "Sentence": "Northern blot and primer extension analyses indicated that [PROTEIN2] yfhS [/PROTEIN2] is transcribed by [PROTEIN1] E sigma E [/PROTEIN1] during sporulation."}
|
| 24 |
+
{"Unnamed: 0": 33, "Gene1": "YfhP", "Gene2": "yfhQ", "Keywords": "negative regulator, transcription", "Direct dependency relations": "nmod:for(regulator, transcription); amod(regulator, negative)", "INO Type": "negative regulation of transcription", "INO ID": "INO_0000074", "Num. Keywords": "2", "Sentence": "These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of [PROTEIN2] yfhQ [/PROTEIN2], yfhR, sspE and yfhP."}
|
| 25 |
+
{"Unnamed: 0": 34, "Gene1": "YfhP", "Gene2": "yfhR", "Keywords": "negative regulator, transcription", "Direct dependency relations": "nmod:for(regulator, transcription); amod(regulator, negative)", "INO Type": "negative regulation of transcription", "INO ID": "INO_0000074", "Num. Keywords": "2", "Sentence": "These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, [PROTEIN2] yfhR [/PROTEIN2], sspE and yfhP."}
|
| 26 |
+
{"Unnamed: 0": 35, "Gene1": "YfhP", "Gene2": "sspE", "Keywords": "negative regulator, transcription", "Direct dependency relations": "nmod:for(regulator, transcription); amod(regulator, negative)", "INO Type": "negative regulation of transcription", "INO ID": "INO_0000074", "Num. Keywords": "2", "Sentence": "These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, yfhR, [PROTEIN2] sspE [/PROTEIN2] and yfhP."}
|
| 27 |
+
{"Unnamed: 0": 36, "Gene1": "YfhP", "Gene2": "yfhP", "Keywords": "negative regulator, transcription", "Direct dependency relations": "nmod:for(regulator, transcription); amod(regulator, negative)", "INO Type": "negative regulation of transcription", "INO ID": "INO_0000074", "Num. Keywords": "2", "Sentence": "These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, yfhR, sspE and [PROTEIN2] yfhP [/PROTEIN2]."}
|
| 28 |
+
{"Unnamed: 0": 37, "Gene1": "sigmaK", "Gene2": "Spo0A", "Keywords": "production, affect", "Direct dependency relations": "nsubj(affect, production)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "Production of [PROTEIN1] sigmaK [/PROTEIN1] about 1 h earlier than normal does affect [PROTEIN2] Spo0A [/PROTEIN2], which when phosphorylated is an activator of sigE transcription."}
|
| 29 |
+
{"Unnamed: 0": 38, "Gene1": "Spo0A", "Gene2": "sigE", "Keywords": "phosphorylated, activator, transcription", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "activation of gene transcription by phosphorylated protein", "INO ID": "INO_0000081", "Num. Keywords": "3", "Sentence": "Production of sigmaK about 1 h earlier than normal does affect [PROTEIN1] Spo0A [/PROTEIN1], which when phosphorylated is an activator of [PROTEIN2] sigE [/PROTEIN2] transcription."}
|
| 30 |
+
{"Unnamed: 0": 39, "Gene1": "sigmaA", "Gene2": "ald", "Keywords": "promoter, recognized", "Direct dependency relations": "nsubjpass(recognized, promoter)", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "The [PROTEIN2] ald [/PROTEIN2] promoter, like the sigE promoter, is believed to be recognized by [PROTEIN1] sigmaA [/PROTEIN1] RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation."}
|
| 31 |
+
{"Unnamed: 0": 40, "Gene1": "sigmaA", "Gene2": "sigE", "Keywords": "promoter, recognized", "Direct dependency relations": "nsubjpass(recognized, promoter)", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "The ald promoter, like the [PROTEIN2] sigE [/PROTEIN2] promoter, is believed to be recognized by [PROTEIN1] sigmaA [/PROTEIN1] RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation."}
|
| 32 |
+
{"Unnamed: 0": 41, "Gene1": "sigmaK", "Gene2": "sigmaA", "Keywords": "inhibit, activity", "Direct dependency relations": "dobj(inhibit, activity)", "INO Type": "inhibition of protein activity", "INO ID": "INO_0000070", "Num. Keywords": "2", "Sentence": "The ald promoter, like the sigE promoter, is believed to be recognized by [PROTEIN2] sigmaA [/PROTEIN2]RNA polymerase, suggesting that [PROTEIN1] sigmaK [/PROTEIN1] may inhibit sigmaA activity late in sporulation."}
|
| 33 |
+
{"Unnamed: 0": 42, "Gene1": "sigmaK", "Gene2": "sigE", "Keywords": "expression, negatively regulated", "Direct dependency relations": "nsubjpass(regulated, expression); advmod(regulated, negatively)", "INO Type": "negative regulation of gene expression", "INO ID": "INO_0000039", "Num. Keywords": "2", "Sentence": "In the mother cell compartment of sporulating cells, expression of the [PROTEIN2] sigE [/PROTEIN2] gene, encoding the earlier-acting sigma factor, sigmaE, is negatively regulated by the later-acting sigma factor, [PROTEIN1] sigmaK [/PROTEIN1]."}
|
| 34 |
+
{"Unnamed: 0": 43, "Gene1": "FtsZ", "Gene2": "SpoIIE", "Keywords": "depends", "Direct dependency relations": "ONE WORD", "INO Type": "regulation", "INO ID": "INO_0000157", "Num. Keywords": "1", "Sentence": "The first stage, which involves the phosphatase function of [PROTEIN2] SpoIIE [/PROTEIN2], depends on the cell division protein [PROTEIN1] FtsZ [/PROTEIN1] and could correspond to the FtsZ-dependent assembly of SpoIIE into E-rings."}
|
| 35 |
+
{"Unnamed: 0": 44, "Gene1": "FtsZ", "Gene2": "SpoIIE", "Keywords": "dependent, assembly", "Direct dependency relations": "amod(assembly, FtsZ-dependent)", "INO Type": "regulation of assembly", "INO ID": "INO_0000100", "Num. Keywords": "2", "Sentence": "The first stage, which involves the phosphatase function of [PROTEIN2] SpoIIE [/PROTEIN2], depends on the cell division protein [PROTEIN1] FtsZ [/PROTEIN1] and could correspond to the FtsZ-dependent assembly of SpoIIE into E-rings."}
|
| 36 |
+
{"Unnamed: 0": 45, "Gene1": "SpoIIE", "Gene2": "SpoIIAA", "Keywords": "blocks", "Direct dependency relations": "ONE WORD", "INO Type": "inhibition", "INO ID": "INO_0000124", "Num. Keywords": "1", "Sentence": "Evidence based on the use of modified and mutant forms of the phosphatase protein indicates that [PROTEIN1] SpoIIE [/PROTEIN1] blocks the capacity of unphosphorylated [PROTEIN2] SpoIIAA [/PROTEIN2] to activate sigmaF until formation of the polar septum is completed."}
|
| 37 |
+
{"Unnamed: 0": 46, "Gene1": "SpoIIAA", "Gene2": "sigmaF", "Keywords": "activate", "Direct dependency relations": "ONE WORD", "INO Type": "activation", "INO ID": "INO_0000024", "Num. Keywords": "1", "Sentence": "Evidence based on the use of modified and mutant forms of the phosphatase protein indicates that SpoIIE blocks the capacity of unphosphorylated [PROTEIN1] SpoIIAA [/PROTEIN1] to activate [PROTEIN2] sigmaF [/PROTEIN2] until formation of the polar septum is completed."}
|
| 38 |
+
{"Unnamed: 0": 47, "Gene1": "SpoIIE", "Gene2": "sigmaF", "Keywords": "activation, requires", "Direct dependency relations": "nsubj(requires, activation)\r\n", "INO Type": "regulation of gene activation", "INO ID": "INO_0000037", "Num. Keywords": "2", "Sentence": "Cell-specific activation of transcription factor [PROTEIN2] sigmaF [/PROTEIN2]during sporulation in Bacillus subtilis requires the formation of the polar septum and the activity of a serine phosphatase ([PROTEIN1] SpoIIE [/PROTEIN1]) located in the septum."}
|
| 39 |
+
{"Unnamed: 0": 48, "Gene1": "SpoIIE", "Gene2": "SpoIIAA-P", "Keywords": "dephosphorylating", "Direct dependency relations": "ONE WORD", "INO Type": "dephosphorylation reaction", "INO ID": "MI:0203", "Num. Keywords": "1", "Sentence": "The [PROTEIN1] SpoIIE [/PROTEIN1] phosphatase indirectly activates sigmaF by dephosphorylating a protein ([PROTEIN2] SpoIIAA-P [/PROTEIN2]) in the pathway that controls the activity of the transcription factor."}
