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 216

8 diseases · 16 shared-gene connections
8 Diseases
3 Unique genes
0.396 Avg. similarity score
Dicer1 syndrome Most-connected disease (5 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 ⇵
Dicer1 syndrome 5 5 1
Dicer1 tumor-predisposition syndrome 5 5 1
Dicer1-related tumor predisposition 5 5 1
Granulosa cell tumor of ovary 5 5 2
Sertoli-leydig cell tumor of ovary 5 5 1
Vertebral anomalies with endocrine and t-cell dysfunction 5 5 2
Blepharophimosis-ptosis-epicanthus inversus syndrome 1 1 1
vertebral anomalies and variable endocrine and t-cell dysfunction 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
DICER1 6 / 8 Dicer1 syndrome, Dicer1 tumor-predisposition syndrome, Dicer1-related tumor predisposition, Granulosa cell tumor of ovary and 2 more
FOXL2 2 / 8 Blepharophimosis-ptosis-epicanthus inversus syndrome, Granulosa cell tumor of ovary
TBX2 2 / 8 vertebral anomalies and variable endocrine and t-cell dysfunction, Vertebral anomalies with endocrine and t-cell dysfunction
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 ⇵
Small interfering RNA (siRNA) biogenesis
DICER1
 Reactome 1 / 9 445× 2.25e-3 2.48e-2 ✓ sig.
SUMOylation of transcription factors
FOXL2
 Reactome 1 / 18 222× 4.49e-3 4.08e-2 ✓ sig.
MicroRNA (miRNA) biogenesis
DICER1
 Reactome 1 / 24 167× 5.98e-3 4.92e-2 ✓ sig.
MicroRNAs in cancer
DICER1
 KEGG 1 / 311 12.9× 7.57e-2 2.13e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
apoptotic DNA fragmentation
FOXL2, DICER1
 GO:0006309 2 / 12 1,038× 1.13e-6 9.16e-5 ✓ sig.
negative regulation of transcription by RNA polymerase II
FOXL2, DICER1, TBX2
 GO:0000122 3 / 1,002 18.6× 1.54e-4 4.18e-3 ✓ sig.
negative regulation of heart looping
TBX2
 GO:1901208 1 / 1 6,229× 1.61e-4 4.31e-3 ✓ sig.
negative regulation of cardiac chamber formation
TBX2
 GO:1901211 1 / 1 6,229× 1.61e-4 4.31e-3 ✓ sig.
female somatic sex determination
FOXL2
 GO:0019101 1 / 1 6,229× 1.61e-4 4.31e-3 ✓ sig.
granulosa cell differentiation
FOXL2
 GO:0060014 1 / 1 6,229× 1.61e-4 4.31e-3 ✓ sig.
muscle cell fate determination
TBX2
 GO:0007521 1 / 2 3,115× 3.21e-4 7.03e-3 ✓ sig.
pigment metabolic process involved in pigmentation
TBX2
 GO:0043474 1 / 2 3,115× 3.21e-4 7.03e-3 ✓ sig.
ureteric peristalsis
TBX2
 GO:0072105 1 / 2 3,115× 3.21e-4 7.03e-3 ✓ sig.
positive regulation of Schwann cell differentiation
DICER1
 GO:0014040 1 / 3 2,076× 4.82e-4 9.31e-3 ✓ sig.
peripheral nervous system myelin formation
DICER1
 GO:0032290 1 / 3 2,076× 4.82e-4 9.31e-3 ✓ sig.
developmental growth involved in morphogenesis
TBX2
 GO:0060560 1 / 3 2,076× 4.82e-4 9.31e-3 ✓ sig.
mammary placode formation
TBX2
 GO:0060596 1 / 3 2,076× 4.82e-4 9.31e-3 ✓ sig.
global gene silencing by mRNA cleavage
DICER1
 GO:0098795 1 / 3 2,076× 4.82e-4 9.31e-3 ✓ sig.
cardiac jelly development
TBX2
 GO:1905072 1 / 4 1,557× 6.42e-4 1.13e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Dicer1 syndrome Dicer1 tumor-predisposition syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dicer1 syndrome Dicer1-related tumor predisposition 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dicer1 syndrome Sertoli-leydig cell tumor of ovary 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dicer1 tumor-predisposition syndrome Dicer1-related tumor predisposition 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dicer1 tumor-predisposition syndrome Sertoli-leydig cell tumor of ovary 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Dicer1-related tumor predisposition Sertoli-leydig cell tumor of ovary 0.500 1 6.49e-5 2.34e-4 ✓ sig.
Blepharophimosis-ptosis-epicanthus inversus syndrome Granulosa cell tumor of ovary 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dicer1 syndrome Granulosa cell tumor of ovary 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dicer1 syndrome Vertebral anomalies with endocrine and t-cell dysfunction 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dicer1 tumor-predisposition syndrome Granulosa cell tumor of ovary 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dicer1 tumor-predisposition syndrome Vertebral anomalies with endocrine and t-cell dysfunction 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dicer1-related tumor predisposition Granulosa cell tumor of ovary 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Dicer1-related tumor predisposition Vertebral anomalies with endocrine and t-cell dysfunction 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Granulosa cell tumor of ovary Sertoli-leydig cell tumor of ovary 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Sertoli-leydig cell tumor of ovary Vertebral anomalies with endocrine and t-cell dysfunction 0.333 1 1.30e-4 3.90e-4 ✓ sig.
vertebral anomalies and variable endocrine and t-cell dysfunction Vertebral anomalies with endocrine and t-cell dysfunction 0.333 1 1.30e-4 3.90e-4 ✓ sig.