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 39

17 diseases · 35 shared-gene connections
17 Diseases
126 Unique genes
0.139 Avg. similarity score
Hereditary breast cancer Most-connected disease (10 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 ⇵
Hereditary breast cancer 10 10 32
Constitutional mismatch repair deficiency 7 7 13
Muir-torre syndrome 7 7 4
Rhabdomyosarcoma 6 6 27
mismatch repair cancer syndrome 1 6 6 4
Fanconi anemia 5 5 39
Hereditary breast and ovarian cancer syndrome 5 5 15
Lynch syndrome 5 5 49
Intellectual developmental disorder dysmorphic behavioral 3 3 3
Turcot syndrome 3 3 3
nijmegen breakage syndrome 3 3 1
BARD1-related cancer predisposition 2 2 1
Cystic leukoencephalopathy 2 2 2
Fanconi anemia complementation group U 2 2 1
fanconi anemia complementation group p 2 2 1
ciliary dyskinesia, primary, 47, and lissencephaly 1 1 1
fanconi anemia complementation group f 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
MLH1 7 / 17 Constitutional mismatch repair deficiency, Hereditary breast cancer, Lynch syndrome, mismatch repair cancer syndrome 1 and 3 more
MSH6 7 / 17 Constitutional mismatch repair deficiency, Hereditary breast cancer, Intellectual developmental disorder dysmorphic behavioral, Lynch syndrome and 3 more
PMS2 7 / 17 Constitutional mismatch repair deficiency, Hereditary breast cancer, Lynch syndrome, mismatch repair cancer syndrome 1 and 3 more
MSH2 6 / 17 Constitutional mismatch repair deficiency, Hereditary breast cancer, Lynch syndrome, mismatch repair cancer syndrome 1 and 2 more
NBN 4 / 17 Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer, nijmegen breakage syndrome, Rhabdomyosarcoma
PALB2 4 / 17 Fanconi anemia, Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer, Lynch syndrome
APC 3 / 17 Constitutional mismatch repair deficiency, Lynch syndrome, Turcot syndrome
ATM 3 / 17 Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer, Lynch syndrome
BARD1 3 / 17 BARD1-related cancer predisposition, Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer
BRCA1 3 / 17 Fanconi anemia, Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer
BRCA2 3 / 17 Fanconi anemia, Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer
BRIP1 3 / 17 Fanconi anemia, Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer
CHEK2 3 / 17 Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer, Lynch syndrome
MRE11 3 / 17 Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer, Lynch syndrome
RAD51 3 / 17 Fanconi anemia, Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer
RNASET2 3 / 17 Constitutional mismatch repair deficiency, Cystic leukoencephalopathy, Lynch syndrome
SLX4 3 / 17 Fanconi anemia, fanconi anemia complementation group p, Hereditary breast cancer
XRCC2 3 / 17 Fanconi anemia, Fanconi anemia complementation group U, Hereditary breast cancer
ASTE1 2 / 17 Constitutional mismatch repair deficiency, Lynch syndrome
EPCAM 2 / 17 Hereditary breast cancer, Lynch syndrome
FANCF 2 / 17 Fanconi anemia, fanconi anemia complementation group f
FANCM 2 / 17 Fanconi anemia, Hereditary breast cancer
FBXO11 2 / 17 Intellectual developmental disorder dysmorphic behavioral, Lynch syndrome
GSTM1 2 / 17 Fanconi anemia, Lynch syndrome
GSTT1 2 / 17 Fanconi anemia, Lynch syndrome
MUTYH 2 / 17 Hereditary breast cancer, Lynch syndrome
PIK3CA 2 / 17 Hereditary breast cancer, Lynch syndrome
RAD50 2 / 17 Hereditary breast and ovarian cancer syndrome, Hereditary breast cancer
RAD51C 2 / 17 Fanconi anemia, Hereditary breast and ovarian cancer syndrome
RAD51D 2 / 17 Hereditary breast and ovarian cancer syndrome, Lynch syndrome
SLC22A9 2 / 17 Constitutional mismatch repair deficiency, Lynch syndrome
SLC67A1 2 / 17 Hereditary breast cancer, Rhabdomyosarcoma
TAF1B 2 / 17 Constitutional mismatch repair deficiency, Lynch syndrome
TGFBR2 2 / 17 Constitutional mismatch repair deficiency, Lynch syndrome
TP53 2 / 17 Constitutional mismatch repair deficiency, Hereditary breast and ovarian cancer syndrome
TP73 2 / 17 ciliary dyskinesia, primary, 47, and lissencephaly, Rhabdomyosarcoma
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 ⇵
Fanconi anemia pathway
MLH1, PALB2, PMS2, FANCM, BRCA1, BRCA2, BRIP1, ERCC4, FAAP100, FANCA, FANCB, FANCC
 KEGG 24 / 54 42.4× 3.41e-34 1.40e-30 ✓ sig.
