Classify gene pair expression

Classifying the expression of a gene pair.

Overall Gene Pair Patterns

Automatically classified patterns of expression for a gene pair

db: Both Dead

Criteria: neither gene is expressed >= 1 FPKM in any dataset in the analysis. These gene pairs are not necessarily dead, but their are either only turned on under conditions not studied in the analysis or are expressed at such a low level pattern analysis is useless.

d1: Gene1 Dead

Criteria: gene1 is expressed < 1 FPKM in all datasets in the analysis AND is always expressed at least 10x less than the average expression of gene2.

d2: Gene2 Dead

Criteria: same as above just switch gene1 and gene2

nc: No Correlation

Criteria: The p-value of the spearman correlation between the expression of the two genes (after removing omitted conditions) is > .01 or the R value is .65 and greater than -.65.

c1: Correlated, Gene1 dominates

Criteria: Gene pair didn't fail the no-correlation test, and the average expression of gene1 is at least 2x that og gene2 (after removing omitted conditions).

c2: Correlated, Gene2 dominates

Criteria: Same as above just switch gene1 and gene2

ce: Correlated, Genes even

Criteria: Didn't fail the no correlation test, less than a two fold difference in mean expression between the expression of the two genes. The direction of correlation is positive.

ic: Inverse Correlation

Criteria: Any correlated gene (p-value < .01, absolute value of R > .65) where the correlation is negative.