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 98

12 diseases · 35 shared-gene connections
12 Diseases
145 Unique genes
0.249 Avg. similarity score
Thrombocythemia Most-connected disease (9 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Thrombocythemia 9 9 6
Thrombocytosis 9 9 6
Amegakaryocytic thrombocytopenia 8 8 2
Congenital amegakaryocytic thrombocytopenia 8 8 2
Essential thrombocythemia 6 6 13
Myeloproliferative disorder 5 5 53
Thrombocythemia with distal limb defects 5 5 1
congenital amegakaryocytic thrombocytopenia 1 5 5 1
thrombocythemia 1 5 5 1
thrombocythemia 2 5 5 1
Myelodysplastic syndrome 3 3 46
Clonal hematopoiesis 2 2 56

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
MPL 8 / 12 Amegakaryocytic thrombocytopenia, Congenital amegakaryocytic thrombocytopenia, congenital amegakaryocytic thrombocytopenia 1, Essential thrombocythemia and 4 more
THPO 7 / 12 Amegakaryocytic thrombocytopenia, Congenital amegakaryocytic thrombocytopenia, Essential thrombocythemia, Thrombocythemia and 3 more
JAK2 6 / 12 Clonal hematopoiesis, Essential thrombocythemia, Myelodysplastic syndrome, Myeloproliferative disorder and 2 more
CALR 4 / 12 Essential thrombocythemia, Myeloproliferative disorder, Thrombocythemia, Thrombocytosis
SH2B3 4 / 12 Essential thrombocythemia, Myeloproliferative disorder, Thrombocythemia, Thrombocytosis
DLK1 3 / 12 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloproliferative disorder
RUNX1 3 / 12 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloproliferative disorder
TERT 3 / 12 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloproliferative disorder
TP53 3 / 12 Essential thrombocythemia, Myelodysplastic syndrome, Myeloproliferative disorder
ATM 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
CHEK2 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
CYRIA 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
DNMT3A 2 / 12 Myelodysplastic syndrome, Myeloproliferative disorder
GATA2 2 / 12 Clonal hematopoiesis, Myelodysplastic syndrome
HBS1L 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
PARP1 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
STN1 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
TCL1A 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
TET2 2 / 12 Essential thrombocythemia, Myelodysplastic syndrome
TUNAR 2 / 12 Clonal hematopoiesis, Myeloproliferative disorder
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 ⇵
Pathways in cancer
JAK2, RUNX1, TERT, TP53, GNB1, CDKN2B, CTNNA1, DAPK1, EPO, HDAC1, KRAS, MYC
 KEGG 27 / 533 4.2× 1.82e-10 2.49e-8 ✓ sig.
PI3K-Akt signaling pathway
JAK2, TCL1A, TP53, EFNA5, GNB1, EPO, KRAS, MYC, TLR2, BCL2, BCL2L1, MYB
 KEGG 20 / 361 4.6× 1.22e-8 1.04e-6 ✓ sig.
Chronic myeloid leukemia
RUNX1, TP53, HDAC1, KRAS, MYC, BCL2L1, MECOM, BCR, TGFB1
 KEGG 9 / 77 9.7× 3.41e-7 1.92e-5 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
JAK2, KRAS, BCL2, BCL2L1, PDGFRB, IGF1R, FGF2, PDGFA, PDGFB
 KEGG 9 / 80 9.3× 4.76e-7 2.56e-5 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
JAK2, TP53, IRF4, MYC, BCL2, BCL2L1, FOXO1, FGF2, TGFB1, IL1B
 Reactome 10 / 108 7.7× 6.80e-7 3.48e-5 ✓ sig.
JAK-STAT signaling pathway
MPL, THPO, IL20RB, JAK2, EPO, MYC, BCL2, BCL2L1, PDGFRB, IFNA2, PDGFA, PDGFB
 KEGG 12 / 168 5.9× 8.56e-7 4.27e-5 ✓ sig.
Signaling by FGFR1 in disease
KRAS, BCR, FGFR1, FGFR1OP2, ZMYM2, FGF2
 Reactome 6 / 33 15.1× 2.36e-6 1.02e-4 ✓ sig.
Melanoma
TP53, KRAS, PDGFRB, FGFR1, IGF1R, FGF2, PDGFA, PDGFB
 KEGG 8 / 73 9.1× 2.58e-6 1.10e-4 ✓ sig.
Prostate cancer
TP53, KRAS, BCL2, FOXO1, PDGFRB, FGFR1, IGF1R, PDGFA, PDGFB
 KEGG 9 / 98 7.6× 2.69e-6 1.13e-4 ✓ sig.