Fanconi Anemia Pathway
FANCM, ERCC4, FAAP100, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL
 Reactome 17 / 40 40.5× 5.37e-24 8.80e-21 ✓ sig.
Resolution of D-loop Structures through Holliday Junction Intermediates
ATM, PALB2, RAD51D, BRCA1, BRCA2, BRIP1, RAD51, RAD51C, SLX4, XRCC2, BARD1, MRE11
 Reactome 16 / 33 46.2× 8.11e-24 1.23e-20 ✓ sig.
Homologous DNA Pairing and Strand Exchange
ATM, PALB2, RAD51D, BRCA1, BRCA2, BRIP1, RAD51, RAD51C, XRCC2, BARD1, MRE11, NBN
 Reactome 14 / 25 53.4× 3.77e-22 4.43e-19 ✓ sig.
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)
ATM, PALB2, RAD51D, BRCA1, BRCA2, BRIP1, RAD51, RAD51C, XRCC2, BARD1, MRE11, NBN
 Reactome 14 / 26 51.3× 8.10e-22 8.77e-19 ✓ sig.
HDR through Homologous Recombination (HRR)
ATM, PALB2, RAD51D, POLE, BRCA1, BRCA2, BRIP1, RAD51, RAD51C, XRCC2, BARD1, MRE11
 Reactome 15 / 48 29.8× 7.13e-19 4.86e-16 ✓ sig.
Presynaptic phase of homologous DNA pairing and strand exchange
ATM, RAD51D, BRCA1, BRCA2, BRIP1, RAD51, RAD51C, XRCC2, BARD1, MRE11, NBN, RAD50
 Reactome 14 / 39 34.2× 1.13e-18 7.51e-16 ✓ sig.
Homologous recombination
ATM, PALB2, RAD51D, BRCA1, BRCA2, BRIP1, RAD51, RAD51C, XRCC2, BARD1, MRE11, NBN
 KEGG 14 / 41 32.5× 2.59e-18 1.60e-15 ✓ sig.
HDR through Single Strand Annealing (SSA)
ATM, BRCA1, BRIP1, ERCC4, RAD51, BARD1, MRE11, NBN, RAD50, ATRIP, EXO1
 Reactome 11 / 37 28.3× 7.38e-14 1.93e-11 ✓ sig.
Colorectal cancer
MLH1, MSH2, MSH6, TGFBR2, APC, TP53, PIK3CA, KRAS, MSH3, SMAD2, SMAD3, SMAD4
 KEGG 14 / 87 15.3× 2.66e-13 6.30e-11 ✓ sig.
Cellular senescence
ATM, CHEK2, RB1, TGFBR2, TP53, MRE11, NBN, PTEN, RAD50, PIK3CA, E2F4, KRAS
 KEGG 17 / 157 10.3× 5.39e-13 1.23e-10 ✓ sig.
Hepatocellular carcinoma
RB1, TGFBR2, APC, TP53, GSTM1, GSTT1, PTEN, PIK3CA, SMARCA4, KRAS, SMAD2, SMAD3
 KEGG 17 / 170 9.5× 2.00e-12 4.13e-10 ✓ sig.
Pathways in cancer
MLH1, MSH2, MSH6, RB1, TGFBR2, APC, TP53, BRCA2, GSTM1, GSTT1, RAD51, VHL
 KEGG 27 / 533 4.8× 5.95e-12 1.11e-9 ✓ sig.
Pancreatic cancer
RB1, TGFBR2, TP53, BRCA2, RAD51, PIK3CA, KRAS, SMAD2, SMAD3, SMAD4, TGFBR1, VEGFA
 KEGG 12 / 77 14.9× 2.16e-11 3.58e-9 ✓ sig.