|
| 40 |
+
{"Unnamed: 0": 49, "Gene1": "SpoIIE", "Gene2": "sigmaF", "Keywords": "activates", "Direct dependency relations": "ONE WORD", "INO Type": "activation", "INO ID": "INO_0000024", "Num. Keywords": "1", "Sentence": "The [PROTEIN1] SpoIIE [/PROTEIN1] phosphatase indirectly activates [PROTEIN2] sigmaF [/PROTEIN2] by dephosphorylating a protein (SpoIIAA-P) in the pathway that controls the activity of the transcription factor."}
|
| 41 |
+
{"Unnamed: 0": 50, "Gene1": "SpoIIAA-P", "Gene2": "sigmaF", "Keywords": "controls, activity", "Direct dependency relations": "dobj(controls, activity)", "INO Type": "regulation of protein activity", "INO ID": "INO_0000055", "Num. Keywords": "2", "Sentence": "The SpoIIE phosphatase indirectly activates [PROTEIN2] sigmaF [/PROTEIN2] by dephosphorylating a protein ([PROTEIN1] SpoIIAA-P [/PROTEIN1]) in the pathway that controls the activity of the transcription factor."}
|
| 42 |
+
{"Unnamed: 0": 52, "Gene1": "sigmaB", "Gene2": "bmrUR", "Keywords": "control", "Direct dependency relations": "ONE WORD", "INO Type": "controling", "INO ID": "INO_0000057", "Num. Keywords": "1", "Sentence": "(i) The finding that the [PROTEIN2] bmrUR [/PROTEIN2] operon is under [PROTEIN1] sigmaB [/PROTEIN1] control indicates that the elimination of multidrug compounds might be a new function in multiple stress resistance."}
|
| 43 |
+
{"Unnamed: 0": 53, "Gene1": "sigmaB", "Gene2": "ydaP", "Keywords": "dependent", "Direct dependency relations": "ONE WORD", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "1", "Sentence": "The [PROTEIN1] ydaP [/PROTEIN1] gene might belong to the increasing number of [PROTEIN2] sigmaB [/PROTEIN2]-dependent genes whose orthologues are under the control of sigmas in Escherichia coli, indicating that both regulons may fulfil similar functions."}
|
| 44 |
+
{"Unnamed: 0": 54, "Gene1": "sigmaB", "Gene2": "ydaE", "Keywords": "dependent", "Direct dependency relations": "ONE WORD", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "1", "Sentence": "Three new [PROTEIN1] sigmaB [/PROTEIN1]-dependent genes ([PROTEIN2] ydaE [/PROTEIN2], ydaG and yfkM) encoding proteins with still unknown functions were also described."}
|
| 45 |
+
{"Unnamed: 0": 56, "Gene1": "sigmaB", "Gene2": "yfkM", "Keywords": "dependent", "Direct dependency relations": "ONE WORD", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "1", "Sentence": "Three new [PROTEIN1] sigmaB [/PROTEIN1]-dependent genes (ydaE, ydaG and [PROTEIN2] yfkM [/PROTEIN2]) encoding proteins with still unknown functions were also described."}
|
| 46 |
+
{"Unnamed: 0": 57, "Gene1": "SpoIIE", "Gene2": "sigma F", "Keywords": "activated, action", "Direct dependency relations": "nmod:through(activated, action)", "INO Type": "gene activation", "INO ID": "INO_0000075", "Num. Keywords": "2", "Sentence": "Cell specificity is first established in the forespore under the control of the [PROTEIN2] sigma F [/PROTEIN2] factor, which is itself activated through the action of the [PROTEIN1] SpoIIE [/PROTEIN1] serine phosphatase, an enzyme targeted to the septum between the two cells."}
|
| 47 |
+
{"Unnamed: 0": 58, "Gene1": "sigmaK", "Gene2": "cot", "Keywords": "transcribed", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": "1", "Sentence": "Most [PROTEIN1] cot [/PROTEIN1] genes, and the gerE gene, are transcribed by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase."}
|
| 48 |
+
{"Unnamed: 0": 59, "Gene1": "sigmaK", "Gene2": "gerE", "Keywords": "transcribed", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": "1", "Sentence": "Most cot genes, and the [PROTEIN1] gerE [/PROTEIN1] gene, are transcribed by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase."}
|
| 49 |
+
{"Unnamed: 0": 60, "Gene1": "GerE", "Gene2": "sigK", "Keywords": "inhibits, transcription", "Direct dependency relations": "dobj(inhibits, transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "Previously, it was shown that the [PROTEIN1] GerE [/PROTEIN1] protein inhibits transcription in vitro of the [PROTEIN2] sigK [/PROTEIN2] gene encoding sigmaK."}
|
| 50 |
+
{"Unnamed: 0": 61, "Gene1": "sigmaK", "Gene2": "gerE", "Keywords": "dependent, transcription", "Direct dependency relations": "amod(transcription-6, sigmaK-dependent-5)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "2", "Sentence": "These results demonstrate that [PROTEIN1] sigmaK [/PROTEIN1]-dependent transcription of [PROTEIN2] gerE [/PROTEIN2] initiates a negative feedback loop in which GerE acts as a repressor to limit production of sigmaK."}
|
| 51 |
+
{"Unnamed: 0": 62, "Gene1": "GerE", "Gene2": "sigmaK", "Keywords": "repressor, limit production", "Direct dependency relations": "acl(repressor, limit); dobj(limit, production)\r\n", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "These results demonstrate that sigmaK-dependent transcription of gerE initiates a negative feedback loop in which [PROTEIN1] GerE [/PROTEIN1] acts as a repressor to limit production of [PROTEIN2] sigmaK [/PROTEIN1]."}
|
| 52 |
+
{"Unnamed: 0": 63, "Gene1": "GerE", "Gene2": "sigmaK", "Keywords": "activated, transcription", "Direct dependency relations": "dobj(activated, transcription)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "2", "Sentence": "A low level of [PROTEIN1] GerE [/PROTEIN1] activated transcription of cotD by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription."}
|
| 53 |
+
{"Unnamed: 0": 64, "Gene1": "GerE", "Gene2": "cotD", "Keywords": "low level, activated, transcription", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "activation of gene transcription by low level protein", "INO ID": "INO_0000052", "Num. Keywords": "3", "Sentence": "A low level of GerE activated transcription of cotD by sigmaK RNA polymerase in vitro, but a higher level of [PROTEIN1] GerE [/PROTEIN1] repressed [PROTEIN2] cotD [/PROTEIN2] transcription."}
|
| 54 |
+
{"Unnamed: 0": 65, "Gene1": "sigmaK", "Gene2": "cotD", "Keywords": "transcription", "Direct dependency relations": "ONE WORD", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "1", "Sentence": "A low level of GerE activated transcription of [PROTEIN2] cotD [/PROTEIN2] by [PROTEIN1] sigmaK [/PROTEIN1] RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription."}
|
| 55 |
+
{"Unnamed: 0": 67, "Gene1": "GerE", "Gene2": "sigK", "Keywords": "binds, transcriptional, act, repressor", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "negative regulation of gene transcription", "INO ID": "INO_0000042", "Num. Keywords": "4", "Sentence": "Here, we show that [PROTEIN1] GerE [/PROTEIN1] binds near the [PROTEIN2] sigK [/PROTEIN2] transcriptional start site, to act as a repressor."}
|
| 56 |
+
{"Unnamed: 0": 68, "Gene1": "GerE", "Gene2": "cotD", "Keywords": "binds, promoter", "Direct dependency relations": "-1", "INO Type": "regulation of transcription by binding to promoter", "INO ID": "INO_0000071", "Num. Keywords": "2", "Sentence": "We show that [PROTEIN1] GerE [/PROTEIN1] binds to two sites that span the -35 region of the [PROTEIN2] cotD [/PROTEIN2] promoter."}
|
| 57 |
+
{"Unnamed: 0": 69, "Gene1": "GerE", "Gene2": "cotD", "Keywords": "activate, transcription, repress, transcription", "Direct dependency relations": "dobj(activate, transcription); advmod(transcription, repress)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "2 (2 events with two keywords each)", "Sentence": "These results suggest that a rising level of [PROTEIN1] GerE [/PROTEIN1] in sporulating cells may first activate [PROTEIN2] cotD [/PROTEIN2] transcription from the upstream site then repress transcription as the downstream site becomes occupied."}
