Help: co-expressed gene network

last update; May. 29. 2008

Nodes (genes)

Node Color	Description
Yellow	Target gene in gene page
Lighter gray	Additional genes
Orange	Commonly appeared genes in an orholog page

Edges (lines between genes)

Co-expressed gene networks in COXPRESdb are drawn based on rank of correlation. Use of correlation rank partially normalizes the density of genes in correlation space.

Correlation rank is asymmetric, namely the rank of gene B from gene A is not the same as the rank of gene A from gene B. Thus, the geometric averaged rank is used.
AveRank(AB) = √ (Rank(A→B) x Rank(B→A))

AveRank Edge thickness

[1 ~ 5) bold

[5 ~ 30) normal

[30 weak

Edge color indecates support data between the genes.

Edge type Description Data Source

Red dotted PPI Human Protein Reference Database

Orange Conserved coexpression NCBI HomoloGene and COXPRESdb

AveRank	Edge thickness
[1 ~ 5)	bold
[5 ~ 30)	normal
[30	weak

Edge type	Description	Data Source
Red dotted	PPI	Human Protein Reference Database
Orange	Conserved coexpression	NCBI HomoloGene and COXPRESdb

Example

Human SSR1	Mouse Ssr1