Salavati Lab


Institute of Parasitology


McGill University








Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei

Supplementary Information


Najafabadi H.S. and Salavati R.


NOTE: All the files that can be directly downloaded from this page are compressed. You will need to unzip the files, using an application such as 7-zip, before viewing or editing them.


Part 1: Coexpression networks of Trypanosoma brucei genes

The coexpression networks CoExp1Tbr and CoExp2Tbr can be found here (you need Cytoscape to open this file). This file also contains the conserved coexpression network based on comparison of expression profiles of T. brucei genes and their orthologs in L. infantum.


Part2: Finding informative regulatory elements from clusters of coexpressed genes

T. brucei genes were clustered using either Iclust or a K-means approach. To download the gene clusters based on Iclust, click here. To download the gene clusters based on K-means with 82 clusters, click here, and for K-means with 19 clusters click here. Two different sets of sequences were used, complete 3′ UTR sequences based on predictions of Benz et al., and truncated 3′ UTR sequences that were at most 1000nt long. The results of running FIRE on these datasets are as follows:



Iclust-based gene clusters

K-means-based 82 gene clusters

K-means-based 19 gene clusters

Complete 3′ UTR sequences




Truncated 3í UTR sequences







Reza Salavatiís profile at McGill

Last updated on 9/9/2010 11:23:50 AM