Table 1.
Comparison of significant pathways enriched by DEGs associated with cytogenetic risk in paired bulk MNCs versus VLBs
| Cytogenetic-Related Genes in MNCs (N = 392) | Cytogenetic-Related Genes in VLBs (N = 455) | ||||
|---|---|---|---|---|---|
| Pathway Rank (N = 835) | Pathway Name | Entities FDR | Pathway Rank (N = 1020) | Pathway Name | Entities FDR |
| 1 | Phosphorylation of CD3 and TCR zeta chains | 1.09E-11 | 1 | Transcriptional regulation of granulopoiesis | 8.70E-05 |
| 2 | Translocation of ZAP-70 to Immunological synapse | 2.46E-11 | 2 | NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport & efflux | 0.003861 |
| 3 | PD-1 signaling | 4.86E-11 | 3 | NR1H2 and NR1H3-mediated signaling | 0.006610 |
| 4 | Generation of second messenger molecules | 2.46E-09 | 4 | RUNX3 regulates CDKN1A transcription | 0.061994 |
| 5 | Neutrophil degranulation | 4.79E-07 | 13 | Neutrophil degranulation | 0.450842 |
| 6 | MHC class II antigen presentation | 4.79E-07 | 53 | Cytokine Signaling in Immune system | 0.593232 |
| 7 | Costimulation by the CD28 family | 4.94E-07 | 90 | Immune System | 0.593232 |
| 8 | Downstream TCR signaling | 6.04E-05 | 128 | Interferon Signaling | 0.593232 |
| 9 | TCR signaling | 1.22E-04 | 359 | MHC class II antigen presentation | 0.593232 |
| 10 | Interferon Signaling | 7.42E-04 | 535 | Generation of second messenger molecules | 0.626337 |
| 11 | Immune System | 7.42E-04 | 687 | Translocation of ZAP-70 to Immunological synapse | 0.779539 |
| 12 | Interferon gamma signaling | 0.001212 | 718 | Phosphorylation of CD3 and TCR zeta chains | 0.802141 |
| 13 | Cytokine Signaling in Immune system | 0.003510 | 799 | Costimulation by the CD28 family | 0.871081 |
| 17 | RUNX3 regulates CDKN1A transcription | 0.107059 | 828 | TCR signaling | 0.898506 |
| 41 | Transcriptional regulation of granulopoiesis | 0.500239 | 991 | Interferon gamma signaling | 0.998825 |
| 55 | NR1H2 and NR1H3-mediated signaling | 0.557604 | Not Identified | PD-1 signaling | N/A |
| 59 | NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport & efflux | 0.557604 | Not Identified | Downstream TCR signaling | N/A |
The lists of DEGs significantly associated with cytogenetic risk groups from paired bulk MNCs and VLBs were downloaded into Reactome to identify pathways enriched in the lists. Pathways significantly associated with cytogenetic risk in bulked MNCs and VLBs were examined separately. Table shows the significance and rank by FDR of individual pathways that were significant in MNCs and VLBs using the list derived from bulk MNCs (left columns) and VLBs (right columns). Those pathways significant associated with the list of genes from bulk MNCs and VLBs are highlighted in light blue and gold, respectively. The significant pathways identified in the bulk MNCs (N = 13) were not significantly enriched for in the VLBs, and vice versa