Gene selections for coexpressed gene networks

last update; Aug. 24. 2018

Gene selections for coexpressed gene networks

COXPRESdb provides four types of coxpressed gene networks.

Type	Target gene	Requirements for Additional genes	Maximum number of genes to select	Indication of conserved nodes in the orthologus gene(s)	Edges	Genes without any edge
For a perticular gene	one target gene (yellow node)	upto 4-path coexpression	20	yes (orange nodes)	Top 3 MR	not draw
GO network	genes in a GO term (lighter gray or orenge nodes)	1-path coexpression for at least 2 target genes	200	yes (orange nodes)	Top 3 MR	not draw
Tissue-specific network	genes expressed in a tissue (white nodes)	no addition	1000	no	Top 2 MR	not draw
User-defined gene network	all user-defined genes (lighter gray)	upto 2-path coexpression	100	no	Top 3 MR	draw (default)

Mutual Rank (MR)

Coexpressed 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. And thus, the geometric averaged rank between the two directional ranks is used, which we call Mutual Rank (MR).

MR(AB) = √ (Rank(A→B) x Rank(B→A))

Selection of the most correlated pair of genes

After the extraction of genes, all relationships in the drawing gene list are drawn according to the following thresholds;

AveRank	Line thickness
1 ~ 5	Bold lines
5 ~ 30	Normal lines
30 ~	Weak lines