|
| 58 |
+
{"Unnamed: 0": 70, "Gene1": "GerE", "Gene2": "sspG", "Keywords": "transcription, requires", "Direct dependency relations": "nsubj(requires,transcription); \r\n", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "2", "Sentence": "[PROTEIN2] sspG [/PROTEIN2] transcription also requires the DNA binding protein [PROTEIN1] GerE [/PROTEIN1]."}
|
| 59 |
+
{"Unnamed: 0": 71, "Gene1": "sigmaG", "Gene2": "sspJ", "Keywords": "transcribed", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": "1", "Sentence": "In contrast, [PROTEIN1] sspJ [/PROTEIN1] is transcribed in the forespore compartment by RNA polymerase with the forespore-specific [PROTEIN2] sigmaG [/PROTEIN2] and appears to give a monocistronic transcript."}
|
| 60 |
+
{"Unnamed: 0": 72, "Gene1": "ComK", "Gene2": "FlgM", "Keywords": "stimulating, transcription", "Direct dependency relations": "dobj(stimulating,transcription)", "INO Type": "positive regulation of gene transcription", "INO ID": "INO_0000049", "Num. Keywords": "2", "Sentence": "[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the [PROTEIN2] FlgM [/PROTEIN2] antisigma factor that inhibits sigmaD activity."}
|
| 61 |
+
{"Unnamed: 0": 73, "Gene1": "ComK", "Gene2": "hag", "Keywords": "negatively controls, transcription", "Direct dependency relations": "dobj(controls, transcription); advmod(controls, negatively)", "INO Type": "negative regulation of gene transcription", "INO ID": "INO_0000042", "Num. Keywords": "2", "Sentence": "[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of [PROTEIN2] hag [/PROTEIN2] by stimulating the transcription of comF-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity."}
|
| 62 |
+
{"Unnamed: 0": 74, "Gene1": "ComK", "Gene2": "comF", "Keywords": "stimulating, transcription", "Direct dependency relations": "dobj(stimulating,transcription)", "INO Type": "positive regulation of gene transcription", "INO ID": "INO_0000049", "Num. Keywords": "2", "Sentence": "[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of hag by stimulating the transcription of [PROTEIN2] comF [/PROTEIN2]-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity."}
|
| 63 |
+
{"Unnamed: 0": 76, "Gene1": "FlgM", "Gene2": "sigmaD", "Keywords": "inhibit, activity", "Direct dependency relations": "dobj(inhibits,activity)", "INO Type": "inhibition of protein activity", "INO ID": "INO_0000070", "Num. Keywords": "2", "Sentence": "ComK negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the [PROTEIN1] FlgM [/PROTEIN1] antisigma factor that inhibits [PROTEIN2] sigmaD [/PROTEIN2] activity."}
|
| 64 |
+
{"Unnamed: 0": 77, "Gene1": "sigmaB", "Gene2": "ykzA", "Keywords": "increase, expression, dependent", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of gene expression", "INO ID": "INO_0000038", "Num. Keywords": "3", "Sentence": "This stress-induced increase in [PROTEIN2] ykzA [/PROTEIN2] expression is absolutely dependent on the alternative sigma factor [PROTEIN1] sigmaB [/PROTEIN1], which controls a large stationary-phase and stress regulon."}
|
| 65 |
+
{"Unnamed: 0": 78, "Gene1": "sigma X", "Gene2": "CsbB", "Keywords": "contributes, expression", "Direct dependency relations": "nmod(contributes,expression)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "[PROTEIN1] sigma X [/PROTEIN1] also contributes to the expression of [PROTEIN2] CsbB [/PROTEIN2], a putative membrane-bound glucosyl transferase that is partially controlled by the sigma B stress response sigma factor."}
|
| 66 |
+
{"Unnamed: 0": 79, "Gene1": "sigma B", "Gene2": "CsbB", "Keywords": "controlled", "Direct dependency relations": "ONE WORD", "INO Type": "controling", "INO ID": "INO_0000057", "Num. Keywords": "1", "Sentence": "sigma X also contributes to the expression of [PROTEIN2] CsbB [/PROTEIN2], a putative membrane-bound glucosyl transferase that is partially controlled by the [PROTEIN1] sigma B [/PROTEIN1] stress response sigma factor."}
|
| 67 |
+
{"Unnamed: 0": 80, "Gene1": "sigma B", "Gene2": "nadE", "Keywords": "induced, dependent", "Direct dependency relations": "-1", "INO Type": "positive regulation of gene expression", "INO ID": "INO_0000038", "Num. Keywords": "2", "Sentence": "Transcriptional studies showed that [PROTEIN2] nadE [/PROTEIN2] is strongly induced in response to heat, ethanol and salt stress or after starvation for glucose in a [PROTEIN1] sigma B [/PROTEIN1]-dependent manner."}
|
| 68 |
+
{"Unnamed: 0": 81, "Gene1": "sigma(B)", "Gene2": "YtxH", "Keywords": "induced, dependent", "Direct dependency relations": "-1", "INO Type": "positive regulation of gene expression", "INO ID": "INO_0000038", "Num. Keywords": "2", "Sentence": "Furthermore, [PROTEIN2] YtxH [/PROTEIN2] and YvyD seemed to be induced after phosphate starvation in the wild type in a [PROTEIN1] sigma(B) [/PROTEIN1]-dependent manner and in the sigB mutant probably via sigma(H)."}
|
| 69 |
+
{"Unnamed: 0": 82, "Gene1": "sigma(B)", "Gene2": "YvyD", "Keywords": "induced, dependent", "Direct dependency relations": "-1", "INO Type": "positive regulation of gene expression", "INO ID": "INO_0000038", "Num. Keywords": "2", "Sentence": "Furthermore, YtxH and [PROTEIN1] YvyD [/PROTEIN1] seemed to be induced after phosphate starvation in the wild type in a [PROTEIN2] sigma(B) [/PROTEIN2]-dependent manner and in the sigB mutant probably via sigma(H)."}
|
| 70 |
+
{"Unnamed: 0": 83, "Gene1": "sigma(H)", "Gene2": "YtxH", "Keywords": "induced, via", "Direct dependency relations": "-1", "INO Type": "induction", "INO ID": "INO_0000122", "Num. Keywords": "2", "Sentence": "Furthermore, [PROTEIN1] YtxH [/PROTEIN1] and YvyD seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner and in the sigB mutant probably via [PROTEIN2] sigma(H) [/PROTEIN2]."}
|
| 71 |
+
{"Unnamed: 0": 84, "Gene1": "sigma(H)", "Gene2": "YvyD", "Keywords": "induced, via", "Direct dependency relations": "-1", "INO Type": "induction", "INO ID": "INO_0000122", "Num. Keywords": "2", "Sentence": "Furthermore, YtxH and [PROTEIN2] YvyD [/PROTEIN2] seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner and in the sigB mutant probably via [PROTEIN1] sigma(H) [/PROTEIN1]."}
|
| 72 |
+
{"Unnamed: 0": 86, "Gene1": "ComK", "Gene2": "sigmaD", "Keywords": "preventing, transcription", "Direct dependency relations": "dobj(preventing,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates degR expression by preventing [PROTEIN2] sigmaD [/PROTEIN2]-driven transcription of degR, possibly through interaction with the control region."}
|
| 73 |
+
{"Unnamed: 0": 87, "Gene1": "ComK", "Gene2": "degR", "Keywords": "negatively regulates, expression", "Direct dependency relations": "dobj(regulates,expression)", "INO Type": "negative regulation of gene expression", "INO ID": "INO_0000039", "Num. Keywords": "2", "Sentence": "From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates [PROTEIN2] degR [/PROTEIN2] expression by preventing sigmaD-driven transcription of degR, possibly through interaction with the control region."}
|
| 74 |
+
{"Unnamed: 0": 88, "Gene1": "ComK", "Gene2": "degR", "Keywords": "preventing, transcription", "Direct dependency relations": "dobj(preventing,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates [PROTEIN2] degR [/PROTEIN2] expression by preventing sigmaD-driven transcription of degR, possibly through interaction with the control region."}
|
| 75 |
+
