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 52

15 diseases · 30 shared-gene connections
15 Diseases
339 Unique genes
0.176 Avg. similarity score
Essential thrombocythemia Most-connected disease (7 links)
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Disease Searched: immunodeficiency, common variable, 14 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 ⇵
Essential thrombocythemia 7 7 13
Myeloproliferative disorder 6 6 53
Thrombocythemia 6 6 6
Thrombocytosis 6 6 6
Amegakaryocytic thrombocytopenia 5 5 2
Congenital amegakaryocytic thrombocytopenia 5 5 2
Myelodysplastic syndrome 5 5 46
Myeloid leukemia 5 5 150
Thrombocythemia with distal limb defects 5 5 1
Leukemia 3 3 43
Clonal hematopoiesis 2 2 56
Promyelocytic leukemia 2 2 50
SYNCRIP-related neurodevelopmental disorder 1 1 1
hypotaurinemic retinal degeneration and cardiomyopathy 1 1 1
immunodeficiency, common variable, 14 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
JAK2 8 / 15 Clonal hematopoiesis, Essential thrombocythemia, Leukemia, Myelodysplastic syndrome and 4 more
MPL 6 / 15 Amegakaryocytic thrombocytopenia, Congenital amegakaryocytic thrombocytopenia, Essential thrombocythemia, Myeloproliferative disorder and 2 more
THPO 6 / 15 Amegakaryocytic thrombocytopenia, Congenital amegakaryocytic thrombocytopenia, Essential thrombocythemia, Thrombocythemia and 2 more
DNMT3A 5 / 15 Leukemia, Myelodysplastic syndrome, Myeloid leukemia, Myeloproliferative disorder and 1 more
CALR 4 / 15 Essential thrombocythemia, Myeloproliferative disorder, Thrombocythemia, Thrombocytosis
CHEK2 4 / 15 Clonal hematopoiesis, Leukemia, Myeloid leukemia, Myeloproliferative disorder
RUNX1 4 / 15 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloid leukemia, Myeloproliferative disorder
SH2B3 4 / 15 Essential thrombocythemia, Myeloproliferative disorder, Thrombocythemia, Thrombocytosis
TERT 4 / 15 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloid leukemia, Myeloproliferative disorder
AQP9 3 / 15 Leukemia, Myeloid leukemia, Promyelocytic leukemia
DLK1 3 / 15 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloproliferative disorder
GATA2 3 / 15 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloid leukemia
PTPN11 3 / 15 Leukemia, Myeloid leukemia, Promyelocytic leukemia
TET2 3 / 15 Essential thrombocythemia, Myelodysplastic syndrome, Promyelocytic leukemia
TP53 3 / 15 Essential thrombocythemia, Myelodysplastic syndrome, Myeloproliferative disorder
WT1 3 / 15 Leukemia, Myeloid leukemia, Promyelocytic leukemia
ASXL1 2 / 15 Myelodysplastic syndrome, Promyelocytic leukemia
ATG2B 2 / 15 Myeloid leukemia, Myeloproliferative disorder
ATM 2 / 15 Clonal hematopoiesis, Myeloproliferative disorder
BCL2 2 / 15 Myeloid leukemia, Myeloproliferative disorder
BCR 2 / 15 Myeloid leukemia, Myeloproliferative disorder
BMI1 2 / 15 Myelodysplastic syndrome, Myeloid leukemia
CD44 2 / 15 Myeloid leukemia, Promyelocytic leukemia
CEBPA 2 / 15 Myeloid leukemia, Promyelocytic leukemia
CFLAR 2 / 15 Leukemia, Myelodysplastic syndrome
CTNNA1 2 / 15 Myelodysplastic syndrome, Myeloid leukemia
CYRIA 2 / 15 Clonal hematopoiesis, Myeloproliferative disorder
