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Cluster 127

10 diseases · 18 shared-gene connections
10 Diseases
705 Unique genes
0.159 Avg. similarity score
Bone fragility with contractures, arterial rupture, and deafness Most-connected disease (7 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)

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

Gene ⇵ Member diseases ⇵ Linked diseases
P4HB 6 / 10 Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Desbuquois syndrome, Osteogenesis imperfecta and 2 more
B4GALT7 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, ehlers-danlos syndrome, spondylodysplastic type, 1, Larsen syndrome and 1 more
COL1A1 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
COL1A2 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
CRTAP 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Desbuquois syndrome, Osteogenesis imperfecta and 1 more
GORAB 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis and 1 more
IFITM5 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
LRP5 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
PLS3 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
SEC24D 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Cole-carpenter syndrome, Desbuquois syndrome, Osteogenesis imperfecta and 1 more
SERPINF1 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
SP7 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
WNT1 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis and 1 more
XYLT2 5 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteogenesis imperfecta and 1 more
ALPL 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
B3GALT6 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
B3GAT3 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
BMP1 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
CCDC134 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
CHST3 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
CREB3L1 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
FKBP10 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
KDELR2 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
MBTPS2 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
MESD 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
P3H1 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
PLOD2 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
PPIB 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
SERPINH1 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
SPARC 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
TENT5A 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
TMEM38B 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
XYLT1 4 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
COPB2 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis, Osteoporosis-pseudoglioma syndrome
CSGALNACT1 3 / 10 Desbuquois syndrome, Larsen syndrome, skeletal dysplasia, mild, with joint laxity and advanced bone age
LIFR 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome
NBAS 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome
P4HA1 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
PHLDB1 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteogenesis imperfecta, Osteoporosis-pseudoglioma syndrome
PLOD3 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Larsen syndrome, Osteoporosis-pseudoglioma syndrome
SGMS2 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome
SLC10A7 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome
TAPT1 3 / 10 Bone fragility with contractures, arterial rupture, and deafness, Desbuquois syndrome, Osteoporosis-pseudoglioma syndrome
AMBN 2 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
ANO5 2 / 10 Desbuquois syndrome, Osteogenesis imperfecta
ANTXR2 2 / 10 Desbuquois syndrome, Osteoporosis
BMP2 2 / 10 Desbuquois syndrome, Osteoporosis
CA2 2 / 10 Desbuquois syndrome, Osteoporosis
CANT1 2 / 10 Desbuquois syndrome, Larsen syndrome
COL11A1 2 / 10 Desbuquois syndrome, Osteogenesis imperfecta
DSPP 2 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
