Disease Clusters?
Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.
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Cluster 79
14
Diseases
193
Unique genes
0.209
Avg. similarity score
Malignant peripheral nerve sheath tumor
Most-connected disease (7 links)
Disease
Searched: Clear cell sarcoma
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Clear cell sarcoma
Malignant peripheral nerve sheath tumor
Malignant soft tissue neoplasm
Soft tissue sarcoma
Synovial sarcoma
Desmoplastic small round cell tumor
Solitary fibrous tumor
Extraskeletal myxoid chondrosarcoma
Neurofibroma
Dermatofibrosarcoma protuberans
Lipoma
Spindle cell rhabdomyosarcoma
Myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies
Uterine benign neoplasm
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| Malignant peripheral nerve sheath tumor | 7 | 7 | 51 |
| Clear cell sarcoma | 6 | 6 | 26 |
| Malignant soft tissue neoplasm | 6 | 6 | 25 |
| Soft tissue sarcoma | 6 | 6 | 69 |
| Synovial sarcoma | 6 | 6 | 77 |
| Desmoplastic small round cell tumor | 5 | 5 | 34 |
| Solitary fibrous tumor | 5 | 5 | 34 |
| Extraskeletal myxoid chondrosarcoma | 4 | 4 | 29 |
| Neurofibroma | 4 | 4 | 20 |
| Dermatofibrosarcoma protuberans | 3 | 3 | 20 |
| Lipoma | 3 | 3 | 27 |
| Spindle cell rhabdomyosarcoma | 3 | 3 | 13 |
| Myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies | 1 | 1 | 1 |
| Uterine benign neoplasm | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CREB3L2 | 9 / 14 | Dermatofibrosarcoma protuberans, Extraskeletal myxoid chondrosarcoma, Lipoma, Malignant peripheral nerve sheath tumor and 5 more |
| FUS | 9 / 14 | Dermatofibrosarcoma protuberans, Extraskeletal myxoid chondrosarcoma, Lipoma, Malignant peripheral nerve sheath tumor and 5 more |
| SS18 | 9 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Extraskeletal myxoid chondrosarcoma, Malignant peripheral nerve sheath tumor and 5 more |
| SSX1 | 9 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Extraskeletal myxoid chondrosarcoma, Malignant peripheral nerve sheath tumor and 5 more |
| SSX2 | 9 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Extraskeletal myxoid chondrosarcoma, Malignant peripheral nerve sheath tumor and 5 more |
| CREB3L1 | 8 / 14 | Extraskeletal myxoid chondrosarcoma, Lipoma, Malignant peripheral nerve sheath tumor, Malignant soft tissue neoplasm and 4 more |
| ETV6 | 8 / 14 | Clear cell sarcoma, Dermatofibrosarcoma protuberans, Desmoplastic small round cell tumor, Malignant peripheral nerve sheath tumor and 4 more |
| EWSR1 | 8 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Extraskeletal myxoid chondrosarcoma, Lipoma and 4 more |
| NTRK3 | 8 / 14 | Clear cell sarcoma, Dermatofibrosarcoma protuberans, Desmoplastic small round cell tumor, Malignant peripheral nerve sheath tumor and 4 more |
| TP53 | 8 / 14 | Clear cell sarcoma, Dermatofibrosarcoma protuberans, Extraskeletal myxoid chondrosarcoma, Malignant peripheral nerve sheath tumor and 4 more |
| ALK | 7 / 14 | Dermatofibrosarcoma protuberans, Extraskeletal myxoid chondrosarcoma, Lipoma, Malignant peripheral nerve sheath tumor and 3 more |
| NPM1 | 7 / 14 | Dermatofibrosarcoma protuberans, Extraskeletal myxoid chondrosarcoma, Lipoma, Malignant peripheral nerve sheath tumor and 3 more |
| PIK3CA | 7 / 14 | Desmoplastic small round cell tumor, Lipoma, Malignant peripheral nerve sheath tumor, Neurofibroma and 3 more |
| PTEN | 7 / 14 | Clear cell sarcoma, Dermatofibrosarcoma protuberans, Extraskeletal myxoid chondrosarcoma, Lipoma and 3 more |
