README.md

---
license: mit
task_categories:
- tabular-regression
tags:
- biology
pretty_name: Toxoplasma gondii Coexpression Network
size_categories:
- 10M<n<100M
---
# ToxoCEN: A Co-expression network for *Toxoplasma gondii*
Elucidating gene function is a major goal in biology, especially among non-model organisms.
However, doing so is complicated by the fact that molecular conservation does not always
mirror functional conservation, and that complex relationships among genes are responsible
for encoding pathways and higher-order biological processes. Co-expression, a promising
approach for predicting gene function, relies on the general principal that genes with
similar expression patterns across multiple conditions will likely be involved in the
same biological process. For Toxoplasma gondii, a prevalent human eukaryotic pathogen
greatly diverged from malaria, approximately 47% of the predicted genes in the genome
lack functional annotations. Here, we leveraged a large amount of publicly available
transcriptomic data to generate a T. gondii Co-Expression Network (ToxoCEN),
recapitulating known protein networks, predicting gene function, and
enabling insights into the principles influencing co-expression. Overall, co-expression
is a powerful tool for uncovering gene function, and decreases the experimental tests
needed to identify functions for currently under-annotated genes.

    CS Arnold, Y Wang, VB Carruthers, MJ O'Meara
    ToxoCEN: A Co-Expression Network for Toxoplasma gondii
    Code available at https://github.com/maomlab/CalCEN/tree/master/vignettes/ToxoCEN

**TGME49_transcript_annotations.tsv**
* [Toxoplasma gondii ME49](https://toxodb.org/toxo/app/record/dataset/NCBITAXON_508771) (NCBI Taxon:508771) annotated protein features collected from [ToxoDB](https://toxodb.org/toxo/app) Release 64

**top_coexp_hits.tsv**
* top 50 ToxoCEN associations for each gene

**top_coexp_hits_0.15.tsv**
* top ToxoCEN associations for each gene filtered by score > 0.85 and at most 50 per gene

**Data/estimated_expression_meta.tsv**
* Metadata for RNAseq estimated expression runs

**Data/estimated_expression.tsv**
* gene by RNA-seq run estimated expression

**Networks/ToxoCEN_network.tsv**
* ToxoCEN Co-expression network

**Networks/BlastP_network.tsv**
* Protein sequence similarity network