DAPK1 2 / 15 Myelodysplastic syndrome, Myeloid leukemia
ERG 2 / 15 Leukemia, Myeloid leukemia
FLT3 2 / 15 Myeloid leukemia, Promyelocytic leukemia
FOXO1 2 / 15 Myeloid leukemia, Myeloproliferative disorder
GSKIP 2 / 15 Myeloid leukemia, Myeloproliferative disorder
HBS1L 2 / 15 Clonal hematopoiesis, Myeloproliferative disorder
IDH1 2 / 15 Myeloid leukemia, Promyelocytic leukemia
IDH2 2 / 15 Myeloid leukemia, Promyelocytic leukemia
IRF2BP2 2 / 15 immunodeficiency, common variable, 14, Promyelocytic leukemia
IRF4 2 / 15 Leukemia, Myelodysplastic syndrome
KIT 2 / 15 Myeloid leukemia, Promyelocytic leukemia
KMT2A 2 / 15 Leukemia, Myeloid leukemia
KMT2E 2 / 15 Leukemia, Myeloid leukemia
KRAS 2 / 15 Myelodysplastic syndrome, Myeloid leukemia
LYL1 2 / 15 Myelodysplastic syndrome, Myeloid leukemia
MECOM 2 / 15 Myeloid leukemia, Myeloproliferative disorder
MYC 2 / 15 Myelodysplastic syndrome, Myeloid leukemia
MYNN 2 / 15 Leukemia, Myeloproliferative disorder
NPM1 2 / 15 Myeloid leukemia, Promyelocytic leukemia
NRAS 2 / 15 Myeloid leukemia, Promyelocytic leukemia
PARP1 2 / 15 Clonal hematopoiesis, Myeloproliferative disorder
RTEL1 2 / 15 Clonal hematopoiesis, Myeloid leukemia
SLC6A6 2 / 15 hypotaurinemic retinal degeneration and cardiomyopathy, Myeloid leukemia
SMPD3 2 / 15 Leukemia, Myelodysplastic syndrome
SPHK1 2 / 15 Leukemia, Myelodysplastic syndrome
STAG2 2 / 15 Myelodysplastic syndrome, Myeloid leukemia
STN1 2 / 15 Clonal hematopoiesis, Myeloproliferative disorder
SYNCRIP 2 / 15 Leukemia, SYNCRIP-related neurodevelopmental disorder
TCL1A 2 / 15 Clonal hematopoiesis, Myeloproliferative disorder
TNFSF10 2 / 15 Leukemia, Myeloid leukemia
TUNAR 2 / 15 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
CEBPA, RUNX1, TERT, CSF3R, ABL1, BCR, JAK2, TP53, AR, BAD, BIRC2, BIRC3
 KEGG 77 / 533 5.1× 4.06e-34 1.36e-30 ✓ sig.
Transcriptional misregulation in cancer
CEBPA, ETV6, RUNX1, ATM, MEIS1, TP53, BIRC2, BIRC3, ERG, KMT2A, WT1, FLT3
 KEGG 36 / 198 6.4× 1.92e-19 1.29e-16 ✓ sig.
Acute myeloid leukemia
CEBPA, RUNX1, BAD, CCND1, FLT3, KIT, KRAS, SPI1, CSF1R, CSF2, EIF4EBP1, MYC
 KEGG 22 / 68 11.5× 5.15e-18 2.81e-15 ✓ sig.
PI3K-Akt signaling pathway
CSF3R, JAK2, TCL1A, TP53, BAD, CCND1, DDIT4, FGF1, IL2, PTEN, FLT3, KIT
 KEGG 43 / 361 4.2× 7.02e-16 2.47e-13 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
JAK2, TP53, CCND1, IRF4, VEGFA, BCL2, CEBPD, FOXO1, HGF, IL4R, MYC, STAT3
 Reactome 22 / 108 7.2× 2.24e-13 4.93e-11 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
JAK2, BAD, PTEN, KRAS, VEGFA, BCL2, EIF4EBP1, HGF, MET, NF1, NRAS, STAT3
 KEGG 19 / 80 8.4× 5.36e-13 1.11e-10 ✓ sig.
Melanoma
TP53, BAD, CCND1, FGF1, PTEN, KRAS, CDK6, HGF, MET, NRAS, AKT1, PDGFRB
 KEGG 17 / 73 8.3× 1.29e-11 2.12e-9 ✓ sig.
Chronic myeloid leukemia
RUNX1, ABL1, BCR, TP53, BAD, CCND1, PTPN11, KRAS, HDAC2, MECOM, CDK6, MYC
 KEGG 17 / 77 7.8× 3.24e-11 4.88e-9 ✓ sig.
Rap1 signaling pathway
FGF1, PRKCZ, KIT, KRAS, VEGFA, ADCY7, CSF1R, ENAH, HGF, LPAR1, MET, NRAS
 KEGG 27 / 211 4.5× 4.39e-11 6.39e-9 ✓ sig.
JAK-STAT signaling pathway
MPL, THPO, CSF3R, IL20RB, JAK2, CCND1, IL2, PTPN11, BCL2, CCND2, CSF2, CSF3
 KEGG 24 / 168 5.1× 5.33e-11 7.62e-9 ✓ sig.
