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Among the 1213 genes, 344 were significantly stronger upregulated on wheat straw (transcript group C) and 65 on lactose (transcript group D; Table 1), whereas 804 were equally strong upregulated on wheat straw and lactose (transcript group E).
The codes of each subsequent transcript group were compared with those from the prior group.
The p-value was then calculated as the portion of random samples with higher Zelda enrichment than the transcript group.
We categorized two patients with both major and minor BCR ABL transcripts into the major BCR ABL transcript group.
We should like to stress that both xyr1 and clr2 belonged to transcript group E, i.e. they were expressed to similar levels on lactose and wheat straw.
Within the 3120 genes, five patterns (further called "transcript groups") could be distinguished: 1213 genes were significantly upregulated both on wheat straw and on lactose (Table 1); 1619 genes were upregulated only on wheat straw (transcript group A), in contrast to only 288 genes that were upregulated on lactose (transcript group B) only.
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To test the activation state of the cells, we selected transcript groups representative of cellular stress response, apoptosis, cell cycle, and hypoxia including genes of the MAPK pathway, Nfkb pathway, and TNF pathway (Additional file 2: Table S1).
Over-represented sequence motifs were found in several co-regulated transcript groups and were conserved in other kinetoplastids.
Figure 1A depicts the distributions of these transcript groups (TFED > SFED and TFED < SFED) with regard to BINs.
The number of transcript groups containing different numbers of paralogs did not vary significantly between species.
Clustering analysis revealed demarcated transcript groups with maximum gene activity at distinct developmental intervals.
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