Cellular senescence
ATM, CHEK2, HLA-C, ITPR2, TP53, HLA-B, CDKN2B, KRAS, MYC, FOXO1, TGFB1
 KEGG 11 / 157 5.8× 3.01e-6 1.25e-4 ✓ sig.
Human T-cell leukemia virus 1 infection
ATM, CHEK2, HLA-C, TERT, CALR, TP53, HLA-B, CDKN2B, KRAS, MYC, BCL2L1, MAD1L1
 KEGG 13 / 224 4.8× 3.07e-6 1.27e-4 ✓ sig.
Transcriptional misregulation in cancer
ATM, MEIS1, RUNX1, TP53, BMI1, HDAC1, LYL1, MYC, BCL2L1, FOXO1, IGF1R, PDGFA
 KEGG 12 / 198 5.0× 4.80e-6 1.84e-4 ✓ sig.
MicroRNAs in cancer
ATM, TP53, DNMT3A, EFNA5, BMI1, DNMT1, DNMT3B, EZH2, HDAC1, KRAS, MYC, BCL2
 KEGG 15 / 311 4.0× 5.16e-6 1.95e-4 ✓ sig.
Human immunodeficiency virus 1 infection
ATM, HLA-C, ITPR2, CALR, GNB1, HLA-B, KRAS, TLR2, BCL2, BCL2L1, CXCR4, IFNA2
 KEGG 12 / 213 4.7× 1.01e-5 3.39e-4 ✓ sig.
MAPK signaling pathway
TP53, EFNA5, PLA2G4A, KRAS, MYC, MECOM, PDGFRB, FGFR1, IGF1R, FGF2, PDGFA, PDGFB
 KEGG 14 / 299 3.9× 1.51e-5 4.74e-4 ✓ 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 DNA-templated transcription
CHEK2, ELF1, GATA2, NPAT, PARP1, RUNX1, ZFHX3, ZNF318, TP53, IRF4, TAF2, EPO
 GO:0045893 25 / 778 4.1× 1.42e-9 3.08e-7 ✓ sig.
cell population proliferation
THPO, BTC, IFT80, TP53, GNB1, GATA1, KRAS, LGR6, MYC, SPHK1, BCL2, FGFR1
 GO:0008283 15 / 263 7.4× 2.10e-9 4.32e-7 ✓ sig.
positive regulation of cell population proliferation
THPO, BTC, JAK2, MEIS1, CALR, EPO, EZH2, HDAC1, MYC, SPHK1, BCL2, TNFSF13
 GO:0008284 20 / 532 4.8× 5.55e-9 1.03e-6 ✓ sig.
positive regulation of transcription by RNA polymerase II
AHI1, ATM, ELF1, GATA2, JAK2, MEIS1, NPAT, NRIP1, PARP1, PURB, RUNX1, THRB
 GO:0045944 30 / 1,208 3.2× 1.10e-8 1.85e-6 ✓ sig.
positive regulation of miRNA transcription
GATA2, TERT, TP53, MYC, MYB, FGF2, PDGFB, TGFB1
 GO:1902895 8 / 56 18.4× 1.12e-8 1.89e-6 ✓ sig.
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
TERT, EYA2, CTNNA1, GATA1, BCL2, BCL2L1, IL1B
 GO:2001240 7 / 37 24.4× 1.24e-8 2.06e-6 ✓ sig.
hemopoiesis
CD164, MEIS1, RUNX1, SH2B3, ASXL1, BMI1, EZH2, BCL2, PDGFB
 GO:0030097 9 / 89 13.0× 2.98e-8 4.37e-6 ✓ sig.
apoptotic process
BTC, CHEK2, IFT80, JAK2, PARP1, PPIA, TP53, EFNA5, CFLAR, CTNNA1, DAPK1, EPO
 GO:0006915 22 / 747 3.8× 7.26e-8 9.21e-6 ✓ sig.
positive regulation of mitotic nuclear division
BTC, SMPD3, SPHK1, PDGFRB, PDGFB, IL1B
 GO:0045840 6 / 29 26.7× 8.07e-8 1.00e-5 ✓ sig.
regulation of gene expression
ATM, SLC8A1, TET2, DNMT3A, BMI1, DNMT1, DNMT3B, EZH2, MYC, SPHK1, BCL2, MYB
 GO:0010468 16 / 402 5.1× 9.63e-8 1.17e-5 ✓ sig.
thrombopoietin-mediated signaling pathway
MPL, THPO, JAK2, SH2B3
 GO:0038163 4 / 7 73.6× 1.20e-7 1.40e-5 ✓ sig.