{"Unnamed: 0": 89, "Gene1": "sigmaD", "Gene2": "degR", "Keywords": "driven, transcription", "Direct dependency relations": "amod(transcription, sigmaD-driven)", "INO Type": "positive regulation of gene transcription", "INO ID": "INO_0000049", "Num. Keywords": "2", "Sentence": "From these results we conclude that ComK negatively regulates degR expression by preventing [PROTEIN1] sigmaD [/PROTEIN1]-driven transcription of [PROTEIN2] degR [/PROTEIN2], possibly through interaction with the control region."}
|
| 76 |
+
{"Unnamed: 0": 90, "Gene1": "sigmaD", "Gene2": "degR", "Keywords": "transcription, driven", "Direct dependency relations": "nsubjpass(driven,transcription)", "INO Type": "positive regulation of gene transcription", "INO ID": "INO_0000049", "Num. Keywords": "2", "Sentence": "We have shown previously that the transcription of [PROTEIN2] degR [/PROTEIN2] is driven by an alternative sigma factor, [PROTEIN1] sigmaD [/PROTEIN1]."}
|
| 77 |
+
{"Unnamed: 0": 91, "Gene1": "SpoIIID", "Gene2": "cotC", "Keywords": "binds", "Direct dependency relations": "ONE WORD", "INO Type": "direct interaction", "INO ID": "MI_0407", "Num. Keywords": "1", "Sentence": "DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the [PROTEIN2] cotC [/PROTEIN2] promoter region, binds weakly to one site in the cotX promoter, and does not bind specifically to cotB."}
|
| 78 |
+
{"Unnamed: 0": 92, "Gene1": "SpoIIID", "Gene2": "cotX", "Keywords": "binds", "Direct dependency relations": "ONE WORD", "INO Type": "direct interaction", "INO ID": "MI_0407", "Num. Keywords": "1", "Sentence": "DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the cotC promoter region, binds weakly to one site in the [PROTEIN2] cotX [/PROTEIN2] promoter, and does not bind specifically to cotB."}
|
| 79 |
+
{"Unnamed: 0": 93, "Gene1": "SpoIIID", "Gene2": "cotB", "Keywords": "bind", "Direct dependency relations": "ONE WORD", "INO Type": "direct interaction", "INO ID": "MI_0407", "Num. Keywords": "1", "Sentence": "DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the cotC promoter region, binds weakly to one site in the cotX promoter, and does not bind specifically to [PROTEIN2] cotB [/PROTEIN2]."}
|
| 80 |
+
{"Unnamed: 0": 94, "Gene1": "sigma(K)", "Gene2": "cotB", "Keywords": "transcription", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": "1", "Sentence": "Transcription of the [PROTEIN1] cotB [/PROTEIN1], cotC, and cotX genes by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase is activated by a small, DNA-binding protein called GerE."}
|
| 81 |
+
{"Unnamed: 0": 96, "Gene1": "sigma(K)", "Gene2": "cotX", "Keywords": "transcription", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": "1", "Sentence": "Transcription of the cotB, cotC, and [PROTEIN1] cotX [/PROTEIN1] genes by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase is activated by a small, DNA-binding protein called GerE."}
|
| 82 |
+
{"Unnamed: 0": 97, "Gene1": "GerE", "Gene2": "cotB", "Keywords": "transcription, activated", "Direct dependency relations": "nsubjpass(activated,transcription)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": "2", "Sentence": "Transcription of the [PROTEIN2] cotB [/PROTEIN2], cotC, and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1]."}
|
| 83 |
+
{"Unnamed: 0": 98, "Gene1": "GerE", "Gene2": "cotC", "Keywords": "transcription ,activated", "Direct dependency relations": "nsubjpass(activated,transcription)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": "2", "Sentence": "Transcription of the cotB, [PROTEIN2] cotC [/PROTEIN2], and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1]."}
|
| 84 |
+
{"Unnamed: 0": 99, "Gene1": "GerE", "Gene2": "cotX", "Keywords": "transcription, activated", "Direct dependency relations": "nsubjpass(activated,transcription)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": "2", "Sentence": "Transcription of the cotB, cotC, and [PROTEIN2] cotX [/PROTEIN2] genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1]."}
|
| 85 |
+
{"Unnamed: 0": 100, "Gene1": "GerE", "Gene2": "cot", "Keywords": "gene expression, action", "Direct dependency relations": "-1", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "In vitro transcription experiments suggest that the differential pattern of [PROTEIN2] cot [/PROTEIN2] gene expression results from the combined action of [PROTEIN1] GerE [/PROTEIN1] and another transcription factor, SpoIIID."}
|
| 86 |
+
{"Unnamed: 0": 102, "Gene1": "GerE", "Gene2": "sigma(K)", "Keywords": "low concentration, activated, transcription", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": "3", "Sentence": "A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated cotB transcription by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC."}
|
| 87 |
+
{"Unnamed: 0": 103, "Gene1": "GerE", "Gene2": "cotB", "Keywords": "low concentration, activated, transcription", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "activation of gene transcription by low level protein", "INO ID": "INO_0000052", "Num. Keywords": "3", "Sentence": "A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated [PROTEIN2] cotB [/PROTEIN2] transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC."}
|
| 88 |
+
{"Unnamed: 0": 104, "Gene1": "GerE", "Gene2": "cotX", "Keywords": "activate, transcription", "Direct dependency relations": "amod(transcription, activate)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": "2", "Sentence": "A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated cotB transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of [PROTEIN2] cotX [/PROTEIN2] or cotC."}
|
| 89 |
+
{"Unnamed: 0": 106, "Gene1": "sigma(K)", "Gene2": "cotB", "Keywords": "activated, transcription", "Direct dependency relations": "dobj(activated,transcription)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": "2", "Sentence": "A low concentration of GerE activated [PROTEIN2] cotB [/PROTEIN2] transcription by final [PROTEIN1] sigma(K) [/PROTEIN1] RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC."}
|
| 90 |
+
{"Unnamed: 0": 107, "Gene1": "SpoIIID", "Gene2": "cotC", "Keywords": "repressed, transcription", "Direct dependency relations": "dobj(repressed,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed [PROTEIN2] cotC [/PROTEIN2] transcription, whereas a higher concentration only partially repressed cotX transcription and had little effect on cotB transcription."}
|
| 91 |
+
{"Unnamed: 0": 108, "Gene1": "SpoIIID", "Gene2": "cotX", "Keywords": "repressed, transcription", "Direct dependency relations": "dobj(repressed,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed cotC transcription, whereas a higher concentration only partially repressed [PROTEIN2] cotX [/PROTEIN2] transcription and had little effect on cotB transcription."}
|
| 92 |
+
{"Unnamed: 0": 109, "Gene1": "SpoIIID", "Gene2": "cotB", "Keywords": "repressed, transcription", "Direct dependency relations": "dobj(repressed,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed cotC transcription, whereas a higher concentration only partially repressed cotX transcription and had little effect on [PROTEIN2] cotB [/PROTEIN2] transcription."}
|
| 93 |
+
{"Unnamed: 0": 110, "Gene1": "sigmaA", "Gene2": "kdgR", "Keywords": "dependent, promoter", "Direct dependency relations": "amod(promoter, sigmaA-dependent)", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "Primer extension experiments and Northern blot analysis show that an active [PROTEIN1] sigmaA [/PROTEIN1]-dependent promoter precedes [PROTEIN2] kdgR [/PROTEIN2] and transcription is terminated at the putative p-independent terminator downstream of kdgT."}
