Fig. 2

TCGA-STAD data results comparing normal versus tumor samples using CeTF. (A) Smear plot showing the difference of expression for 8,037 genes, which 151 are up-regulated (colored in red), 118 are down-regulated (blue color), and the dots in black color are not differentially expressed based in a difference of expression module cutoff of 2.57. There are 7 TFs up-regulated (green color), 9 TFs down-regulated (pink color), and 504 not differentially expressed TFs (grey color). (B) Smear plot showing the 163 HOXB3 targets. Of these, 76 are up-regulated, 58 are down-regulated, and 29 are not differentially expressed. The yellow dots represent the 149 targets associated with NT samples, and the green dots represent the 4 targets associated with TP samples. (C) Heatmap with 163 HOXB3 targets in NT samples. The bottom annotation has clinical information as tumor stage, AJCC pathologic N, AJCC pathologic T, AJCC pathologic stage, primary diagnosis, AJCC system edition, gender, and race. (D) Enrichment of 163 HOXB3 targets with Gene Ontology Biological Process showing which genes are enriched with the pathways and their expression difference. The bar plot on the left side shows the enrichment ratio. The left sidebar shows the enriched pathway significance with an asterisk if significant, a p-value less than 0.05. Finally, the top annotation shows the match between HOXB3 targets from CeTF and ChIP-seq. (E) Circos plot representing the HOXB3 targets and their chromosome position. HOXB3 is located on chromosome 17. The red line shows the 10 cis interactions (the target is located at the same chromosome HOXB3), and the black lines indicate a trans interaction (the target is locatedon a different chromosome than HOXB3). (F) Network with 134 down and up-regulated HOXB3 targets. The network has 135 nodes and 2520 edges. HOXB3 is represented in the center of the network in blue color. The green nodes represent the 79 targets found in CeTF that match with ChIP-seq targets for HOXB3 and the yellow nodes represent the 55 targets that don’t fit with them