README.md

---
license: mit
task_categories:
- tabular-regression
tags:
- biology
pretty_name: Cryptococcus Coexpression Network
size_categories:
- 10M<n<100M
---
# 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