Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms

Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (April 2022) Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. Nucleic Acids Research. ISSN 0305-1048

PDF 2022.Crow.coexpression.pdf Available under License Creative Commons Attribution Non-commercial. Download (4MB)

Abstract

What makes a mouse a mouse, and not a hamster? Differences in gene regulation between the two organisms play a critical role. Comparative analysis of gene coexpression networks provides a general framework for investigating the evolution of gene regulation across species. Here, we compare coexpression networks from 37 species and quantify the conservation of gene activity 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. We find that ancient genes are expressed in multiple cell types and have well conserved coexpression patterns, however they are expressed at different levels across cell types. Thus, differential regulation of ancient gene programs contributes to transcriptional cell identity. We propose that this differential regulation may play a role in cell diversification in both the animal and plant kingdoms.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > annotation bioinformatics bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > animal bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > animal > mammal organism description > animal > mammal > rodent > mouse organism description > animal > mammal > rodent
CSHL Authors:	Gillis, Jesse Crow, Megan Suresh, Hamsini Lee, John
Communities:	CSHL labs > Gillis Lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	22 April 2022
Date Deposited:	02 May 2022 13:41
Last Modified:	11 Jan 2024 19:31
PMCID:	PMC9071420
URI:	https://repository.cshl.edu/id/eprint/40595

Actions (login required)

Administrator's edit/view item