positive regulation of smooth muscle cell proliferation
HDAC1, SMPD3, MYB, PDGFRB, FGF2, PDGFB, TGFB1
 GO:0048661 7 / 52 17.3× 1.46e-7 1.67e-5 ✓ sig.
positive regulation of fibroblast proliferation
BTC, BMI1, MYC, SPHK1, PDGFA, PDGFB, TGFB1
 GO:0048146 7 / 55 16.4× 2.18e-7 2.33e-5 ✓ sig.
myeloid cell differentiation
GATA2, JAK2, RUNX1, TET2, GATA1, MYB
 GO:0030099 6 / 35 22.1× 2.65e-7 2.75e-5 ✓ sig.
negative regulation of DNA-templated transcription
NPAT, PARP1, PURB, THRB, ZNF318, CALR, TP53, DNMT3A, DNMT1, EZH2, HDAC1, PLCB1
 GO:0045892 19 / 631 3.9× 4.42e-7 4.21e-5 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Clonal hematopoiesis Myeloproliferative disorder 0.122 12 3.62e-19 6.95e-18 ✓ sig.
Thrombocythemia Thrombocytosis 0.625 5 4.99e-18 9.09e-17 ✓ sig.
Essential thrombocythemia Thrombocythemia 0.333 5 1.07e-15 1.69e-14 ✓ sig.
Essential thrombocythemia Thrombocytosis 0.333 5 1.07e-15 1.69e-14 ✓ sig.
Essential thrombocythemia Myeloproliferative disorder 0.081 5 5.02e-10 4.95e-9 ✓ sig.
Myeloproliferative disorder Thrombocytosis 0.071 4 1.87e-9 1.74e-8 ✓ sig.
Myeloproliferative disorder Thrombocythemia 0.071 4 1.87e-9 1.74e-8 ✓ sig.
Amegakaryocytic thrombocytopenia Congenital amegakaryocytic thrombocytopenia 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Myelodysplastic syndrome Myeloproliferative disorder 0.064 6 1.05e-8 8.86e-8 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Thrombocytosis 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Amegakaryocytic thrombocytopenia Thrombocytosis 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Thrombocythemia 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Amegakaryocytic thrombocytopenia Thrombocythemia 0.286 2 1.27e-7 9.20e-7 ✓ sig.
Clonal hematopoiesis Myelodysplastic syndrome 0.051 5 6.49e-7 4.17e-6 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Essential thrombocythemia 0.143 2 6.58e-7 4.21e-6 ✓ sig.
Amegakaryocytic thrombocytopenia Essential thrombocythemia 0.143 2 6.58e-7 4.21e-6 ✓ sig.
Essential thrombocythemia Myelodysplastic syndrome 0.053 3 6.99e-6 3.74e-5 ✓ sig.
congenital amegakaryocytic thrombocytopenia 1 thrombocythemia 2 0.500 1 6.49e-5 2.34e-4 ✓ sig.
thrombocythemia 1 Thrombocythemia with distal limb defects 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Amegakaryocytic thrombocytopenia Thrombocythemia with distal limb defects 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Amegakaryocytic thrombocytopenia thrombocythemia 2 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Amegakaryocytic thrombocytopenia congenital amegakaryocytic thrombocytopenia 1 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Amegakaryocytic thrombocytopenia thrombocythemia 1 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital amegakaryocytic thrombocytopenia thrombocythemia 2 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital amegakaryocytic thrombocytopenia congenital amegakaryocytic thrombocytopenia 1 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Thrombocythemia with distal limb defects 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Congenital amegakaryocytic thrombocytopenia thrombocythemia 1 0.333 1 1.30e-4 3.90e-4 ✓ sig.
congenital amegakaryocytic thrombocytopenia 1 Thrombocythemia 0.143 1 3.90e-4 8.52e-4 ✓ sig.
thrombocythemia 1 Thrombocytosis 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Thrombocythemia thrombocythemia 1 0.143 1 3.90e-4 8.52e-4 ✓ sig.
thrombocythemia 2 Thrombocytosis 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Thrombocythemia thrombocythemia 2 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Thrombocythemia with distal limb defects Thrombocytosis 0.143 1 3.90e-4 8.52e-4 ✓ sig.
Thrombocythemia Thrombocythemia with distal limb defects 0.143 1 3.90e-4 8.52e-4 ✓ sig.
congenital amegakaryocytic thrombocytopenia 1 Thrombocytosis 0.143 1 3.90e-4 8.52e-4 ✓ sig.