| ERG | 6 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Malignant peripheral nerve sheath tumor, Malignant soft tissue neoplasm and 2 more |
| FLI1 | 6 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Malignant peripheral nerve sheath tumor, Malignant soft tissue neoplasm and 2 more |
| FOXO1 | 6 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Malignant soft tissue neoplasm, Soft tissue sarcoma and 2 more |
| PAX3 | 6 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Malignant soft tissue neoplasm, Soft tissue sarcoma and 2 more |
| PAX7 | 6 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Malignant soft tissue neoplasm, Soft tissue sarcoma and 2 more |
| WT1 | 6 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Malignant soft tissue neoplasm, Soft tissue sarcoma and 2 more |
| ATF1 | 5 / 14 | Clear cell sarcoma, Malignant peripheral nerve sheath tumor, Malignant soft tissue neoplasm, Soft tissue sarcoma and 1 more |
| DDIT3 | 5 / 14 | Clear cell sarcoma, Extraskeletal myxoid chondrosarcoma, Lipoma, Malignant soft tissue neoplasm and 1 more |
| FGFR1 | 5 / 14 | Dermatofibrosarcoma protuberans, Malignant peripheral nerve sheath tumor, Soft tissue sarcoma, Solitary fibrous tumor and 1 more |
| KMT2D | 5 / 14 | Extraskeletal myxoid chondrosarcoma, Malignant peripheral nerve sheath tumor, Solitary fibrous tumor, Spindle cell rhabdomyosarcoma and 1 more |
| NUTM2B | 5 / 14 | Clear cell sarcoma, Dermatofibrosarcoma protuberans, Malignant peripheral nerve sheath tumor, Solitary fibrous tumor and 1 more |
| YWHAE | 5 / 14 | Clear cell sarcoma, Dermatofibrosarcoma protuberans, Malignant peripheral nerve sheath tumor, Solitary fibrous tumor and 1 more |
| BRAF | 4 / 14 | Clear cell sarcoma, Malignant peripheral nerve sheath tumor, Soft tissue sarcoma, Synovial sarcoma |
| COL1A1 | 4 / 14 | Dermatofibrosarcoma protuberans, Malignant peripheral nerve sheath tumor, Neurofibroma, Synovial sarcoma |
| EGFR | 4 / 14 | Clear cell sarcoma, Desmoplastic small round cell tumor, Soft tissue sarcoma, Synovial sarcoma |
| FAT1 | 4 / 14 | Malignant peripheral nerve sheath tumor, Soft tissue sarcoma, Solitary fibrous tumor, Spindle cell rhabdomyosarcoma |
| NRAS | 4 / 14 | Clear cell sarcoma, Malignant peripheral nerve sheath tumor, Soft tissue sarcoma, Synovial sarcoma |
| PDGFB | 4 / 14 | Dermatofibrosarcoma protuberans, Malignant peripheral nerve sheath tumor, Neurofibroma, Synovial sarcoma |
| ROS1 | 4 / 14 | Desmoplastic small round cell tumor, Extraskeletal myxoid chondrosarcoma, Soft tissue sarcoma, Synovial sarcoma |
| ARID2 | 3 / 14 | Malignant peripheral nerve sheath tumor, Soft tissue sarcoma, Synovial sarcoma |
| BCOR | 3 / 14 | Malignant peripheral nerve sheath tumor, Spindle cell rhabdomyosarcoma, Synovial sarcoma |
| CDKN2A | 3 / 14 | Clear cell sarcoma, Malignant peripheral nerve sheath tumor, Soft tissue sarcoma |
| CIC | 3 / 14 | Desmoplastic small round cell tumor, Malignant soft tissue neoplasm, Soft tissue sarcoma |
| CTNNB1 | 3 / 14 | Malignant peripheral nerve sheath tumor, Soft tissue sarcoma, Synovial sarcoma |
| ETV4 | 3 / 14 | Malignant soft tissue neoplasm, Soft tissue sarcoma, Synovial sarcoma |
| KDR | 3 / 14 | Extraskeletal myxoid chondrosarcoma, Soft tissue sarcoma, Synovial sarcoma |
| KMT2C | 3 / 14 | Desmoplastic small round cell tumor, Spindle cell rhabdomyosarcoma, Synovial sarcoma |
| KRAS | 3 / 14 | Lipoma, Malignant peripheral nerve sheath tumor, Synovial sarcoma |
| MED12 | 3 / 14 | Dermatofibrosarcoma protuberans, Malignant peripheral nerve sheath tumor, Synovial sarcoma |
