Table 1.
Cellular processes that are associated with a lethal tumor micro-environment in human breast cancer (Cav-1 deficient stroma)
| Data Set | p-value | Detailed Description |
| Stem Cells, HGF/MET Signaling, the EMT and Metastasis | ||
| STEMCELL_NEURAL_UP | 1.45E-17 | Enriched in mouse neural stem cells, compared to differentiated brain and bone marrow cells |
| MORF_BMI1 | 3.74E-10 | Neighborhood of BMI1 B lymphoma Mo-MLV insertion region (mouse) in the MORF expression compendium |
| STEMCELL_EMBRYONIC_UP | 6.51E-09 | Enriched in mouse embryonic stem cells, compared to differentiated brain and bone marrow cells |
| HSC_LATEPROGENITORS_SHARED | 8.03E-09 | Upregulated in mouse hematopoietic late progenitors from both adult bone marrow and fetal liver (Cluster VI, Late Progenitors Shared) |
| STEMCELL_HEMATOPOIETIC_UP | 8.50E-09 | Enriched in mouse hematopoietic stem cells, compared to differentiated brain and bone marrow cells |
| HSC_LATEPROGENITORS_FETAL | 2.72E-08 | Up regulated in mouse hematopoietic late progenitors from fetal liver (Late Progenitors Shared + Fetal) |
| RUTELLA_HEPATGFSNDCS_UP | 6.88E-06 | Genes upregulated by HGF treatments |
| MORF_TPR | 1.59E-05 | Neighborhood of TPR translocated promoter region (to activated MET oncogene) in the MORF expression compendium |
| Inflammation, Host Defense and Graft Rejection | ||
| WIELAND_HEPATITIS_B_INDUCED | 5.92E-12 | Genes induced in the liver during hepatitis B viral clearance in chimpanzees |
| REOVIRUS_HEK293_UP | 1.56E-06 | Upregulated at any timepoint up to 24 hours following infection of HEK293 cells with reovirus strain T3Abney |
| DEFENSE_RESPONSE | 1.73E-06 | Genes annotated by the GO term GO:0006952. Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack |
| FLECHNER_KIDNEY_TRANSPLANT_ | ||
| REJECTION_UP | 3.80E-06 | Genes upreglated in acute rejection transplanted kidney biopsies relative to well functioning transplanted kidney biopsies from stable, immunosuppressed, recipients (median FDR <0.14% per comparison) |
| CARIES_PULP_UP | 2.02E-05 | Up-regulated in pulpal tissue from extracted carious teeth (cavities), compared to tissue from extracted healthy teeth |
| ER Negative Breast Cancer, BRCA1 Mutations, Cancer-Related Genes and Resistance to Chemotherapy | ||
| BRCA_ER_NEG | 6.60E-11 | Genes whose expression is consistently negatively correlated with estrogen receptor status in breast cancer] |
| MORF_DEK | 1.30E-08 | Neighborhood of DEK oncogene (DNA binding) in the MORF expression compendium |
| BRCA_BRCA1_POS | 7.38E-05 | Genes whose expression is consistently positively correlated with brca1 germline status in breast cancer |
| BRENTANI_SIGNALING | 1.19E-04 | Cancer related genes involved in the cell signaling |
| DOX_RESIST_GASTRIC_UP | 2.45E-04 | Upregulated in gastric cancer cell lines resistant to doxorubicin, compared to parent chemosensitive lines |
| MORF_SS18 | 3.32E-04 | Neighborhood of SS18 synovial sarcoma translocation, chromosome 18 in the MORF expression compendium |
| IL4/STAT6 Signaling | ||
| GNF2_STAT6 | 2.67E-10 | Neighborhood of STAT6 |
| LU_IL4BCELL | 9.16E-05 | Genes induced in peripheral B cells by 4 hours of incubation with the cytokine IL-4 |
| TNF/NFκB Signaling | ||
