ver. 6.0

last update; Feb. 03. 2015

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 Example
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;

AveRankLine thickness
1 ~ 5Bold lines
  5 ~ 30Normal lines
30 ~  Weak lines