| NF1 | 3 / 14 | Dermatofibrosarcoma protuberans, Neurofibroma, Solitary fibrous tumor |
| PIK3R1 | 3 / 14 | Soft tissue sarcoma, Solitary fibrous tumor, Synovial sarcoma |
| PTCH1 | 3 / 14 | Extraskeletal myxoid chondrosarcoma, Malignant peripheral nerve sheath tumor, Soft tissue sarcoma |
| SMARCB1 | 3 / 14 | Extraskeletal myxoid chondrosarcoma, Malignant peripheral nerve sheath tumor, Soft tissue sarcoma |
| SUZ12 | 3 / 14 | Dermatofibrosarcoma protuberans, Malignant peripheral nerve sheath tumor, Solitary fibrous tumor |
| APC | 2 / 14 | Desmoplastic small round cell tumor, Solitary fibrous tumor |
| ARID1A | 2 / 14 | Extraskeletal myxoid chondrosarcoma, Neurofibroma |
| BET1L | 2 / 14 | Lipoma, Uterine benign neoplasm |
| CBL | 2 / 14 | Malignant peripheral nerve sheath tumor, Solitary fibrous tumor |
| CDH1 | 2 / 14 | Soft tissue sarcoma, Synovial sarcoma |
| CDH11 | 2 / 14 | Malignant peripheral nerve sheath tumor, Synovial sarcoma |
| CREB1 | 2 / 14 | Clear cell sarcoma, Malignant soft tissue neoplasm |
| EED | 2 / 14 | Malignant peripheral nerve sheath tumor, Soft tissue sarcoma |
| EP300 | 2 / 14 | Desmoplastic small round cell tumor, Solitary fibrous tumor |
| ERBB4 | 2 / 14 | Solitary fibrous tumor, Synovial sarcoma |
| FBXW7 | 2 / 14 | Soft tissue sarcoma, Solitary fibrous tumor |
| FEV | 2 / 14 | Clear cell sarcoma, Malignant soft tissue neoplasm |
| FGFR3 | 2 / 14 | Soft tissue sarcoma, Solitary fibrous tumor |
| HGF | 2 / 14 | Dermatofibrosarcoma protuberans, Synovial sarcoma |
| HLA-A | 2 / 14 | Neurofibroma, Soft tissue sarcoma |
| HRAS | 2 / 14 | Soft tissue sarcoma, Synovial sarcoma |
| JAK2 | 2 / 14 | Desmoplastic small round cell tumor, Malignant soft tissue neoplasm |
| KDM6A | 2 / 14 | Soft tissue sarcoma, Spindle cell rhabdomyosarcoma |
| KMT2A | 2 / 14 | Soft tissue sarcoma, Synovial sarcoma |
| MYOD1 | 2 / 14 | Myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies, Spindle cell rhabdomyosarcoma |
| NF2 | 2 / 14 | Malignant peripheral nerve sheath tumor, Neurofibroma |
| NR4A3 | 2 / 14 | Clear cell sarcoma, Extraskeletal myxoid chondrosarcoma |
| PALB2 | 2 / 14 | Soft tissue sarcoma, Synovial sarcoma |
| PDGFRA | 2 / 14 | Malignant peripheral nerve sheath tumor, Synovial sarcoma |
| RASA1 | 2 / 14 | Desmoplastic small round cell tumor, Synovial sarcoma |
| SF3B1 | 2 / 14 | Extraskeletal myxoid chondrosarcoma, Synovial sarcoma |
| SPEN | 2 / 14 | Soft tissue sarcoma, Solitary fibrous tumor |
| STAG2 | 2 / 14 | Desmoplastic small round cell tumor, Malignant peripheral nerve sheath tumor |
| TERT | 2 / 14 | Lipoma, Soft tissue sarcoma |
| USP6 | 2 / 14 | Malignant peripheral nerve sheath tumor, Synovial sarcoma |
What do these columns mean?
- Connections in cluster
- How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
- Significant partners
- How many of those links are statistically significant (FDR q < 0.05).
- Curated genes
- Distinct curated genes linked to that disease in GeDiPNet.
- Member diseases (Top shared genes)
- How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
- Overlap genes (x / y)
- x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
- Cluster gene count
- Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
- Fold enrichment
- Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
- P-value / FDR q-value
- Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
- Shared genes (Pairs within this cluster)
- Number of curated genes the two diseases in that row have in common.
- Similarity score (Pairs within this cluster)
- Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.
