ATTED-II

ver. 9.0

last update; Feb. 03. 2015

Help: Gene selection for coexpressed gene network of functional categories

Rank correlation between pairwise genes

Coexpressed gene networks in ATTED-II 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))

Selection of the most correlated pair of genes

For drawing coexpressed gene network of a functional category, the genes for the networks are first selected.

  1. Select pair of the genes that are most strongly correlated in the functional category.
  2. Add the pair of genes to drawing gene list.
  3. Stop to extract genes in following cases.

    • When the AveRank between the pair of genes are larger than 50.
    • When the number of non-redundant genes in drawing gene list reaches 15.
      In each step of the gene extractions, the number of genes in the drawing gene list increase 0, 1 or 2. Thus in some cases, the number of genes in the drawing gene list could be 16.
  4. Back to the step 1.


Example of the gene selection for MF:0004190

Genes in MF:0004190 is shown in this table. They are sorted for their AveRank.

Locus1Locus2AveRankCor* Drawing gene list
At3g61820At1g01300 14.50.66 At3g61820, At1g01300
At4g22050At5g33340 19.50.54 → At3g61820, At1g01300, At4g22050, At5g33340
At1g69100At1g31450 25  0.47 → At3g61820, At1g01300, At4g22050, At5g33340, At1g69100, At1g31450
At1g31450At5g33340 33.50.46 → At3g61820, At1g01300, At4g22050, At5g33340, At1g69100, At1g31450
At4g04460At2g03200 46  0.57 → At3g61820, At1g01300, At4g22050, At5g33340, At1g69100, At1g31450, At4g04460, At2g03200
At1g25510At4g35880109.50.58Stop because the AveRank is larger than 50
............
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 ~ 50Weak lines
50 ~      No lines