COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

Abstract

Coexpressed gene databases are valuable resources for identifying new gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases are a fundamental platform in the field of plant biology, their use in animal studies is relatively limited. The COXPRESdb (http://coxpresdb.jp) provides coexpression relationships for multiple animal species, as comparisons of coexpressed gene lists can enhance the reliability of gene coexpression determinations. Here, we report the updates of the database, mainly focusing on the following two points. First, we updated our coexpression data by including recent microarray data for the previous seven species (human, mouse, rat, chicken, fly, zebrafish and nematode) and adding four new species (monkey, dog, budding yeast and fission yeast), along with a new human microarray platform. A reliability scoring function was also implemented, based on coexpression conservation to filter out coexpression with low reliability. Second, the network drawing function was updated, to implement automatic cluster analyses with enrichment analyses in Gene Ontology and in cis elements, along with interactive network analyses with Cytoscape Web. With these updates, COXPRESdb will become a more powerful tool for analyses of functional and regulatory networks of genes in a variety of animal species.

Systematic Identification of Molecular Links between Core and Candidate Genes in Breast Cancer

“…In order to assess the degree of coexpression between the novel interactions discovered after cDNA library screening, we downloaded human coexpression data from COXPRESdb v4 67 . Using full coexpression profiles of core genes as a background, we performed a significance test analogous to gene set enrichment analysis (GSEA) 68 , where gene pairs were rank-ordered according to their coexpression correlation, and the overall high rank of pairs corresponding to our experimental interactions was tested.…”

Exome sequencing reveals recurrent germ line variants in patients with familial Waldenström macroglobulinemia

“…Given the selected potential familial WM-associated variants/genes, we used Gene Relationships Across Implicated Loci (GRAIL) 30 coupled with global coexpressed gene database (COXPRESdb) 31 to assess the functional relatedness between these genes and those that were differentially expressed between bone marrow-derived primary WM cells compared with their normal counterparts, using GSE12668.…”

“…We next assessed the functional relatedness between potential familial WM-associated genes and the observed WM mRNA signature using the GRAIL algorithm 30 coupled with a global coexpression network COXPRESdb, as reported. 31 Using an FDR cutoff of 5%, 13 genes were predicted to be functionally related to the WM mRNA signature ( Figure 2B). In addition, the observed germ line variants were annotated and interpreted by implementing PolyPhen-2, as described, 35 thus allowing us to prioritize the deleteriousness of SNVs shared among all 3 affected WM family members.…”

Gene Expression: edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test

“…It is reasonable to hypothesize that true differentially expressed genes uniquely reported by a differential expression tool are functionally connected to genes in the consensus group. We use GRAIL (Raychaudhuri et al, 2009) coupled with a global coexpression network COXPRESdb (Obayashi et al, 2013) to assess the relatedness between a gene and the consensus group. As expected, nearly half of these seed genes are correlated with other members of the seed group, meaning that these consensus genes form a tightly connected network.…”