TP53 Regulates Transcription of DNA Repair Genes
ATM, MLH1, MSH2, PMS2, RAD51D, TP53, BRCA1, FANCC, FANCD2, FANCI, CDK9
 Reactome 11 / 65 16.1× 6.04e-11 9.10e-9 ✓ 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 ⇵
DNA repair
ATM, CHEK2, MLH1, MLH3, MSH2, MSH6, MUTYH, PALB2, PMS1, PMS2, RAD51D, POLE
 GO:0006281 51 / 420 18.0× 5.52e-51 1.21e-46 ✓ sig.
DNA damage response
ATM, CHEK2, MLH1, MLH3, MSH2, MSH6, MUTYH, PALB2, PMS1, PMS2, RAD51D, APC
 GO:0006974 55 / 577 14.1× 1.95e-49 3.79e-45 ✓ sig.
interstrand cross-link repair
RAD51D, FANCM, BRIP1, FAAP100, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI
 GO:0036297 18 / 39 68.5× 1.30e-29 6.49e-26 ✓ sig.
double-strand break repair via homologous recombination
ATM, PALB2, RAD51D, ASTE1, BRCA1, BRCA2, ERCC4, RAD51, RAD51C, RFWD3, SLX4, XRCC2
 GO:0000724 19 / 119 23.7× 3.84e-21 7.31e-18 ✓ sig.
DNA recombination
PALB2, RAD51D, ASTE1, BRCA1, BRCA2, RAD51, RAD51C, SLX4, XRCC2, MRE11, RAD50, RAD54L
 GO:0006310 16 / 110 21.6× 2.81e-17 3.03e-14 ✓ sig.
mismatch repair
MLH1, MLH3, MSH2, MSH6, MUTYH, PMS1, PMS2, EXO1, MSH3, TP73, SETD2
 GO:0006298 11 / 30 54.4× 4.11e-17 4.29e-14 ✓ sig.
double-strand break repair
ATM, CHEK2, MSH2, TP53, BRCA1, BRCA2, BRIP1, MAD2L2, VCP, MRE11, NBN, RAD50
 GO:0006302 14 / 87 23.9× 6.84e-16 5.53e-13 ✓ sig.
homologous recombination
FANCM, BRCA1, BRIP1, BARD1, MRE11, NBN, RAD50
 GO:0035825 7 / 12 86.5× 4.12e-13 2.03e-10 ✓ sig.
reciprocal meiotic recombination
ATM, MLH1, MLH3, RAD51D, RAD51, RAD51C, MRE11, RAD50, RAD54L
 GO:0007131 9 / 33 40.4× 7.26e-13 3.42e-10 ✓ sig.
DNA strand resection involved in replication fork processing
ATM, BRCA1, BARD1, MRE11, NBN, RAD50, EXO1
 GO:0110025 7 / 14 74.2× 1.77e-12 7.67e-10 ✓ sig.
regulation of cell cycle
ATM, MSH2, RAD51D, RB1, TFDP1, TP53, BRCA1, BARD1, NBN, PTEN, CDK9, CDKN1B
 GO:0051726 16 / 262 9.1× 2.54e-11 8.42e-9 ✓ sig.
somatic recombination of immunoglobulin gene segments
MLH1, MSH2, MSH6, PMS2, MSH3
 GO:0016447 5 / 6 124× 7.68e-11 2.25e-8 ✓ sig.
intrinsic apoptotic signaling pathway in response to DNA damage
ATM, CHEK2, MLH1, MSH2, MSH6, BRCA1, BRCA2, TNF, TP73
 GO:0008630 9 / 54 24.7× 8.88e-11 2.57e-8 ✓ sig.
positive regulation of transcription by RNA polymerase II
ATM, EPCAM, RB1, KMT2D, TFDP1, TP53, BRCA1, TNF, PTEN, CDK9, NFKBIZ, SMARCA4
 GO:0045944 30 / 1,208 3.7× 3.15e-10 7.99e-8 ✓ sig.
telomeric 3' overhang formation
DCLRE1B, MRE11, NBN, RAD50
 GO:0031860 4 / 4 148× 1.97e-9 4.08e-7 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hereditary breast and ovarian cancer syndrome Hereditary breast cancer 0.297 11 6.08e-28 1.82e-26 ✓ sig.
Constitutional mismatch repair deficiency Lynch syndrome 0.189 10 1.13e-23 2.72e-22 ✓ sig.