Ras signaling pathway
ABL1, BAD, FGF1, PTPN11, FLT3, KIT, KRAS, VEGFA, CSF1R, HGF, MET, NF1
 KEGG 27 / 237 4.0× 6.33e-10 7.08e-8 ✓ sig.
Apoptosis
ATM, ITPR2, PARP1, TP53, BAD, BIRC2, BIRC3, CFLAR, TNFSF10, KRAS, BCL2, CAPN2
 KEGG 20 / 137 5.2× 1.52e-9 1.54e-7 ✓ sig.
Cellular senescence
CHEK2, ATM, HLA-C, ITPR2, TP53, CCND1, FOXM1, PTEN, KRAS, CAPN2, CCND2, CDK6
 KEGG 21 / 157 4.7× 3.00e-9 2.85e-7 ✓ sig.
Regulation of RUNX1 Expression and Activity
CBFB, RUNX1, CCND1, PTPN11, AGO2, CCND2, CDK6, PML
 Reactome 8 / 16 17.7× 3.92e-9 3.64e-7 ✓ sig.
Human cytomegalovirus infection
HLA-C, ITPR2, CALR, TP53, CCND1, KRAS, VEGFA, ADCY7, CDK6, EIF4EBP1, FAS, MYC
 KEGG 25 / 226 3.9× 5.15e-9 4.65e-7 ✓ 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
CBFB, CEBPA, ETV6, GATA2, RUNX1, ABL1, AHI1, ATM, ELF1, JAK2, MEIS1, NPAT
 GO:0045944 76 / 1,208 3.5× 3.73e-22 8.08e-19 ✓ sig.
positive regulation of cell population proliferation
THPO, CSF3R, BTC, JAK2, MEIS1, CALR, AR, CCND1, FGF1, FOXM1, IL2, PRAME
 GO:0008284 46 / 532 4.8× 1.01e-18 1.31e-15 ✓ sig.
negative regulation of apoptotic process
TERT, AHI1, JAK2, TP53, BAD, BIRC2, BIRC3, CFLAR, IL2, MGMT, PLK1, PRAME
 GO:0043066 45 / 524 4.7× 3.26e-18 3.89e-15 ✓ sig.
apoptotic process
CHEK2, ABL1, BTC, IFT80, JAK2, PARP1, PPIA, TP53, BAD, BIRC2, BIRC3, CFLAR
 GO:0006915 53 / 747 3.9× 1.15e-17 1.27e-14 ✓ sig.
negative regulation of transcription by RNA polymerase II
CBFB, CEBPA, ETV6, GATA2, RUNX1, NRIP1, PARP1, PURB, THRB, ZFHX3, CALR, TP53
 GO:0000122 59 / 1,002 3.2× 7.63e-16 6.10e-13 ✓ sig.
positive regulation of gene expression
CEBPA, GATA2, ATM, RLN2, CALR, TP53, AR, KMT2A, WT1, KIT, KRAS, AGO2
 GO:0010628 41 / 504 4.5× 7.67e-16 6.12e-13 ✓ sig.
positive regulation of DNA-templated transcription
CEBPA, CHEK2, GATA2, RUNX1, ELF1, NPAT, PARP1, ZFHX3, ZNF318, TP53, AR, BIRC2
 GO:0045893 50 / 778 3.5× 5.63e-15 3.85e-12 ✓ sig.
cell population proliferation
CEBPA, THPO, BTC, IFT80, TP53, BAP1, CCND1, SPHK1, KIT, KRAS, VEGFA, BCL2
 GO:0008283 29 / 263 6.1× 7.24e-15 4.82e-12 ✓ sig.
regulation of gene expression
ABL1, ATM, SLC8A1, TET2, AR, BAP1, DNMT3A, KMT2A, KMT2E, SETD2, SPHK1, BMI1
 GO:0010468 34 / 402 4.7× 8.65e-14 4.80e-11 ✓ sig.
myeloid cell differentiation
CBFB, CEBPA, GATA2, RUNX1, JAK2, TET2, CSF2, CEBPE, PML, ZBTB16, GATA1, MYB
 GO:0030099 12 / 35 18.9× 6.01e-13 2.81e-10 ✓ sig.
regulation of cell cycle
CEBPA, ABL1, BCR, ATM, TP53, BAP1, BIRC2, BIRC3, CCND1, FOXM1, KMT2E, PLK1
 GO:0051726 26 / 262 5.5× 2.21e-12 9.35e-10 ✓ sig.
