Table 2.
Enriched or depleted gene sets in CUPs compared to metastases of known origin
| Up-regulated in CUP | ||||
|---|---|---|---|---|
| Gene Set name | Transcripts | Overlap | k/K | p value |
| PUJANA_BRCA1_PCC_NERWORK | ||||
| Genes constituting the BRCA1-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC > = 0.4) with that of BRCA1 | 1671 | 159 | 0.0952 | 0.00E + 00 |
| KINSEY_TARGETS_OF_EWSR1_FLII_UP | ||||
| Genes up-regulated in TC71 and EWS502 cells (Ewing’s sarcoma) upon knockdown of theEWSR1-FLII fusion | 1281 | 133 | 0.1038 | 0.00E + 00 |
| PUJANA_ATM_PCC_NETWORK | ||||
| Genes constituting the ATM-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC > = 0.4) with that of ATM | 1461 | 152 | 0.104 | 0.00E + 00 |
| PUJANA_CHEK2_PCC_NETWORK | ||||
| Genes constituting the CHEK2-PCC network of transcripts whose expression positively correlates (Pearson correlation coefficient, PCC > 0.4) with that of CHEK2 | 782 | 89 | 0.1138 | 0.00E + 00 |
| DODD_NASOPHARYNGEAL_CARCINOMA_DN | ||||
| Genes down-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. | 1375 | 157 | 0.1142 | 0.00E+00 |
| RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP | ||||
| Genes up-regulated in anaplastic thyroid carcinoma (ATC) compared to normal tissue. | 721 | 93 | 0.129 | 0.00+00 |
| MILI_PSEUDOPODIA_HAPTOTAXIS_UP | ||||
| Transcripts enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to haptotactic migratory stimulus by fibronectin, FN1 | 552 | 74 | 0.1341 | 0.00E+00 |
| RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP | ||||
| Genes up-regulated in poorly diffrentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue. | 640 | 94 | 0.1469 | 0.00E+00 |
| DECOSTA_UV_RESPONSE_VIA_ERCC3_DN | ||||
| Genes down-regulated transcripts in fibrolasts expressing ethier XP/CS or TDD mutant forms of ERCC3 [Gene ID=2071], after UVC irradiation | 855 | 126 | 0.1474 | 0.00E+00 |
| DECOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN | ||||
| Common down -regulated transcripts in fibroblasts expressing either XP/CS orTDD mutant forms of ERCC3 [Gene ID=2071], after UVC irradiation | 420 | 64 | 0.1524 | 0.00E+00 |
| OSMAN_BLADDER_CANCER_UP | ||||
| Common down-regulated in blood samples from bladder cancer patients | 402 | 57 | 0.1418 | 5.55E-16 |
| SENUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP | ||||
| Genes up-regulated in nasopharyngeal carcinoma (NPC) positive for LMP1 [Gene ID=9260], a latent gene of Epstein Barr virus (EBV) | 399 | 56 | 0.1404 | 155E-15 |
| SENUPTA_NASOPHARYNGEAL_CARCINOMA_UP | ||||
| Genes up-regulated in nsopharyngeal carcinoma relative to the normal tissue. | 286 | 46 | 0.1608 | 3.33E+15 |
| PUJANA_XPRSS_INT_NETWORK | ||||
| Genes constituting the XPRSS-Int network: intersection of genes whose expression correlates with BRCA1, BRCA2, ATM, and CHEK2 [Gene ID=672, 675, 472, 11200] in a compendium of normal tissues. | 167 | 34 | 0.2036 | 1.21E-14 |
| Down-regulated in CUP | ||||
| Gene Set Name | Transcripts | Overlap | k/K | p value |
| SHEN_SMARCA2_TARGETS_DN | ||||
| Genes whose expression negatively correlated with that of SMARCA2 [GeneID=6595] in prostate cancer samples | 360 | 73 | 032028 | 0.00E+00 |
| GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN | ||||
| Genes doen-regulated in non-metastic breast cancer tumors having type 1 amplifications in the 20q13 region; involves ZNF217 [Gene ID=7764] locus only. | 336 | 49 | 0.1458 | 7.71E-11 |
Gene set enrichments among up or down regulated mRNAs in the CUP core set were examined in the molecular signatures database (MSig) among the C2 curated gene sets comprising profiles from chemical and genetic perturbations, canonical pathways, BIOCARTA, KEGG and the reactome collections. The uncorrected p values are indicated. In all cases the false positive discovery rate was set to q < 0.01.