|
| 94 |
+
{"Unnamed: 0": 111, "Gene1": "sigmaW", "Gene2": "sigW", "Keywords": "dependent, promoter, precedes", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "3", "Sentence": "A [PROTEIN1] sigmaW [/PROTEIN1]-dependent promoter (PW) precedes [PROTEIN2] sigW [/PROTEIN2], demonstrating that this transcription factor is positively autoregulated."}
|
| 95 |
+
{"Unnamed: 0": 112, "Gene1": "sigma(A)", "Gene2": "sigX", "Keywords": "recognize, promoter ", "Direct dependency relations": "-1", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both [PROTEIN1] sigma(A) [/PROTEIN1] and sigma(X) holoenzymes recognize promoter elements within the [PROTEIN2] sigX [/PROTEIN2]-ypuN control region."}
|
| 96 |
+
{"Unnamed: 0": 113, "Gene1": "sigma(A)", "Gene2": "ypuN", "Keywords": "recognize, promoter ", "Direct dependency relations": "-1", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both [PROTEIN1] sigma(A) [/PROTEIN1] and sigma(X) holoenzymes recognize promoter elements within the sigX-[PROTEIN2] ypuN [/PROTEIN2] control region."}
|
| 97 |
+
{"Unnamed: 0": 114, "Gene1": "sigma(X)", "Gene2": "sigX", "Keywords": "recognize, promoter ", "Direct dependency relations": "-1", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "We overproduced and purified [PROTEIN1] sigma(X) [/PROTEIN1] from Escherichia coli and demonstrate that in vitro, both sigma(A) and sigma(X) holoenzymes recognize promoter elements within the [PROTEIN2] sigX [/PROTEIN2]-ypuN control region."}
|
| 98 |
+
{"Unnamed: 0": 116, "Gene1": "PhoP~P", "Gene2": "tagA", "Keywords": "repress, transcription", "Direct dependency relations": "dobj(repress,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the [PROTEIN2] tagA [/PROTEIN2] and tagD promoters and also to activate the transcription of the tuaA promoter."}
|
| 99 |
+
{"Unnamed: 0": 117, "Gene1": "PhoP~P", "Gene2": "tagD", "Keywords": "repress, transcription", "Direct dependency relations": "dobj(repress,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the tagA and [PROTEIN2] tagD [/PROTEIN2] promoters and also to activate the transcription of the tuaA promoter."}
|
| 100 |
+
{"Unnamed: 0": 118, "Gene1": "PhoP~P", "Gene2": "tuaA", "Keywords": "activate, transcription", "Direct dependency relations": "dobj(activate,transcription)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": "2", "Sentence": "The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the tagA and tagD promoters and also to activate the transcription of the [PROTEIN2] tuaA [/PROTEIN2] promoter."}
|
| 101 |
+
{"Unnamed: 0": 119, "Gene1": "AraR", "Gene2": "araE", "Keywords": "expression, promoter, negatively regulated", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "negative regulation of transcription by binding to promoter", "INO ID": "INO_0000074", "Num. Keywords": "3", "Sentence": "Transcriptional studies demonstrated that the expression from the [PROTEIN2] araE [/PROTEIN2] promoter is induced by L-arabinose, repressed by glucose, and negatively regulated by [PROTEIN1] AraR [/PROTEIN1]."}
|
| 102 |
+
{"Unnamed: 0": 120, "Gene1": "GerE", "Gene2": "sigmaK", "Keywords": "stimulates, transcription, promoters", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of transcription by binding to promoter", "INO ID": "INO_0000072", "Num. Keywords": "3", "Sentence": "During endospore formation in Bacillus subtilis, the DNA binding protein [PROTEIN2] GerE [/PROTEIN2] stimulates transcription from several promoters that are used by RNA polymerase containing [PROTEIN1] sigmaK [/PROTEIN1]"}
|
| 103 |
+
{"Unnamed: 0": 121, "Gene1": "GerE", "Gene2": "cotX", "Keywords": "binds, promoter", "Direct dependency relations": "-1", "INO Type": "regulation of transcription by binding to promoter", "INO ID": "INO_0000071", "Num. Keywords": "2", "Sentence": "[PROTEIN1] GerE [/PROTEIN1] binds to a site on one of these promoters, [PROTEIN2] cotX [/PROTEIN2], that overlaps its -35 region."}
|
| 104 |
+
{"Unnamed: 0": 122, "Gene1": "Spo0A", "Gene2": "sigma(A)", "Keywords": "stimulate, transcription, dependent", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of gene transcription", "INO ID": "INO_0000049", "Num. Keywords": "3", "Sentence": "However, the mutant was unable to stimulate transcription by final [PROTEIN2] sigma(A) [/PROTEIN2]-RNA polymerase from the [PROTEIN1] Spo0A [/PROTEIN1]-dependent spoIIG operon promoter."}
|
| 105 |
+
{"Unnamed: 0": 123, "Gene1": "Spo0A", "Gene2": "spoIIG", "Keywords": "dependent, promoter", "Direct dependency relations": "amod(promoter,Spo0A-dependent)", "INO Type": "promoter-based regulation of transcription", "INO ID": "INO_0000079", "Num. Keywords": "2", "Sentence": "However, the mutant was unable to stimulate transcription by final sigma(A)-RNA polymerase from the [PROTEIN1] Spo0A [/PROTEIN1]-dependent [PROTEIN2] spoIIG [/PROTEIN2] operon promoter."}
|
| 106 |
+
{"Unnamed: 0": 124, "Gene1": "sigma(A)", "Gene2": "spoIIG", "Keywords": "stimulate transcription; ", "Direct dependency relations": "dobj(stimulate,transcription)", "INO Type": "positive regulation of gene transcription", "INO ID": "INO_0000049", "Num. Keywords": "2", "Sentence": "However, the mutant was unable to stimulate transcription by final [PROTEIN1] sigma(A) [/PROTEIN1]-RNA polymerase from the Spo0A-dependent [PROTEIN2] spoIIG [/PROTEIN2] operon promoter."}
|
| 107 |
+
{"Unnamed: 0": 125, "Gene1": "sigmaB", "Gene2": "clpC", "Keywords": "regulated, relying on", "Direct dependency relations": "xcomp(regulated, relying)", "INO Type": "regulation", "INO ID": "INO_0000157", "Num. Keywords": "2", "Sentence": "The Bacillus subtilis [PROTEIN2] clpC [/PROTEIN2] operon is regulated by two stress induction pathways relying on either [PROTEIN1] sigmaB [/PROTEIN1] or a class III stress induction mechanism acting at a sigmaA-like promoter."}
|
| 108 |
+
{"Unnamed: 0": 126, "Gene1": "sigmaA", "Gene2": "clpC", "Keywords": "regulated, relying on", "Direct dependency relations": "xcomp(regulated, relying)", "INO Type": "regulation", "INO ID": "INO_0000157", "Num. Keywords": "2", "Sentence": "The Bacillus subtilis [PROTEIN2] clpC [/PROTEIN2] operon is regulated by two stress induction pathways relying on either sigmaB or a class III stress induction mechanism acting at a [PROTEIN1] sigmaA [/PROTEIN1]-like promoter."}
|
| 109 |
+
{"Unnamed: 0": 127, "Gene1": "CtsR", "Gene2": "clpC", "Keywords": "acts, repressor", "Direct dependency relations": "nmod:as(acts,repressor)", "INO Type": "gene expression inhibition", "INO ID": "INO_0000085", "Num. Keywords": "2", "Sentence": "Our data demonstrate that the [PROTEIN1] CtsR [/PROTEIN1] protein acts as a global repressor of the [PROTEIN2] clpC [/PROTEIN2] operon, as well as other class III heat shock genes, by preventing unstressed transcription from either the sigmaB- or sigmaA-dependent promoter and might be inactivated or dissociate under inducing stress conditions."}
|
| 110 |
+
{"Unnamed: 0": 128, "Gene1": "sigmaB", "Gene2": "clpC", "Keywords": "preventing, transcription", "Direct dependency relations": "dobj(preventing,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "Our data demonstrate that the CtsR protein acts as a global repressor of the [PROTEIN2] clpC [/PROTEIN2] operon, as well as other class III heat shock genes, by preventing unstressed transcription from either the [PROTEIN1] sigmaB [/PROTEIN1]- or sigmaA-dependent promoter and might be inactivated or dissociate under inducing stress conditions."}
|
| 111 |