| GNF2_TNFRSF1B | 2.08E-08 | Neighborhood of TNFRSF1B |
| GNF2_TYK2 | 3.63E-06 | Neighborhood of TYK2 |
| GNF2_CARD15 | 6.32E-06 | Neighborhood of CARD15 |
| MORF_BUB3 | 7.64E-06 | Neighborhood of BUB3 |
| I_KAPPAB_KINASE_NF_KAPPAB_ CASCADE | 2.05E-04 | Genes annotated by the GO term GO:0007249. A series of reactions initiated by the activation of the transcription factor NF-kappaB. |
| ST_FAS_SIGNALING_PATHWAY | 2.89E-04 | The Fas receptor induces apoptosis and NFκB activation when bound to Fas ligand |
| DNA Damage and Repair | ||
| MORF_BMI1 | 3.74E-10 | Neighborhood of BMI1 B lymphoma Mo-MLV insertion region (mouse) in the MORF expression compendium |
| MORF_RAD23A | 3.80E-08 | Neighborhood of RAD23A homolog A (S. cerevisiae) in the MORF expression compendium |
| MORF_PRKDC | 3.18E-07 | Neighborhood of PRKDC protein kinase, DNA-activated, catalytic polypeptide in the MORF expression compendium |
| MORF_DDB1 | 5.42E-07 | Neighborhood of DDB1 damage-specific DNA binding protein 1, 127 kDa in the MORF expression compendium |
| DNA_METABOLIC_PROCESS | 1.01E-06 | Genes annotated by the GO term GO:0006259. The chemical reactions and pathways involving DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. |
| DNA_BINDING | 3.39E-06 | Genes annotated by the GO term GO:0003677. Interacting selectively with DNA (deoxyribonucleic acid). |
| MORF_RPA2 | 9.64E-06 | Neighborhood of RPA2 replication protein A2, 32 kDa in the MORF expression compendium |
| MORF_XRCC5 | 1.72E-05 | Neighborhood of XRCC5 X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kDa) in the MORF expression compendium |
| MORF_RFC4 | 2.18E-05 | Neighborhood of RFC4 replication factor C (activator 1) 4, 37kDa in the MORF expression compendium |
| MORF_BUB1B | 5.69E-05 | Neighborhood of BUB1B budding uninhibited by benzimidazoles 1 homolog β (yeast) in the MORF expression compendium |
| MORF_TERF1 | 8.11E-05 | Neighborhood of TERF1 telomeric repeat binding factor (NIMA-interacting) 1 in the MORF expression compendium |
| MORF_RAD21 | 2.73E-04 | Neighborhood of RAD21 homolog (S. pombe) in the MORF expression compendium |
| Aging, Alzheimer Disease and Oxidative Stress | ||
| AGEING_KIDNEY_UP | 4.17E-07 | Upregulation is associated with increasing age in normal human kidney tissue from 74 patients |
| MORF_RAC1 | 1.88E-06 | Neighborhood of RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) in the MORF expression compendium |
| AGED_MOUSE_NEOCORTEX_UP | 4.47E-05 | Upregulated in the neocortex of aged adult mice (30-month) vs. young adult (5-month) |
| ALZHEIMERS_DISEASE_UP | 1.81E-04 | Upregulated in correlation with overt Alzheimer's Disease, in the CA1 region of the hippocampus |
| STRESS_ARSENIC_SPECIFIC_UP | 2.12E-04 | Genes upregulated 4 hours following arsenic treatment that discriminate arsenic from other stress agents |
| Pro- and Anti-Apoptotic Signaling | ||
| GNF2_CASP1 | 1.68E-08 | Neighborhood of CASP1 |
| APOPTOSIS_GO | 2.01E-06 | Genes annotated by the GO term GO:0006915. A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle the cell and result in cell death. Apoptosis begins internally with condensation and subsequent fragmentation of the cell nucleus (blebbing) while the plasma membrane remains intact. Other characteristics of apoptosis include DNA fragmentation and the exposure of phosphatidyl serine on the cell surface |
