CryptoCEN: A Co-expression network for Cryptococcus neoformans

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 Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. 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.

MJ O'Meara, JR Rapala, CB Nichols, C Alexandre, B Billmyre, JL Steenwyk, A Alspaugh, TR O'Meara CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair Code available at https://github.com/maomlab/CalCEN/tree/master/vignettes/CryptoCEN

h99_transcript_annotations.tsv

• Cryptococcus neoforman H99 (NCBI Taxon:235443) annotated protein features collected from FungiDB Release 49

top_coexp_hits.tsv

• top 50 CrypoCEN associations for each gene

top_coexp_hits_0.05.tsv

• top CrypoCEN associations for each gene filtered by score > 0.95 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

Data/sac_complex_interactions.tsv

• C. neoformans genes that are orthologous to S. cerevisiae genes who's proteins are involved in a protein complex

Networks/CryptoCEN_network.tsv

• Co-expression network

Networks/BlastP_network.tsv

• Protein sequence similarity network

Network/CoEvo_network.tsv

• Co-evolution network