+
{"Unnamed: 0": 129, "Gene1": "sigmaA", "Gene2": "clpC", "Keywords": "preventing, transcription", "Direct dependency relations": "dobj(preventing,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": "2", "Sentence": "Our data demonstrate that the CtsR protein acts as a global repressor of the [PROTEIN2] clpC [/PROTEIN2] operon, as well as other class III heat shock genes, by preventing unstressed transcription from either the sigmaB- or [PROTEIN2] sigmaA [/PROTEIN2]-dependent promoter and might be inactivated or dissociate under inducing stress conditions."}
|
| 112 |
+
{"Unnamed: 0": 130, "Gene1": "sigmaB", "Gene2": "yvyD", "Keywords": "dependent, drives, expression, promoter", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of transcription by binding to promoter", "INO ID": "INO_0000072", "Num. Keywords": "4", "Sentence": "The [PROTEIN1] sigmaB [/PROTEIN1]-dependent promoter drives expression of [PROTEIN2] yvyD [/PROTEIN2] under stress conditions and after glucose starvation, whereas a sigmaH-dependent promoter is responsible for yvyD transcription following amino acid limitation."}
|
| 113 |
+
{"Unnamed: 0": 133, "Gene1": "sigmaH", "Gene2": "yvyD", "Keywords": "member of, regulons", "Direct dependency relations": "nmod:of(member, regulons)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "This indicates that the [PROTEIN2] yvyD [/PROTEIN2] gene product, being a member of both the sigmaB and [PROTEIN1] sigmaH [/PROTEIN1] regulons, might negatively regulate the activity of the sigmaL regulon."}
|
| 114 |
+
{"Unnamed: 0": 134, "Gene1": "yvyD", "Gene2": "sigmaL", "Keywords": "negatively regulate, activity", "Direct dependency relations": "dobj(regulate,activity)", "INO Type": "negative regulation of protein activity", "INO ID": "INO_0000067", "Num. Keywords": "2", "Sentence": "This indicates that the [PROTEIN1] yvyD [/PROTEIN1] gene product, being a member of both the sigmaB and sigmaH regulons, might negatively regulate the activity of the [PROTEIN2] sigmaL [/PROTEIN2] regulon."}
|
| 115 |
+
{"Unnamed: 0": 136, "Gene1": "sigma(K)", "Gene2": "ftsY", "Keywords": "expressed, controlled, promoter", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of transcription by binding to promoter", "INO ID": "INO_0000072", "Num. Keywords": "3", "Sentence": "Therefore, ftsY is solely expressed during sporulation from a [PROTEIN1] sigma(K) [/PROTEIN1]- and GerE-controlled promoter that is located immediately upstream of [PROTEIN2] ftsY [/PROTEIN2] inside the smc gene."}
|
| 116 |
+
{"Unnamed: 0": 137, "Gene1": "GerE", "Gene2": "ftsY", "Keywords": "expressed, controlled, promoter", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "positive regulation of transcription by binding to promoter", "INO ID": "INO_0000072", "Num. Keywords": "3", "Sentence": "Therefore, [PROTEIN2] ftsY [/PROTEIN2] is solely expressed during sporulation from a sigma(K)- and [PROTEIN1] GerE [/PROTEIN1]-controlled promoter that is located immediately upstream of ftsY inside the smc gene."}
|
| 117 |
+
{"Unnamed: 0": 138, "Gene1": "sigmaB", "Gene2": "gsiB", "Keywords": "member of, regulon", "Direct dependency relations": "nmod:of(member, regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "In that respect sigB is similar to the previously described gene [PROTEIN2] gsiB [/PROTEIN2] which is also a member of the [PROTEIN1] sigmaB [/PROTEIN1] regulon."}
|
| 118 |
+
{"Unnamed: 0": 139, "Gene1": "sigmaB", "Gene2": "sigB", "Keywords": "member of, regulon", "Direct dependency relations": "nmod:of(member, regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "In that respect [PROTEIN2] sigB [/PROTEIN2] is similar to the previously described gene gsiB which is also a member of the [PROTEIN1] sigmaB [/PROTEIN1] regulon."}
|
| 119 |
+
{"Unnamed: 0": 140, "Gene1": "ClpX", "Gene2": "sigmaH", "Keywords": "dependent, stimulation", "Direct dependency relations": "amod(stimulation, ClpX-dependent)", "INO Type": "positve regulation of protein activity", "INO ID": "INO_0000104", "Num. Keywords": "2", "Sentence": "The addition of [PROTEIN1] ClpX [/PROTEIN1] to in vitro transcription reactions resulted in the stimulation of RNAP holoenzyme activity, but [PROTEIN2] sigmaH [/PROTEIN2]-RNAP was observed to be more sensitive to ClpX-dependent stimulation than sigmaA-RNAP."}
|
| 120 |
+
{"Unnamed: 0": 141, "Gene1": "ClpX", "Gene2": "sigmaA", "Keywords": "dependent, stimulation", "Direct dependency relations": "amod(stimulation, ClpX-dependent)", "INO Type": "positve regulation of protein activity", "INO ID": "INO_0000104", "Num. Keywords": "2", "Sentence": "The addition of ClpX to in vitro transcription reactions resulted in the stimulation of RNAP holoenzyme activity, but sigmaH-RNAP was observed to be more sensitive to [PROTEIN1] ClpX [/PROTEIN1]-dependent stimulation than [PROTEIN2] sigmaA [/PROTEIN2]-RNAP."}
|
| 121 |
+
{"Unnamed: 0": 142, "Gene1": "ClpX", "Gene2": "sigmaH", "Keywords": "dependent, stimulation", "Direct dependency relations": "amod(stimulation, ClpX-dependent)", "INO Type": "positve regulation of protein activity", "INO ID": "INO_0000104", "Num. Keywords": "2", "Sentence": "The addition of ClpX to in vitro transcription reactions resulted in the stimulation of RNAP holoenzyme activity, but [PROTEIN2] sigmaH [/PROTEIN2]-RNAP was observed to be more sensitive to [PROTEIN1] ClpX [/PROTEIN1]-dependent stimulation than sigmaA-RNAP."}
|
| 122 |
+
{"Unnamed: 0": 143, "Gene1": "ClpX", "Gene2": "sigmaA", "Keywords": "dependent, stimulation", "Direct dependency relations": "amod(stimulation, ClpX-dependent)", "INO Type": "positve regulation of protein activity", "INO ID": "INO_0000104", "Num. Keywords": "2", "Sentence": "The addition of [PROTEIN1] ClpX [/PROTEIN1] to in vitro transcription reactions resulted in the stimulation of RNAP holoenzyme activity, but sigmaH-RNAP was observed to be more sensitive to ClpX-dependent stimulation than [PROTEIN2] sigmaA [/PROTEIN2]-RNAP."}
|
| 123 |
+
{"Unnamed: 0": 144, "Gene1": "Spo0", "Gene2": "spo0H", "Keywords": "governs, activity", "Direct dependency relations": "dobj(governs,activity)", "INO Type": "regulation of protein activity", "INO ID": "INO_0000055", "Num. Keywords": "2", "Sentence": "Although [PROTEIN2] spo0H [/PROTEIN2] is transcriptionally regulated by the key regulatory device that controls sporulation initiation, the [PROTEIN1] Spo0 [/PROTEIN1] phosphorelay, there is considerable evidence implicating a mechanism of post-translational control that governs the activity and concentration of sigmaH."}
|
| 124 |
+
{"Unnamed: 0": 146, "Gene1": "SpoIIAB", "Gene2": "sigma G", "Keywords": "inhibits ", "Direct dependency relations": "ONE WORD", "INO Type": "inhibition", "INO ID": "INO_0000124", "Num. Keywords": "1", "Sentence": "The class includes AsiA form bacteriophage T4, which inhibits Escherichia coli sigma 70; FlgM, present in both gram-positive and gram-negative bacteria, which inhibits the flagella sigma factor sigma 28; [PROTEIN1] SpoIIAB [/PROTEIN1], which inhibits the sporulation-specific sigma factor, sigma F and [PROTEIN2] sigma G [/PROTEIN2], of Bacillus subtilis; RbsW of B. subtilis, which inhibits stress response sigma factor sigma B; and DnaK, a general regulator of the heat shock response, which in bacteria inhibits the heat shock sigma factor sigma 32."}
|
| 125 |
+