hemopoiesis
RUNX1, CD164, MEIS1, SH2B3, FLT3, KIT, PICALM, BMI1, BCL2, CDK6, CSF1R, RUNX3
 GO:0030097 16 / 89 9.9× 5.15e-12 2.01e-9 ✓ sig.
negative regulation of DNA-templated transcription
CEBPA, NPAT, PARP1, PURB, THRB, ZNF318, CALR, TP53, BAP1, DNMT3A, FOXM1, PRAME
 GO:0045892 40 / 631 3.5× 5.86e-12 2.26e-9 ✓ sig.
positive regulation of miRNA transcription
GATA2, TERT, TP53, AR, WT1, SPI1, MYC, STAT3, PPARG, MYB, FGF2, PDGFB
 GO:1902895 13 / 56 12.8× 1.72e-11 6.04e-9 ✓ sig.
positive regulation of cell migration
ATM, JAK2, FGF1, SPHK1, KIT, VEGFA, CSF1R, CSF2, CTSH, HGF, NTRK3, STAT3
 GO:0030335 26 / 292 4.9× 2.59e-11 8.73e-9 ✓ 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 6.58e-18 ✓ sig.
Thrombocythemia Thrombocytosis 0.625 5 4.99e-18 8.59e-17 ✓ sig.
Essential thrombocythemia Thrombocytosis 0.333 5 1.07e-15 1.60e-14 ✓ sig.
Essential thrombocythemia Thrombocythemia 0.333 5 1.07e-15 1.60e-14 ✓ sig.
Myelodysplastic syndrome Myeloid leukemia 0.065 12 1.37e-14 1.91e-13 ✓ sig.
Myeloid leukemia Promyelocytic leukemia 0.063 12 4.13e-14 5.50e-13 ✓ sig.
Myeloid leukemia Myeloproliferative disorder 0.057 11 2.78e-12 3.19e-11 ✓ sig.
Leukemia Myeloid leukemia 0.054 10 8.28e-12 9.14e-11 ✓ sig.
Essential thrombocythemia Myeloproliferative disorder 0.081 5 5.02e-10 4.67e-9 ✓ sig.
Myeloproliferative disorder Thrombocytosis 0.071 4 1.87e-9 1.64e-8 ✓ sig.
Myeloproliferative disorder Thrombocythemia 0.071 4 1.87e-9 1.64e-8 ✓ sig.
Leukemia Myelodysplastic syndrome 0.071 6 2.84e-9 2.45e-8 ✓ sig.
Amegakaryocytic thrombocytopenia Congenital amegakaryocytic thrombocytopenia 0.667 2 8.44e-9 6.82e-8 ✓ sig.
Myelodysplastic syndrome Myeloproliferative disorder 0.064 6 1.05e-8 8.39e-8 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Thrombocythemia 0.286 2 1.27e-7 8.71e-7 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Thrombocytosis 0.286 2 1.27e-7 8.71e-7 ✓ sig.
Amegakaryocytic thrombocytopenia Thrombocythemia 0.286 2 1.27e-7 8.71e-7 ✓ sig.
Amegakaryocytic thrombocytopenia Thrombocytosis 0.286 2 1.27e-7 8.71e-7 ✓ sig.
Clonal hematopoiesis Myelodysplastic syndrome 0.051 5 6.49e-7 3.95e-6 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Essential thrombocythemia 0.143 2 6.58e-7 3.99e-6 ✓ sig.
Amegakaryocytic thrombocytopenia Essential thrombocythemia 0.143 2 6.58e-7 3.99e-6 ✓ sig.
Essential thrombocythemia Myelodysplastic syndrome 0.053 3 6.99e-6 3.53e-5 ✓ sig.
Amegakaryocytic thrombocytopenia Thrombocythemia with distal limb defects 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Congenital amegakaryocytic thrombocytopenia Thrombocythemia with distal limb defects 0.333 1 1.30e-4 3.93e-4 ✓ sig.
Thrombocythemia with distal limb defects Thrombocytosis 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Thrombocythemia Thrombocythemia with distal limb defects 0.143 1 3.90e-4 8.66e-4 ✓ sig.
Essential thrombocythemia Thrombocythemia with distal limb defects 0.071 1 8.44e-4 1.50e-3 ✓ sig.
Leukemia SYNCRIP-related neurodevelopmental disorder 0.023 1 2.79e-3 3.75e-3 ✓ sig.
immunodeficiency, common variable, 14 Promyelocytic leukemia 0.020 1 3.25e-3 4.24e-3 ✓ sig.
hypotaurinemic retinal degeneration and cardiomyopathy Myeloid leukemia 0.007 1 9.74e-3 1.11e-2 ✓ sig.