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 150

9 diseases · 11 shared-gene connections
9 Diseases
330 Unique genes
0.054 Avg. similarity score
Myeloid leukemia Most-connected disease (5 links)
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Disease Searched: Clonal hematopoiesis 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 ⇵
Myeloid leukemia 5 5 150
Myelodysplastic syndrome 4 4 46
Leukemia 3 3 43
Myeloproliferative disorder 3 3 53
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
DNMT3A 5 / 9 Leukemia, Myelodysplastic syndrome, Myeloid leukemia, Myeloproliferative disorder and 1 more
JAK2 5 / 9 Clonal hematopoiesis, Leukemia, Myelodysplastic syndrome, Myeloid leukemia and 1 more
CHEK2 4 / 9 Clonal hematopoiesis, Leukemia, Myeloid leukemia, Myeloproliferative disorder
RUNX1 4 / 9 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloid leukemia, Myeloproliferative disorder
TERT 4 / 9 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloid leukemia, Myeloproliferative disorder
AQP9 3 / 9 Leukemia, Myeloid leukemia, Promyelocytic leukemia
DLK1 3 / 9 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloproliferative disorder
GATA2 3 / 9 Clonal hematopoiesis, Myelodysplastic syndrome, Myeloid leukemia
PTPN11 3 / 9 Leukemia, Myeloid leukemia, Promyelocytic leukemia
WT1 3 / 9 Leukemia, Myeloid leukemia, Promyelocytic leukemia
ASXL1 2 / 9 Myelodysplastic syndrome, Promyelocytic leukemia
ATG2B 2 / 9 Myeloid leukemia, Myeloproliferative disorder
ATM 2 / 9 Clonal hematopoiesis, Myeloproliferative disorder
BCL2 2 / 9 Myeloid leukemia, Myeloproliferative disorder
BCR 2 / 9 Myeloid leukemia, Myeloproliferative disorder
BMI1 2 / 9 Myelodysplastic syndrome, Myeloid leukemia
CD44 2 / 9 Myeloid leukemia, Promyelocytic leukemia
CEBPA 2 / 9 Myeloid leukemia, Promyelocytic leukemia
CFLAR 2 / 9 Leukemia, Myelodysplastic syndrome
CTNNA1 2 / 9 Myelodysplastic syndrome, Myeloid leukemia
CYRIA 2 / 9 Clonal hematopoiesis, Myeloproliferative disorder
DAPK1 2 / 9 Myelodysplastic syndrome, Myeloid leukemia
ERG 2 / 9 Leukemia, Myeloid leukemia
FLT3 2 / 9 Myeloid leukemia, Promyelocytic leukemia
FOXO1 2 / 9 Myeloid leukemia, Myeloproliferative disorder
GSKIP 2 / 9 Myeloid leukemia, Myeloproliferative disorder
HBS1L 2 / 9 Clonal hematopoiesis, Myeloproliferative disorder
IDH1 2 / 9 Myeloid leukemia, Promyelocytic leukemia
IDH2 2 / 9 Myeloid leukemia, Promyelocytic leukemia
IRF2BP2 2 / 9 immunodeficiency, common variable, 14, Promyelocytic leukemia
IRF4 2 / 9 Leukemia, Myelodysplastic syndrome
KIT 2 / 9 Myeloid leukemia, Promyelocytic leukemia
KMT2A 2 / 9 Leukemia, Myeloid leukemia
KMT2E 2 / 9 Leukemia, Myeloid leukemia
KRAS 2 / 9 Myelodysplastic syndrome, Myeloid leukemia
LYL1 2 / 9 Myelodysplastic syndrome, Myeloid leukemia
MECOM 2 / 9 Myeloid leukemia, Myeloproliferative disorder
MYC 2 / 9 Myelodysplastic syndrome, Myeloid leukemia
MYNN 2 / 9 Leukemia, Myeloproliferative disorder
NPM1 2 / 9 Myeloid leukemia, Promyelocytic leukemia
NRAS 2 / 9 Myeloid leukemia, Promyelocytic leukemia
PARP1 2 / 9 Clonal hematopoiesis, Myeloproliferative disorder
RTEL1 2 / 9 Clonal hematopoiesis, Myeloid leukemia
SLC6A6 2 / 9 hypotaurinemic retinal degeneration and cardiomyopathy, Myeloid leukemia
SMPD3 2 / 9 Leukemia, Myelodysplastic syndrome
SPHK1 2 / 9 Leukemia, Myelodysplastic syndrome
STAG2 2 / 9 Myelodysplastic syndrome, Myeloid leukemia
STN1 2 / 9 Clonal hematopoiesis, Myeloproliferative disorder
SYNCRIP 2 / 9 Leukemia, SYNCRIP-related neurodevelopmental disorder
TCL1A 2 / 9 Clonal hematopoiesis, Myeloproliferative disorder
TET2 2 / 9 Myelodysplastic syndrome, Promyelocytic leukemia
TNFSF10 2 / 9 Leukemia, Myeloid leukemia
TP53 2 / 9 Myelodysplastic syndrome, Myeloproliferative disorder
TUNAR 2 / 9 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, AR, BAD, BIRC2, BIRC3, CCND1
 KEGG 72 / 533 4.9× 1.05e-30 3.07e-27 ✓ sig.