{"Unnamed: 0": 147, "Gene1": "FlgM", "Gene2": "sigma 28", "Keywords": "inhibits ", "Direct dependency relations": "ONE WORD", "INO Type": "inhibition", "INO ID": "INO_0000124", "Num. Keywords": "1", "Sentence": "The class includes AsiA form bacteriophage T4, which inhibits Escherichia coli sigma 70; [PROTEIN1] FlgM [/PROTEIN1], present in both gram-positive and gram-negative bacteria, which inhibits the flagella sigma factor [PROTEIN2] sigma 28 [/PROTEIN2]; SpoIIAB, which inhibits the sporulation-specific sigma factor, sigma F and sigma G, of Bacillus subtilis; RbsW of B. subtilis, which inhibits stress response sigma factor sigma B; and DnaK, a general regulator of the heat shock response, which in bacteria inhibits the heat shock sigma factor sigma 32."}
|
| 126 |
+
{"Unnamed: 0": 148, "Gene1": "RbsW", "Gene2": "sigma B", "Keywords": "inhibits ", "Direct dependency relations": "ONE WORD", "INO Type": "inhibition", "INO ID": "INO_0000124", "Num. Keywords": "1", "Sentence": "The class includes AsiA form bacteriophage T4, which inhibits Escherichia coli sigma 70; FlgM, present in both gram-positive and gram-negative bacteria, which inhibits the flagella sigma factor sigma 28; SpoIIAB, which inhibits the sporulation-specific sigma factor, sigma F and sigma G, of Bacillus subtilis; [PROTEIN1] RbsW [/PROTEIN1] of B. subtilis, which inhibits stress response sigma factor [PROTEIN2] sigma B [/PROTEIN2]; and DnaK, a general regulator of the heat shock response, which in bacteria inhibits the heat shock sigma factor sigma 32."}
|
| 127 |
+
{"Unnamed: 0": 149, "Gene1": "DnaK", "Gene2": "sigma 32", "Keywords": "inhibits ", "Direct dependency relations": "ONE WORD", "INO Type": "inhibition", "INO ID": "INO_0000124", "Num. Keywords": "1", "Sentence": "The class includes AsiA form bacteriophage T4, which inhibits Escherichia coli sigma 70; FlgM, present in both gram-positive and gram-negative bacteria, which inhibits the flagella sigma factor sigma 28; SpoIIAB, which inhibits the sporulation-specific sigma factor, sigma F and sigma G, of Bacillus subtilis; RbsW of B. subtilis, which inhibits stress response sigma factor sigma B; and [PROTEIN1] DnaK [/PROTEIN1], a general regulator of the heat shock response, which in bacteria inhibits the heat shock sigma factor [PROTEIN2] sigma 32 [/PROTEIN2]."}
|
| 128 |
+
{"Unnamed: 0": 150, "Gene1": "sigmaE", "Gene2": "spoIVA", "Keywords": "localization, under the control", "Direct dependency relations": "-1", "INO Type": "regulation of protein location", "INO ID": "INO_0000031", "Num. Keywords": "2", "Sentence": "Finally, we show that proper localization of [PROTEIN2] SpoIVA [/PROTEIN2] required the expression of one or more genes which, like spoIVA, are under the control of the mother cell transcription factor [PROTEIN1] sigmaE [/PROTEIN1]."}
|
| 129 |
+
{"Unnamed: 0": 151, "Gene1": "sigmaG", "Gene2": "sspH", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": "1", "Sentence": "The [PROTEIN2] sspH [/PROTEIN2]and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, [PROTEIN1] sigmaG [/PROTEIN1]; the sspN-tlp operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, sigmaF."}
|
| 130 |
+
{"Unnamed: 0": 153, "Gene1": "sigmaG", "Gene2": "sspN", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": "1", "Sentence": "The sspH and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, sigmaG; the [PROTEIN2] sspN [/PROTEIN2]-tlp operon is recognized equally well by [PROTEIN1] sigmaG [/PROTEIN1] and the other forespore-specific sigma factor, sigmaF."}
|
| 131 |
+
{"Unnamed: 0": 154, "Gene1": "sigmaG", "Gene2": "tlp", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": "1", "Sentence": "The sspH and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, sigmaG; the sspN-[PROTEIN2] tlp [/PROTEIN2] operon is recognized equally well by [PROTEIN1] sigmaG [/PROTEIN1] and the other forespore-specific sigma factor, sigmaF."}
|
| 132 |
+
{"Unnamed: 0": 155, "Gene1": "sigmaF", "Gene2": "sspN", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": "1", "Sentence": "The sspH and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, sigmaG; the [PROTEIN2] sspN [/PROTEIN2]-tlp operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, [PROTEIN1] sigmaF [/PROTEIN1]."}
|
| 133 |
+
{"Unnamed: 0": 156, "Gene1": "sigmaF", "Gene2": "tlp", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": "1", "Sentence": "The sspH and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, sigmaG; the sspN-[PROTEIN2] tlp [/PROTEIN2] operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, [PROTEIN1] sigmaF [/PROTEIN1]."}
|
| 134 |
+
{"Unnamed: 0": 158, "Gene1": "sigma W", "Gene2": "RacX", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase ([PROTEIN2] RacX [/PROTEIN2]), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
|
| 135 |
+
{"Unnamed: 0": 159, "Gene1": "sigma W", "Gene2": "YteI", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase ([PROTEIN2] YteI [/PROTEIN2]), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
|
| 136 |
+
{"Unnamed: 0": 160, "Gene1": "sigma W", "Gene2": "YuaG", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin ([PROTEIN2] YuaG [/PROTEIN2]), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
|
| 137 |
+
{"Unnamed: 0": 161, "Gene1": "sigma W", "Gene2": "YknXYZ", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters ([PROTEIN2] YknXYZ [/PROTEIN2]), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
|
| 138 |
+
{"Unnamed: 0": 162, "Gene1": "sigma W", "Gene2": "YdjP", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase ([PROTEIN2] YdjP [/PROTEIN2]), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
|
| 139 |
+
{"Unnamed: 0": 163, "Gene1": "sigma W", "Gene2": "YfhM", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": "2", "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase ([PROTEIN2] YfhM [/PROTEIN2]) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
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| 1 |
+
{"Unnamed: 0": 60, "Gene1": "GerE", "Gene2": "sigK", "Keywords": "inhibits, transcription", "Direct dependency relations": "dobj(inhibits, transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": 2, "Sentence": "Previously, it was shown that the [PROTEIN1] GerE [/PROTEIN1] protein inhibits transcription in vitro of the [PROTEIN2] sigK [/PROTEIN2] gene encoding sigmaK."}
|
| 2 |
+
{"Unnamed: 0": 106, "Gene1": "sigma(K)", "Gene2": "cotB", "Keywords": "activated, transcription", "Direct dependency relations": "dobj(activated,transcription)", "INO Type": "activation of gene transcription", "INO ID": "INO_0000051", "Num. Keywords": 2, "Sentence": "A low concentration of GerE activated [PROTEIN2] cotB [PROTEIN2] transcription by final [PROTEIN1] sigma(K) [/PROTEIN1] RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC."}
|
| 3 |
+
{"Unnamed: 0": 78, "Gene1": "sigma X", "Gene2": "CsbB", "Keywords": "contributes, expression", "Direct dependency relations": "nmod(contributes,expression)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "[PROTEIN1] sigma X [/PROTEIN1] also contributes to the expression of [PROTEIN2] CsbB [/PROTEIN2], a putative membrane-bound glucosyl transferase that is partially controlled by the sigma B stress response sigma factor."}
|
| 4 |
+
{"Unnamed: 0": 3, "Gene1": "Spo0A", "Gene2": "spoIIG", "Keywords": "transcription, depends", "Direct dependency relations": "nsubj(depends, transcription)", "INO Type": "regulation of transcription", "INO ID": "INO_0000032", "Num. Keywords": 2, "Sentence": "In this mutant, expression of the [PROTEIN2] spoIIG [/PROTEIN2] gene, whose transcription depends on both sigma(A) and the phosphorylated Spo0A protein, [PROTEIN1] Spo0A [/PROTEIN1]~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C."}
