CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species

Lee, John, Shah, Manthan, Ballouz, Sara, Crow, Megan, Gillis, Jesse (April 2020) CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species. BioRxiv. (Unpublished)

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Abstract

<h4>ABSTRACT</h4> Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to Zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties, or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying co nserved gene modules and co mparing co -expression net works. CoCoCoNet is a resource for both data and methods, providing gold-standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups, and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet , with data and R scripts available at ftp://milton.cshl.edu/data .

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
CSHL Authors:	Lee, John Ballouz, Sara Crow, Megan Gillis, Jesse Shah, Manthan
Communities:	CSHL labs > Gillis Lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	23 April 2020
Date Deposited:	21 May 2021 15:28
Last Modified:	21 May 2021 15:28
URI:	https://repository.cshl.edu/id/eprint/40116

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