| PROGRAMMED_CELL_DEATH | 2.32E-06 | Genes annotated by the GO term GO:0012501. Cell death resulting from activation of endogenous cellular processes |
| MORF_AATF | 2.84E-06 | Neighborhood of AATF apoptosis antagonizing transcription factor in the MORF expression compendium |
| GNF2_MCL1 | 4.95E-06 | Neighborhood of MCL1 |
| GNF2_BNIP2 | 6.86E-06 | Neighborhood of BNIP2 |
| GNF2_CASP8 | 5.41E-05 | Neighborhood of CASP8 |
| MORF_ANP32B | 3.34E-04 | Neighborhood of ANP32B acidic (leucine-rich) nuclear phosphoprotein 32 family, member B in the MORF expression compendium |
| Hypoxia, Mitochondrial Damage and Mitochondrial Respiration | ||
| MORF_PRKDC | 3.18E-07 | Neighborhood of PRKDC protein kinase, DNA-activated, catalytic polypeptide in the MORF expression compendium |
| RCGCANGCGY_V$NRF1_Q6 | 3.24E-07 | Genes with promoter regions [−2 kb, 2 kb] around transcription start site containing the motif RCGCANGCGY which matches annotation for NRF1: nuclear respiratory factor 1 |
| VHL_NORMAL_UP | 3.10E-05 | Upregulated in VHL-null renal carcinoma vs. normal renal cells (Fig. 2c+e) |
| V$NRF1_Q6 | 1.93E-04 | Genes with promoter regions [− 2 kb, 2 kb] around transcription start site containing the motif CGCATGCGCR which matches annotation for NRF1: nuclear respiratory factor 1 |
| MENSE_HYPOXIA_UP | 1.94E-04 | List of Hypoxia-induced genes found in both Astrocytes and HeLa Cells |
| STRESS_ARSENIC_SPECIFIC_UP | 2.12E-04 | Genes upregulated 4 hours following arsenic treatment that discriminate arsenic from other stress agents |
| Metabolic Dys-regulation: Obesity, Catabolism, Starvation and Autophagy | ||
| NADLER_OBESITY_UP | 1.90E-06 | Genes with increased expression with obesity |
| MORF_PRKAG1 | 5.94E-05 | Neighborhood of PRKAG1 protein kinase, AMP-activated, γ1 non-catalytic subunit in the MORF expression compendium |
| PENG_GLUTAMINE_UP | 5.97E-05 | Genes upregulated in response to glutamine starvation |
| BIOPOLYMER_CATABOLIC_PROCESS | 1.22E-04 | Genes annotated by the GO term GO:0043285. The chemical reactions and pathways resulting in the breakdown of biopolymers, long, repeating chains of monomers found in nature e.g., polysaccharides and proteins |
| PENG_LEUCINE_UP | 1.92E-04 | Genes upregulated in response to leucine starvation |
| Other | ||
| MGGAAGTG_V$GABP_B | 8.60E-10 | Genes with promoter regions [− 2 kb, 2 kb] around transcription start site containing the motif MGGAAGTG which matches annotation for GABPA: GA binding protein transcription factor, α subunit 60 kDa<br> GABPB2: GA binding protein transcription factor, β subunit 2 |
| SCGGAAGY_V$ELK1_02 | 1.65E-07 | Genes with promoter regions [− 2 kb, 2 kb] around transcription start site containing the motif SCGGAAGY which matches annotation for ELK1: ELK1, member of ETS oncogene family |
| GNF2_PECAM1 | 3.03E-06 | Neighborhood of PECAM1 |
| ST_GA13_PATHWAY | 2.17E-05 | G-α-13 influences the actin cytoskeleton and activates protein kinase D, PI3K and Pyk2. |
| V$E2F1_Q6 | 1.65E-04 | Genes with promoter regions [−2kb, 2kb] around transcription start site containing the motif TTTSGCGS which matches annotation for E2F1: E2F transcription factor 1 |