Transcriptional misregulation in cancer
CEBPA, ETV6, RUNX1, ATM, MEIS1, BIRC2, BIRC3, ERG, KMT2A, WT1, FLT3, HDAC2
 KEGG 35 / 198 6.4× 6.76e-19 3.99e-16 ✓ sig.
Acute myeloid leukemia
CEBPA, RUNX1, BAD, CCND1, FLT3, KIT, KRAS, SPI1, CSF1R, CSF2, EIF4EBP1, MYC
 KEGG 22 / 68 11.8× 2.89e-18 1.56e-15 ✓ sig.
PI3K-Akt signaling pathway
CSF3R, JAK2, TCL1A, BAD, CCND1, DDIT4, FGF1, IL2, PTEN, FLT3, KIT, KRAS
 KEGG 38 / 361 3.8× 8.42e-13 1.74e-10 ✓ sig.
Interleukin-4 and Interleukin-13 signaling
JAK2, CCND1, IRF4, VEGFA, BCL2, CEBPD, FOXO1, HGF, IL4R, MYC, STAT3, AKT1
 Reactome 19 / 108 6.4× 9.37e-11 1.29e-8 ✓ sig.
Chronic myeloid leukemia
RUNX1, ABL1, BCR, BAD, CCND1, PTPN11, KRAS, HDAC2, MECOM, CDK6, MYC, NRAS
 KEGG 16 / 77 7.6× 2.20e-10 2.76e-8 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
JAK2, BAD, PTEN, KRAS, VEGFA, BCL2, EIF4EBP1, HGF, MET, NF1, NRAS, STAT3
 KEGG 16 / 80 7.3× 4.03e-10 4.74e-8 ✓ sig.
Apoptosis
ATM, ITPR2, PARP1, BAD, BIRC2, BIRC3, CFLAR, TNFSF10, KRAS, BCL2, CAPN2, CASP7
 KEGG 20 / 137 5.3× 9.51e-10 1.02e-7 ✓ sig.
Regulation of RUNX1 Expression and Activity
CBFB, RUNX1, CCND1, PTPN11, AGO2, CCND2, CDK6, PML
 Reactome 8 / 16 18.2× 3.17e-9 3.05e-7 ✓ sig.
Rap1 signaling pathway
FGF1, PRKCZ, KIT, KRAS, VEGFA, ADCY7, CSF1R, ENAH, HGF, LPAR1, MET, NRAS
 KEGG 24 / 211 4.1× 3.56e-9 3.39e-7 ✓ sig.
Central carbon metabolism in cancer
PTEN, FLT3, KIT, KRAS, IDH1, IDH2, MET, MYC, NRAS, NTRK3, AKT1, TP53
 KEGG 14 / 71 7.2× 6.22e-9 5.58e-7 ✓ sig.
Melanoma
BAD, CCND1, FGF1, PTEN, KRAS, CDK6, HGF, MET, NRAS, AKT1, TP53, PDGFRB
 KEGG 14 / 73 7.0× 9.08e-9 7.77e-7 ✓ sig.
Cellular senescence
CHEK2, ATM, HLA-C, ITPR2, CCND1, FOXM1, PTEN, KRAS, CAPN2, CCND2, CDK6, EIF4EBP1
 KEGG 20 / 157 4.6× 1.07e-8 9.00e-7 ✓ sig.
Platinum drug resistance
ATM, BAD, BIRC2, BIRC3, GSTM1, GSTO1, TOP2A, TOP2B, BCL2, FAS, AKT1, BIRC5
 KEGG 14 / 75 6.8× 1.31e-8 1.08e-6 ✓ sig.