Hereditary breast cancer Lynch syndrome 0.155 11 1.24e-20 2.59e-19 ✓ sig.
mismatch repair cancer syndrome 1 Muir-torre syndrome 0.800 4 4.27e-16 6.90e-15 ✓ sig.
Fanconi anemia Hereditary breast cancer 0.125 8 7.92e-15 1.19e-13 ✓ sig.
Constitutional mismatch repair deficiency Muir-torre syndrome 0.286 4 3.05e-13 4.09e-12 ✓ sig.
Constitutional mismatch repair deficiency mismatch repair cancer syndrome 1 0.286 4 3.05e-13 4.09e-12 ✓ sig.
Fanconi anemia Hereditary breast and ovarian cancer syndrome 0.122 6 8.68e-13 1.12e-11 ✓ sig.
Muir-torre syndrome Rhabdomyosarcoma 0.143 4 7.50e-12 8.80e-11 ✓ sig.
mismatch repair cancer syndrome 1 Rhabdomyosarcoma 0.143 4 7.50e-12 8.80e-11 ✓ sig.
Hereditary breast cancer Rhabdomyosarcoma 0.111 6 1.41e-11 1.62e-10 ✓ sig.
Hereditary breast cancer Muir-torre syndrome 0.121 4 1.54e-11 1.77e-10 ✓ sig.
Hereditary breast cancer mismatch repair cancer syndrome 1 0.121 4 1.54e-11 1.77e-10 ✓ sig.
Lynch syndrome Muir-torre syndrome 0.080 4 9.05e-11 9.60e-10 ✓ sig.
Constitutional mismatch repair deficiency Turcot syndrome 0.214 3 4.70e-10 4.65e-9 ✓ sig.
Hereditary breast and ovarian cancer syndrome Lynch syndrome 0.083 5 7.76e-10 7.51e-9 ✓ sig.
Constitutional mismatch repair deficiency Rhabdomyosarcoma 0.108 4 5.30e-9 4.73e-8 ✓ sig.
Muir-torre syndrome Turcot syndrome 0.333 2 1.52e-7 1.09e-6 ✓ sig.
mismatch repair cancer syndrome 1 Turcot syndrome 0.333 2 1.52e-7 1.09e-6 ✓ sig.
Intellectual developmental disorder dysmorphic behavioral Muir-torre syndrome 0.143 1 7.79e-4 1.39e-3 ✓ sig.
Intellectual developmental disorder dysmorphic behavioral mismatch repair cancer syndrome 1 0.143 1 7.79e-4 1.39e-3 ✓ sig.
BARD1-related cancer predisposition Hereditary breast and ovarian cancer syndrome 0.063 1 9.74e-4 1.64e-3 ✓ sig.
Hereditary breast and ovarian cancer syndrome nijmegen breakage syndrome 0.063 1 9.74e-4 1.64e-3 ✓ sig.
Constitutional mismatch repair deficiency Cystic leukoencephalopathy 0.067 1 1.69e-3 2.51e-3 ✓ sig.
nijmegen breakage syndrome Rhabdomyosarcoma 0.036 1 1.75e-3 2.59e-3 ✓ sig.
ciliary dyskinesia, primary, 47, and lissencephaly Rhabdomyosarcoma 0.036 1 1.75e-3 2.59e-3 ✓ sig.
Fanconi anemia complementation group U Hereditary breast cancer 0.030 1 2.08e-3 2.95e-3 ✓ sig.
Hereditary breast cancer nijmegen breakage syndrome 0.030 1 2.08e-3 2.95e-3 ✓ sig.
fanconi anemia complementation group p Hereditary breast cancer 0.030 1 2.08e-3 2.95e-3 ✓ sig.
BARD1-related cancer predisposition Hereditary breast cancer 0.030 1 2.08e-3 2.95e-3 ✓ sig.
Constitutional mismatch repair deficiency Intellectual developmental disorder dysmorphic behavioral 0.063 1 2.53e-3 3.44e-3 ✓ sig.
Fanconi anemia Fanconi anemia complementation group U 0.025 1 2.53e-3 3.44e-3 ✓ sig.
Fanconi anemia fanconi anemia complementation group p 0.025 1 2.53e-3 3.44e-3 ✓ sig.
Fanconi anemia fanconi anemia complementation group f 0.025 1 2.53e-3 3.44e-3 ✓ sig.
Cystic leukoencephalopathy Lynch syndrome 0.020 1 6.35e-3 7.63e-3 ✓ sig.