Enriched Pathways (why this cluster is grouped, biologically)
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Transcriptional misregulation in cancer | KEGG | 36 / 198 | 11.3× | 4.51e-28 | 1.13e-24 ✓ sig. |
| Prostate cancer | KEGG | 28 / 98 | 17.8× | 7.80e-28 | 1.88e-24 ✓ sig. |
| Pathways in cancer | KEGG | 51 / 533 | 6.0× | 4.95e-26 | 9.32e-23 ✓ sig. |
| PI3K-Akt signaling pathway | KEGG | 39 / 361 | 6.7× | 9.83e-22 | 9.98e-19 ✓ sig. |
| EGFR tyrosine kinase inhibitor resistance | KEGG | 22 / 80 | 17.1× | 1.22e-21 | 1.22e-18 ✓ sig. |
| Central carbon metabolism in cancer | KEGG | 21 / 71 | 18.4× | 1.91e-21 | 1.83e-18 ✓ sig. |
| Gastric cancer | KEGG | 26 / 150 | 10.8× | 7.00e-20 | 5.09e-17 ✓ sig. |
| Melanoma | KEGG | 20 / 73 | 17.0× | 9.97e-20 | 7.13e-17 ✓ sig. |
| Hepatocellular carcinoma | KEGG | 27 / 170 | 9.9× | 1.40e-19 | 9.82e-17 ✓ sig. |
| Endometrial cancer | KEGG | 18 / 59 | 19.0× | 8.35e-19 | 5.14e-16 ✓ sig. |
| Non-small cell lung cancer | KEGG | 18 / 73 | 15.3× | 5.83e-17 | 2.58e-14 ✓ sig. |
| Glioma | KEGG | 18 / 76 | 14.7× | 1.27e-16 | 5.19e-14 ✓ sig. |
| Colorectal cancer | KEGG | 18 / 87 | 12.9× | 1.68e-15 | 5.58e-13 ✓ sig. |
| Breast cancer | KEGG | 22 / 148 | 9.3× | 1.69e-15 | 5.60e-13 ✓ sig. |
| MAPK signaling pathway | KEGG | 29 / 299 | 6.0× | 4.89e-15 | 1.48e-12 ✓ sig. |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| positive regulation of transcription by RNA polymerase II | GO:0045944 | 67 / 1,208 | 5.4× | 1.07e-31 | 7.02e-28 ✓ sig. |
| positive regulation of DNA-templated transcription | GO:0045893 | 52 / 778 | 6.5× | 5.53e-28 | 2.50e-24 ✓ sig. |
| regulation of DNA-templated transcription | GO:0006355 | 58 / 1,454 | 3.9× | 5.72e-20 | 9.07e-17 ✓ sig. |
| negative regulation of transcription by RNA polymerase II | GO:0000122 | 47 / 1,002 | 4.5× | 8.14e-19 | 1.09e-15 ✓ sig. |
| positive regulation of cell population proliferation | GO:0008284 | 33 / 532 | 6.0× | 9.08e-17 | 9.00e-14 ✓ sig. |
| chromatin organization | GO:0006325 | 30 / 449 | 6.5× | 3.57e-16 | 3.14e-13 ✓ sig. |
| chromatin remodeling | GO:0006338 | 26 / 320 | 7.9× | 3.71e-16 | 3.24e-13 ✓ sig. |
| regulation of transcription by RNA polymerase II | GO:0006357 | 55 / 1,602 | 3.3× | 5.44e-16 | 4.67e-13 ✓ sig. |
| cell surface receptor protein tyrosine kinase signaling pathway | GO:0007169 | 17 / 120 | 13.7× | 6.37e-15 | 4.53e-12 ✓ sig. |
| positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | GO:0051897 | 21 / 217 | 9.4× | 9.50e-15 | 6.53e-12 ✓ sig. |
| negative regulation of cell population proliferation | GO:0008285 | 28 / 444 | 6.1× | 1.62e-14 | 1.07e-11 ✓ sig. |
| positive regulation of cell differentiation | GO:0045597 | 14 / 83 | 16.3× | 1.39e-13 | 7.76e-11 ✓ sig. |
| peptidyl-tyrosine phosphorylation | GO:0018108 | 11 / 39 | 27.3× | 1.40e-13 | 7.80e-11 ✓ sig. |
| regulation of cell population proliferation | GO:0042127 | 19 / 201 | 9.2× | 2.90e-13 | 1.53e-10 ✓ sig. |
| positive regulation of MAPK cascade | GO:0043410 | 19 / 224 | 8.2× | 2.03e-12 | 9.11e-10 ✓ sig. |