Figure 1.
A: Percentage of copy number gains and losses in tumor samples compared with their normal corresponding tissue for all chromosomes in fifteen study subjects. Losses are marked in Red below the baseline whereas gains are represented in Blue bars above the baseline. Circled chromosome numbers (12 and 14) reflect events of loss and gain solely observed in our dataset. B: Gender wise copy number changes in context of overall CNAs: The slight loss in the short arm of chromosomes 4, throughout chromosome 6 and 10 are frequent in the female group.
Table 1.
Counts of copy number gains and losses per subject.
Table 2.
Different CNAs in six recent studies on CRC (including our study).
Figure 2.
LOH and copy neutral LOH (Uniparental Disomy) events.
A: Segmental UPD events spanning multiple microRNA regions in chromosome 4 in patient 9F. B: LOH event in chromosome 17 of the same sample above. LOH is associated with copy number variations. C: Target Prediction analysis of miRNAs exhibit the probable involvement of known signaling pathways in colorectal cancer. Y-axis represents the numerical score indicative of predictive value. D: TPM3 and MUC1 are affected by UPD events in patient 7F. E: MYC region sustain LOH events and copy gains in patient 10F.
Table 3.
Regions of LOH and UPD.
Figure 3.
CNAs affecting transcription factor binding sites that may affect CRC related genes.
A: TFBS in regions where the copy number changes in excess of +/−35% are marked on chromosomes 7 (gain), 14 (loss), 20 (short arm gain (males), loss (females), long arm gain (both sexes)), 21 (loss) and X (somewhat similar to chromosome 20). The marking is by the gene names corresponding to these TFBS. B: Association of TFBS genes with significant functions and C: pathways. Cancer and TGF-β signaling were statistically the most significant associations for these affected genes.
Figure 4.
Chromosome wide GISTIC results.
A: Amplitude of gains and losses reveal 144 genes of different GISTIC scores across all chromosomes (numbered accordingly). The spikes in the grayed out regions of enrichment correspond to GISTIC scores for genes in these regions. B: Molecular network of genes affected by significant copy number aberrations in tumor samples. These events were located on chromosomes 7, 8, 18 and 20. 11 of 24 genes show no association with the colorectal cancer function. This is in conformation with the GISTIC analysis except for the G-score of TSHZ1. Solid lines between nodes indicate direct molecular interaction between connected genes with respect to CRC. Functions are indicated by shapes: enzymes (diamonds), cytokines (squares), kinases (triangles), transcription factors (horizontal ovals), transmembrane receptors (vertical ovals), transporters (trapezoids), and other (circles).
Table 4.
Chromosomes 18, 20,7 and 8 loss and gain.