COXPRESdb

ver. 6.0

last update; Feb. 04. 2015

Rank and Mutual Rank (MR)

Coexpressed gene rank

In COXPRESdb, a rank of correlation value is used rather than correlation value itself. Here,Rab indicates correlation rank from gene A to gene B.

Example: Top 5 co-expressed gene list for gene A

Rank Cor Locus
0 1.00 gene A
1 0.93 gene E
2 0.93 gene D
3 0.93 gene B
4 0.93 gene C
5 0.92 gene F
In this case, Rab = 3.

We do not introduce any cut-off threshold. Namely even if the correlation value between two loci is insignificantly low, the ranks are numbered from the strongest pair to the weakest pair.


Examples of the effictiveness of correlation rank rather than correlation value

The following genes are well coexpressed in the viewpoints of correlation rank, although correlation values are lower than 0.5.


Mutual Rank (MR)

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. 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))