Functional Genome Annotation by Combined Analysis across Microarray Studies of Trypanosoma brucei
(A) Gene pairs that are functionally related are coexpressed in both T. brucei and L. infantum. Therefore, an enrichment of functional linkages can be observed where correlation coefficients are high for both T. brucei and L. infantum (the x-axis represents the correlation coefficients of gene pairs in L. infantum, while the y-axis represents that correlation coefficients in T. brucei). Enrichment was calculated as Pr(ctbr = x±Δ,clif = y±Δ|I)/Pr(ctbr = x±Δ,clif = y±Δ|I′), where I and I′ represent sets of functionally associated and non-associated gene pairs according to KEGG, respectively. Also, ctbr and clif respectively represent correlation coefficients in T. brucei and L. infantum. Δ was chosen to be 0.05. (B) By considering the conservation of coexpression between T. brucei and L. infantum (red), we can more accurately predict functional linkages, compared to predictions that are based solely on T. brucei data (yellow) or L. infantum (light blue). About 50% of gene pairs whose expression profiles have correlation coefficients greater than 0.89 in T. brucei and 0.56 in L. infantum are estimated to be functionally related (black circle). These gene pairs cover ∼11.9% of all T. brucei genes with unambiguous L. infantum orthologs. The resultant conserved coexpression network is provided in Supplementary Dataset S1 and can also be downloaded at http://webpages.mcgill.ca/staff/Group2/rsalav/web/Suppl/20100109/index.htm. (C) Ribosome, proteasome and oxidative phosphrylation genes can be identified based on the conserved coexpression network. See Supplementary Table S9 for complete set of predictions.