JAK-STAT signaling pathway
CSF3R, IL20RB, JAK2, CCND1, IL2, PTPN11, BCL2, CCND2, CSF2, CSF3, IL4R, MYC
 KEGG 20 / 168 4.3× 3.43e-8 2.54e-6 ✓ 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 73 / 1,208 3.4× 5.79e-21 1.05e-17 ✓ sig.
negative regulation of apoptotic process
TERT, AHI1, JAK2, BAD, BIRC2, BIRC3, CFLAR, IL2, MGMT, PLK1, PRAME, PRKCZ
 GO:0043066 45 / 524 4.9× 1.12e-18 1.44e-15 ✓ sig.
apoptotic process
CHEK2, ABL1, BTC, IFT80, JAK2, PARP1, PPIA, BAD, BIRC2, BIRC3, CFLAR, DDIT4
 GO:0006915 50 / 747 3.8× 3.69e-16 3.04e-13 ✓ sig.
negative regulation of transcription by RNA polymerase II
CBFB, CEBPA, ETV6, GATA2, RUNX1, NRIP1, PARP1, PURB, THRB, ZFHX3, AR, CCND1
 GO:0000122 58 / 1,002 3.3× 8.55e-16 6.46e-13 ✓ sig.
positive regulation of cell population proliferation
CSF3R, BTC, JAK2, MEIS1, AR, CCND1, FGF1, FOXM1, IL2, PRAME, PTEN, SPHK1
 GO:0008284 40 / 532 4.3× 9.95e-15 6.31e-12 ✓ sig.
positive regulation of DNA-templated transcription
CEBPA, CHEK2, GATA2, RUNX1, ELF1, NPAT, PARP1, ZFHX3, ZNF318, AR, BIRC2, ESR1
 GO:0045893 47 / 778 3.4× 1.42e-13 7.46e-11 ✓ sig.
positive regulation of gene expression
CEBPA, GATA2, ATM, RLN2, AR, KMT2A, WT1, KIT, KRAS, AGO2, RAD21, SPI1
 GO:0010628 37 / 504 4.2× 2.24e-13 1.14e-10 ✓ sig.
myeloid cell differentiation
CBFB, CEBPA, GATA2, RUNX1, JAK2, CSF2, CEBPE, PML, TET2, ZBTB16, GATA1, MYB
 GO:0030099 12 / 35 19.4× 4.37e-13 2.11e-10 ✓ sig.
regulation of gene expression
ABL1, ATM, SLC8A1, AR, BAP1, DNMT3A, KMT2A, KMT2E, SETD2, SPHK1, BMI1, ATP1B1
 GO:0010468 32 / 402 4.5× 1.20e-12 5.31e-10 ✓ sig.
cell population proliferation
CEBPA, BTC, IFT80, BAP1, CCND1, SPHK1, KIT, KRAS, VEGFA, BCL2, CD9, CSF1R
 GO:0008283 25 / 263 5.4× 8.53e-12 3.16e-9 ✓ sig.
hemopoiesis
RUNX1, CD164, MEIS1, FLT3, KIT, PICALM, BMI1, BCL2, CDK6, CSF1R, RUNX3, ASXL1
 GO:0030097 15 / 89 9.5× 4.33e-11 1.35e-8 ✓ sig.
regulation of cell cycle
CEBPA, ABL1, BCR, ATM, BAP1, BIRC2, BIRC3, CCND1, FOXM1, KMT2E, PLK1, PTEN
 GO:0051726 24 / 262 5.2× 4.92e-11 1.51e-8 ✓ sig.
negative regulation of DNA-templated transcription
CEBPA, NPAT, PARP1, PURB, THRB, ZNF318, BAP1, DNMT3A, FOXM1, PRAME, WT1, HDAC2
 GO:0045892 37 / 631 3.3× 1.64e-10 4.40e-8 ✓ sig.
macrophage differentiation
CEBPA, PARP1, CFLAR, NPM1, SPI1, VEGFA, CSF1R, CSF2, CEBPE, IFNG
 GO:0030225 10 / 37 15.3× 5.88e-10 1.36e-7 ✓ sig.
homeostasis of number of cells within a tissue
GATA2, IL20RB, KMT2A, PTPN11, KRAS, VEGFA, BCL2, RAC3, SMO, GATA1
 GO:0048873 10 / 38 14.9× 7.85e-10 1.74e-7 ✓ 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 6.60e-18 ✓ sig.
Myelodysplastic syndrome Myeloid leukemia 0.065 12 1.37e-14 1.92e-13 ✓ sig.
Myeloid leukemia Promyelocytic leukemia 0.063 12 4.13e-14 5.52e-13 ✓ sig.
Myeloid leukemia Myeloproliferative disorder 0.057 11 2.78e-12 3.20e-11 ✓ sig.
Leukemia Myeloid leukemia 0.054 10 8.28e-12 9.19e-11 ✓ sig.
Leukemia Myelodysplastic syndrome 0.071 6 2.84e-9 2.46e-8 ✓ sig.
Myelodysplastic syndrome Myeloproliferative disorder 0.064 6 1.05e-8 8.41e-8 ✓ sig.
Clonal hematopoiesis Myelodysplastic syndrome 0.051 5 6.49e-7 3.96e-6 ✓ 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.