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))
For drawing coexpressed gene network of a functional category, the genes for the networks are first selected.
- Select pair of the genes that are most strongly correlated in the functional category.
- Add the pair of genes to drawing gene list.
- 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.
- Back to the step 1.
Genes in MF:0004190 is shown in this table. They are sorted for their AveRank.
|Locus1||Locus2||AveRank||Cor* ||Drawing gene list|
|At3g61820||At1g01300|| 14.5||0.66 ||→ At3g61820, At1g01300|
|At4g22050||At5g33340|| 19.5||0.54 ||→ At3g61820, At1g01300, At4g22050, At5g33340|
|At1g69100||At1g31450|| 25 ||0.47 ||→ At3g61820, At1g01300, At4g22050, At5g33340, At1g69100, At1g31450|
|At1g31450||At5g33340|| 33.5||0.46 ||→ At3g61820, At1g01300, At4g22050, At5g33340, At1g69100, At1g31450|
|At4g04460||At2g03200|| 46 ||0.57 ||→ At3g61820, At1g01300, At4g22050, At5g33340, At1g69100, At1g31450, At4g04460, At2g03200|
|At1g25510||At4g35880||109.5||0.58||Stop 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;
|1 ~ 5||Bold lines|
| 5 ~ 30||Normal lines|
|30 ~ 50||Weak lines|
|50 ~ ||No lines|