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 240

7 diseases · 13 shared-gene connections
7 Diseases
52 Unique genes
0.196 Avg. similarity score
Erythroid hypoplasia 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 ⇵
Erythroid hypoplasia 5 5 2
Ovarian agenesis 5 5 2
Auricle malformation 4 4 8
Testicular hydrocele 4 4 11
diamond-blackfan anemia 6 4 4 1
Diamond-blackfan anemia 3 3 37
Degcags syndrome 1 1 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
RPL5 6 / 7 Auricle malformation, Diamond-blackfan anemia, diamond-blackfan anemia 6, Erythroid hypoplasia and 2 more
DIPK1A 5 / 7 Auricle malformation, Diamond-blackfan anemia, Erythroid hypoplasia, Ovarian agenesis and 1 more
ZNF699 2 / 7 Degcags syndrome, Diamond-blackfan anemia
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 ⇵
Viral mRNA Translation
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 89 62.3× 9.30e-39 6.04e-35 ✓ sig.
SRP-dependent cotranslational protein targeting to membrane
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 93 59.6× 3.11e-38 1.91e-34 ✓ sig.
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 95 58.3× 5.57e-38 3.24e-34 ✓ sig.
Formation of a pool of free 40S subunits
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 101 54.9× 2.94e-37 1.54e-33 ✓ sig.
L13a-mediated translational silencing of Ceruloplasmin expression
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 111 49.9× 3.70e-36 1.86e-32 ✓ sig.
GTP hydrolysis and joining of the 60S ribosomal subunit
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 112 49.5× 4.70e-36 2.16e-32 ✓ sig.
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 115 48.2× 9.48e-36 4.19e-32 ✓ sig.
Ribosome
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS10-NUDT3, RPS15A, RPS17
 KEGG 25 / 171 33.8× 3.86e-33 1.47e-29 ✓ sig.
Major pathway of rRNA processing in the nucleolus and cytosol
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 Reactome 24 / 184 30.1× 1.77e-30 5.43e-27 ✓ sig.
Coronavirus disease - COVID-19
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS10-NUDT3, RPS15A, RPS17
 KEGG 25 / 238 24.3× 2.22e-29 5.98e-26 ✓ sig.
Formation of the ternary complex, and subsequently, the 43S complex
RPS10, RPS15A, RPS17, RPS19, RPS20, RPS24, RPS26, RPS28, RPS29, RPS7, RPS15, RPS27
 Reactome 12 / 51 54.3× 1.55e-18 1.02e-15 ✓ sig.
Translation initiation complex formation
RPS10, RPS15A, RPS17, RPS19, RPS20, RPS24, RPS26, RPS28, RPS29, RPS7, RPS15, RPS27
 Reactome 12 / 58 47.8× 8.54e-18 4.67e-15 ✓ sig.
Ribosomal scanning and start codon recognition
RPS10, RPS15A, RPS17, RPS19, RPS20, RPS24, RPS26, RPS28, RPS29, RPS7, RPS15, RPS27
 Reactome 12 / 58 47.8× 8.54e-18 4.67e-15 ✓ sig.
Signaling by FGFR2 amplification mutants
FGFR2
 Reactome 1 / 1 231× 4.33e-3 3.98e-2 ✓ sig.
Signaling by FGFR2 fusions
FGFR2
 Reactome 1 / 1 231× 4.33e-3 3.98e-2 ✓ 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 ⇵
cytoplasmic translation
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 GO:0002181 24 / 126 68.5× 2.80e-39 2.80e-35 ✓ sig.
translation
RPL11, RPL15, RPL18, RPL26, RPL35, RPL35A, RPL5, RPL8, RPS10, RPS15A, RPS17, RPS19
 GO:0006412 25 / 310 29.0× 3.77e-31 2.16e-27 ✓ sig.
rRNA processing
RPL11, RPL26, RPL35A, RPL5, RPS17, RPS19, RPS24, RPS28, RPS7, TSR2, RPL27, RPS15
 GO:0006364 13 / 162 28.8× 4.55e-16 3.80e-13 ✓ sig.
ribosomal small subunit biogenesis
RPS15A, RPS17, RPS19, RPS24, RPS28, RPS7, RPS15, RPS27
 GO:0042274 8 / 75 38.3× 3.00e-11 9.71e-9 ✓ sig.
ribosomal small subunit assembly
RPS19, RPS28, RPS15, RPS27
 GO:0000028 4 / 13 111× 3.74e-8 5.29e-6 ✓ sig.
ribosomal large subunit biogenesis
HEATR3, RPL11, RPL26, RPL35A, RPL5
 GO:0042273 5 / 39 46.1× 7.34e-8 9.30e-6 ✓ sig.
negative regulation of ubiquitin protein ligase activity
RPL11, RPL5, RPS7
 GO:1904667 3 / 9 120× 1.69e-6 1.26e-4 ✓ sig.
positive regulation of signal transduction by p53 class mediator
RPL11, RPS20, RPS15
 GO:1901798 3 / 13 82.9× 5.70e-6 3.33e-4 ✓ sig.
erythrocyte differentiation
GATA1, RPS19, EPO, IKZF1
 GO:0030218 4 / 65 22.1× 3.18e-5 1.28e-3 ✓ sig.
negative regulation of ubiquitin-dependent protein catabolic process
RPL11, RPL5, RPS7
 GO:2000059 3 / 25 43.1× 4.48e-5 1.66e-3 ✓ sig.
metanephric S-shaped body morphogenesis
PAX8, PKD2
 GO:0072284 2 / 4 180× 4.54e-5 1.68e-3 ✓ sig.
negative regulation of protein neddylation
RPL11, RPL5
 GO:2000435 2 / 5 144× 7.55e-5 2.46e-3 ✓ sig.
mesonephric tubule development
PAX8, PKD2
 GO:0072164 2 / 7 103× 1.58e-4 4.26e-3 ✓ sig.
embryonic organ development
TP53, FGFR2, PKD2
 GO:0048568 3 / 42 25.7× 2.16e-4 5.32e-3 ✓ sig.
response to salt stress
TP53, EPO
 GO:0009651 2 / 9 79.9× 2.70e-4 6.24e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Erythroid hypoplasia Ovarian agenesis 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Auricle malformation Ovarian agenesis 0.222 2 2.36e-7 1.64e-6 ✓ sig.
Auricle malformation Erythroid hypoplasia 0.222 2 2.36e-7 1.64e-6 ✓ sig.
Erythroid hypoplasia Testicular hydrocele 0.167 2 4.64e-7 3.06e-6 ✓ sig.
Ovarian agenesis Testicular hydrocele 0.167 2 4.64e-7 3.06e-6 ✓ sig.
Diamond-blackfan anemia Ovarian agenesis 0.053 2 5.62e-6 3.06e-5 ✓ sig.
Diamond-blackfan anemia Erythroid hypoplasia 0.053 2 5.62e-6 3.06e-5 ✓ sig.
Auricle malformation Testicular hydrocele 0.111 2 1.30e-5 6.68e-5 ✓ sig.
diamond-blackfan anemia 6 Ovarian agenesis 0.333 1 1.30e-4 3.90e-4 ✓ sig.
diamond-blackfan anemia 6 Erythroid hypoplasia 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Auricle malformation diamond-blackfan anemia 6 0.111 1 5.20e-4 1.04e-3 ✓ sig.
diamond-blackfan anemia 6 Testicular hydrocele 0.083 1 7.14e-4 1.31e-3 ✓ sig.
Degcags syndrome Diamond-blackfan anemia 0.026 1 2.40e-3 3.30e-3 ✓ sig.