|
| 5 |
+
{"Unnamed: 0": 163, "Gene1": "sigma W", "Gene2": "YfhM", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase ([PROTEIN2] YfhM [/PROTEIN2]) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
|
| 6 |
+
{"Unnamed: 0": 47, "Gene1": "SpoIIE", "Gene2": "sigmaF", "Keywords": "activation, requires", "Direct dependency relations": "nsubj(requires, activation)\r\n", "INO Type": "regulation of gene activation", "INO ID": "INO_0000037", "Num. Keywords": 2, "Sentence": "Cell-specific activation of transcription factor [PROTEIN2] sigmaF [/PROTEIN2] during sporulation in Bacillus subtilis requires the formation of the polar septum and the activity of a serine phosphatase ([PROTEIN1] SpoIIE [/PROTEIN1]) located in the septum."}
|
| 7 |
+
{"Unnamed: 0": 64, "Gene1": "GerE", "Gene2": "cotD", "Keywords": "low level, activated, transcription", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "activation of gene transcription by low level protein", "INO ID": "INO_0000052", "Num. Keywords": 3, "Sentence": "A low level of [PROTEIN1] GerE [/PROTEIN1] activated transcription of [PROTEIN2] cotD [/PROTEIN2] by sigmaK RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription."}
|
| 8 |
+
{"Unnamed: 0": 49, "Gene1": "SpoIIE", "Gene2": "sigmaF", "Keywords": "activates", "Direct dependency relations": "ONE WORD", "INO Type": "activation", "INO ID": "INO_0000024", "Num. Keywords": 1, "Sentence": "The [PROTEIN1] SpoIIE [/PROTEIN1] phosphatase indirectly activates [PROTEIN2] sigmaF [/PROTEIN2] by dephosphorylating a protein (SpoIIAA-P) in the pathway that controls the activity of the transcription factor."}
|
| 9 |
+
{"Unnamed: 0": 154, "Gene1": "sigmaG", "Gene2": "tlp", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": 1, "Sentence": "The sspH and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, [PROTEIN1] sigmaG [/PROTEIN1]; the sspN-[PROTEIN2] tlp [/PROTEIN2] operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, sigmaF."}
|
| 10 |
+
{"Unnamed: 0": 38, "Gene1": "Spo0A", "Gene2": "sigE", "Keywords": "phosphorylated, activator, transcription", "Direct dependency relations": "MORE THAN TWO KEYWORDS", "INO Type": "activation of gene transcription by phosphorylated protein", "INO ID": "INO_0000081", "Num. Keywords": 3, "Sentence": "Production of sigmaK about 1 h earlier than normal does affect [PROTEIN1] Spo0A [/PROTEIN1], which when phosphorylated is an activator of [PROTEIN2] sigE [/PROTEIN2] transcription."}
|
| 11 |
+
{"Unnamed: 0": 96, "Gene1": "sigma(K)", "Gene2": "cotX", "Keywords": "transcription", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": 1, "Sentence": "Transcription of the cotB, cotC, and [PROTEIN2] cotX [/PROTEIN2] genes by final [PROTEIN1] sigma(K) [/PROTEIN1] RNA polymerase is activated by a small, DNA-binding protein called GerE."}
|
| 12 |
+
{"Unnamed: 0": 141, "Gene1": "ClpX", "Gene2": "sigmaA", "Keywords": "dependent, stimulation", "Direct dependency relations": "amod(stimulation, ClpX-dependent)", "INO Type": "positve regulation of protein activity", "INO ID": "INO_0000104", "Num. Keywords": 2, "Sentence": "The addition of [PROTEIN1] ClpX [/PROTEIN1] to in vitro transcription reactions resulted in the stimulation of RNAP holoenzyme activity, but sigmaH-RNAP was observed to be more sensitive to ClpX-dependent stimulation than [PROTEIN2] sigmaA [/PROTEIN2]-RNAP."}
|
| 13 |
+
{"Unnamed: 0": 129, "Gene1": "sigmaA", "Gene2": "clpC", "Keywords": "preventing, transcription", "Direct dependency relations": "dobj(preventing,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": 2, "Sentence": "Our data demonstrate that the CtsR protein acts as a global repressor of the [PROTEIN2] clpC [/PROTEIN2] operon, as well as other class III heat shock genes, by preventing unstressed transcription from either the sigmaB- or [PROTEIN1] sigmaA [/PROTEIN1]-dependent promoter and might be inactivated or dissociate under inducing stress conditions."}
|
| 14 |
+
{"Unnamed: 0": 158, "Gene1": "sigma W", "Gene2": "RacX", "Keywords": "regulon, includes", "Direct dependency relations": "nsubj(includes,regulon)", "INO Type": "gene expression regulation", "INO ID": "INO_0000044", "Num. Keywords": 2, "Sentence": "The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase ([PROTEIN2] RacX [/PROTEIN2]), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides."}
|
| 15 |
+
{"Unnamed: 0": 59, "Gene1": "sigmaK", "Gene2": "gerE", "Keywords": "transcribed", "Direct dependency relations": "ONE WORD", "INO Type": "gene transcription", "INO ID": "INO_0000173", "Num. Keywords": 1, "Sentence": "Most cot genes, and the [PROTEIN2] gerE [/PROTEIN2] gene, are transcribed by [PROTEIN1] sigmaK [/PROTEIN1] RNA polymerase."}
|
| 16 |
+
{"Unnamed: 0": 33, "Gene1": "YfhP", "Gene2": "yfhQ", "Keywords": "negative regulator, transcription", "Direct dependency relations": "nmod:for(regulator, transcription); amod(regulator, negative)", "INO Type": "negative regulation of transcription", "INO ID": "INO_0000074", "Num. Keywords": 2, "Sentence": "These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of [PROTEIN2] yfhQ [/PROTEIN2], yfhR, sspE and yfhP."}
|
| 17 |
+
{"Unnamed: 0": 42, "Gene1": "sigmaK", "Gene2": "sigE", "Keywords": "expression, negatively regulated", "Direct dependency relations": "nsubjpass(regulated, expression); advmod(regulated, negatively)", "INO Type": "negative regulation of gene expression", "INO ID": "INO_0000039", "Num. Keywords": 2, "Sentence": "In the mother cell compartment of sporulating cells, expression of the sigE gene, encoding the earlier-acting sigma factor, [PROTEIN2] sigmaE [/PROTEIN2], is negatively regulated by the later-acting sigma factor, [PROTEIN1] sigmaK [/PROTEIN1]."}
|
| 18 |
+
{"Unnamed: 0": 151, "Gene1": "sigmaG", "Gene2": "sspH", "Keywords": "recognized ", "Direct dependency relations": "ONE WORD", "INO Type": "association", "INO ID": "MI_0914", "Num. Keywords": 1, "Sentence": "The [PROTEIN2] sspH [/PROTEIN2] and sspL genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, [PROTEIN1] sigmaG [/PROTEIN1]; the sspN-tlp operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, sigmaF."}
|
| 19 |
+
{"Unnamed: 0": 73, "Gene1": "ComK", "Gene2": "hag", "Keywords": "negatively controls, transcription", "Direct dependency relations": "dobj(controls, transcription); advmod(controls, negatively)", "INO Type": "negative regulation of gene transcription", "INO ID": "INO_0000042", "Num. Keywords": 2, "Sentence": "[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of [PROTEIN2] hag [/PROTEIN2] by stimulating the transcription of comF-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity."}
|
| 20 |
+
{"Unnamed: 0": 93, "Gene1": "SpoIIID", "Gene2": "cotB", "Keywords": "bind", "Direct dependency relations": "ONE WORD", "INO Type": "direct interaction", "INO ID": "MI_0407", "Num. Keywords": 1, "Sentence": "DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the cotC promoter region, binds weakly to one site in the cotX promoter, and does not bind specifically to [PROTEIN2] cotB [/PROTEIN2]."}
|
| 21 |
+
{"Unnamed: 0": 117, "Gene1": "PhoP~P", "Gene2": "tagD", "Keywords": "repress, transcription", "Direct dependency relations": "dobj(repress,transcription)", "INO Type": "inhibition of gene transcription", "INO ID": "INO_0000046", "Num. Keywords": 2, "Sentence": "The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the [PROTEIN2] tagA [/PROTEIN2]and tagD promoters and also to activate the transcription of the tuaA promoter."}
|