Descriptive class | Cluster description | Cluster ID number | No. of probesets in cluster | No. of genes in cluster | Known markers present in cluster | Gene ontology annotation | Other annotation | Conservation of signature in skin dataset: Cluster number | Conservation of signature in skin dataset: significance of enrichment |
---|---|---|---|---|---|---|---|---|---|
* KEGG pathway, ** Curated gene set, *** Swiss-Prot | |||||||||
(p-value for EASE score) | Keywords (p-value) | ||||||||
(Adjusted Fisher’s test) | |||||||||
Immune | Macrophage | 7 | 220 | 163 | CD68, CD14, CD163, CSF1R, Fc Receptors (CD16, CD32, CD64), MHC II molecules | Immune system process (3.96e-32) | Â | 16 | 1.3E-120 |
Defence response (8.79e-22) | |||||||||
T cell | 8 | 181 | 145 | CD2, CD3, CD6, CD7, CD52, TCR | Immune system process (4.99e-35) | TCR signalling pathway (6.1e-25) * | 6 | 3.29E-93 | |
Signal transduction (7.32e-18) | |||||||||
T cell activation (2.58e-19) | |||||||||
Macrophage/T cell interface | 13 | 87 | 58 | Â | Immune response (7.20e-06) | Â | 34 | 2.6E-13 | |
IFN response | 12 | 115 | 73 | GBP1. IFI27, IFR1, IRF2, OAS1, SP100, STAT1, | Immune response (4.32e-26) | Genes upregulated by IFNB in HT1080 (1.48e-47)** | 51 | 4.06E-56 | |
Response to virus (1.15e-21) | |||||||||
Genes upregulated by IFNA in HT1080 (1.05e-43)** | |||||||||
MHC class I | 19 | 35 | 16 | HLA-A, HLA-B, HLA-C, HLA-E, B2M | Antigen processing and presentation (5.51e-17) | MHC 1 (9.29e-15)*** | 82 | 1.2E-58 | |
Ig/ plasma cell | 14 | 85 | 36 | Ig light and heavy chains, | Immune response (7.49e-10) | Ig C region (1.12e-10) | 21 | 2.48E-129 | |
B-cell | 79, 142 | 10, 7 | 6, 6 | CD19, CD20, CD79 | B-cell receptor complex (2.31e-06) | BCR signalling (1.28e-09)* | 6 | 6.52E-17 | |
Immune response (1.84e-08) | |||||||||
Mast cell | 93 | 9 | 4 | Tryptase, Fc receptor for IgE | Proteolysis (0.008) | Zymogen (4.77e-04)*** | 167 | 2.72E-27 | |
AP1 response | 48, 89 | 13, 9 | 11, 6 | FOS, JUNB, | Sequence specific DNA binding (2.19e-06) | DNA binding (2.75e-09)*** | - | - | |
Regulation of cellular process (1.2e-04) | |||||||||
Stroma | Extracellular matrix | 9 | 163 | 100 | BGN, CALD1, FN1, collagens | Extracellular matrix (1.93e-40) | Â | 88 | 5.5E-34 |
Cell adhesion (1.16e-17) | |||||||||
Adipocyte | 27 | 22 | 15 | ADIPOQ, LPL | Response to wounding (0.004) | PPAR signalling (1.46e-07)* | - | - | |
Adipocyte vs Fibroblast upregulated (1.49e-15)** | |||||||||
Endothelium | 29,38,49 | 20, 17, 13 | 17, 13, 11 | CD31, CD34, Endomucin, Endoglin, vWF | Cell adhesion (1.3e-08) | Upregulated in glomerul in DM vs normal (8.33e-14)** | 58 | 6.75E-16 | |
Blood vessel development (1.28e-10) | |||||||||
Brentani_Angiogenesis (6.87e-08)** | |||||||||
Endothelium/ECM | 59 | 11 | 6 | COL4A1, COL4A2 | Cell adhesion (4.13e-05) | Â | 215 | 1.22E-12 | |
Smooth muscle | 88, 249 | 9,6 | 5, 4 | Alpha SMA, calponin | Smooth muscle contraction (4.75e-05) | Muscle protein (3.95e-08)*** | 907 | 1.27E-11 | |
Skeletal muscle | 46 | 15 | 15 | Myoglobin, CKm, Myosin | Contractile fibre part (1.53e-17) | Â | 23 | 2.55E-31 | |
Muscle development (2.09e-05) | |||||||||
Cell cycle | Cell cycle | 6 | 239 | 182 | AURKA, BUB1, CHEK2, CDC2, MCM2 | Cell cycle (3.06e-59) | Serum fibroblast cell cycle (1.17e-117)** | 101 | 1.31E-26 |
DNA replication (1.48e-39) | |||||||||
Cell cycle related | 10, 16, 26 | 147, 52, 23 | 125, 44, 19 | Â | RNA binding (2.29e-11) | RNA binding (2.29e-14)*** | - | - | |
Ribosomal | Ribosomal | 54, 60, 64, 97 | 12, 11, 11, 8 | 12, 8, 6, 5 | RPL38, RPS10, RPS19 | Cytosolic ribosome (7.91e-13) | Ribosomal protein (8.44e-11)*** | 54 | 4.25E-36 |
Protein biosynthesis (1.62e-06)*** | |||||||||
Other functional classes | Histones | 20 | 30 | 26 | HIST1H1C, HIST1H2AB, HIST1H3H | Nucleosome (9.75e-23) | Nucleosome core (2.61e-21)*** | 160 | 9.15E-35 |
Chromatin assembly (9.24e-21) | |||||||||
Glycolysis | 47 | 13 | 5 | GAPDH, GPI | Glycolysis (1.46e-05) | Gluconeogenesis (9.37e-07)*** | 151 | 6E-30 | |
Haemoglobins | 91 | 9 | 2 | HBA1, HBB | Â | Â | 144 | 6E-31 | |
Affymetrix controls | Affymetrix controls | 23, 28 | 26, 22 | 26, 22 | Â | Â | Â | 99 | 4.57E-59 |