EMILIN1 2 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
FGFR3 2 / 10 Desbuquois syndrome, Larsen syndrome
FLNB 2 / 10 Desbuquois syndrome, Larsen syndrome
GALNT3 2 / 10 Desbuquois syndrome, Osteoporosis
GPC6 2 / 10 Desbuquois syndrome, Osteoporosis
GZF1 2 / 10 Desbuquois syndrome, Larsen syndrome
IDH2 2 / 10 Desbuquois syndrome, Osteoporosis
IGF1R 2 / 10 Desbuquois syndrome, Osteoporosis
IL1RN 2 / 10 Desbuquois syndrome, Osteoporosis
KIF22 2 / 10 Desbuquois syndrome, Larsen syndrome
KIF5B 2 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
KL 2 / 10 Desbuquois syndrome, Osteoporosis
MECOM 2 / 10 Desbuquois syndrome, Osteoporosis
MIA3 2 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
OFD1 2 / 10 Desbuquois syndrome, Osteoporosis
PGGHG 2 / 10 Osteogenesis imperfecta, Osteoporosis
PIEZO2 2 / 10 Larsen syndrome, Osteoporosis
PPP1R21 2 / 10 Desbuquois syndrome, neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities
SEC16B 2 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
SFRP4 2 / 10 Desbuquois syndrome, Osteoporosis
SKI 2 / 10 Desbuquois syndrome, Larsen syndrome
TGFB1 2 / 10 Desbuquois syndrome, Osteoporosis
TNFRSF11A 2 / 10 Desbuquois syndrome, Osteoporosis
TNFRSF11B 2 / 10 Desbuquois syndrome, Osteoporosis
TNFSF11 2 / 10 Desbuquois syndrome, Osteoporosis
WNT11 2 / 10 Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome
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 ⇵
Proteoglycans in cancer KEGG 55 / 204 4.6× 1.82e-22 2.28e-19 ✓ sig.
Pathways in cancer KEGG 91 / 533 2.9× 5.03e-21 4.71e-18 ✓ sig.
Signaling pathways regulating pluripotency of stem cells KEGG 41 / 144 4.9× 5.71e-18 3.25e-15 ✓ sig.
Breast cancer KEGG 41 / 148 4.7× 1.70e-17 8.84e-15 ✓ sig.
Hepatocellular carcinoma KEGG 44 / 170 4.4× 1.87e-17 9.66e-15 ✓ sig.
Parathyroid hormone synthesis, secretion and action KEGG 36 / 115 5.3× 2.10e-17 1.07e-14 ✓ sig.
Gastric cancer KEGG 41 / 150 4.7× 2.88e-17 1.42e-14 ✓ sig.
Hedgehog 'off' state Reactome 24 / 56 7.3× 1.40e-15 5.25e-13 ✓ sig.
Melanogenesis KEGG 31 / 101 5.2× 6.76e-15 2.23e-12 ✓ sig.
Signaling by high-kinase activity BRAF mutants Reactome 17 / 36 8.0× 2.90e-12 5.75e-10 ✓ sig.
Chronic myeloid leukemia KEGG 24 / 77 5.3× 5.41e-12 1.02e-9 ✓ sig.
Endocrine resistance KEGG 27 / 99 4.6× 8.69e-12 1.57e-9 ✓ sig.
AGE-RAGE signaling pathway in diabetic complications KEGG 27 / 101 4.6× 1.45e-11 2.50e-9 ✓ sig.
Human papillomavirus infection KEGG 53 / 333 2.7× 2.15e-11 3.57e-9 ✓ sig.
MAP2K and MAPK activation Reactome 17 / 40 7.2× 2.40e-11 3.93e-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 ⇵
skeletal system development GO:0001501 72 / 151 12.6× 9.38e-62 4.00e-57 ✓ sig.
ossification GO:0001503 43 / 110 10.4× 1.20e-32 7.76e-29 ✓ sig.
embryonic limb morphogenesis GO:0030326 33 / 59 14.8× 8.07e-32 4.71e-28 ✓ sig.
embryonic digit morphogenesis GO:0042733 31 / 57 14.4× 1.91e-29 9.41e-26 ✓ sig.
cartilage development GO:0051216 35 / 89 10.4× 6.76e-27 2.66e-23 ✓ sig.
bone development GO:0060348 32 / 76 11.2× 8.02e-26 2.75e-22 ✓ sig.
bone mineralization GO:0030282 28 / 56 13.3× 2.34e-25 7.64e-22 ✓ sig.
positive regulation of gene expression GO:0010628 75 / 504 3.9× 8.23e-25 2.52e-21 ✓ sig.
embryonic hindlimb morphogenesis GO:0035116 20 / 29 18.3× 1.91e-22 4.39e-19 ✓ sig.
positive regulation of transcription by RNA polymerase II GO:0045944 114 / 1,208 2.5× 3.79e-20 6.40e-17 ✓ sig.
chondrocyte differentiation GO:0002062 25 / 61 10.9× 4.20e-20 7.03e-17 ✓ sig.
osteoblast differentiation GO:0001649 35 / 137 6.8× 8.92e-20 1.40e-16 ✓ sig.
bone morphogenesis GO:0060349 19 / 32 15.7× 1.56e-19 2.36e-16 ✓ sig.
cilium assembly GO:0060271 44 / 237 4.9× 1.11e-18 1.47e-15 ✓ sig.
heart development GO:0007507 47 / 273 4.6× 1.74e-18 2.24e-15 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Bone fragility with contractures, arterial rupture, and deafness Osteoporosis-pseudoglioma syndrome 0.980 49 4.28e-143 7.93e-141 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Osteogenesis imperfecta 0.459 28 1.14e-65 8.16e-64 ✓ sig.
Osteogenesis imperfecta Osteoporosis-pseudoglioma syndrome 0.459 28 1.14e-65 8.16e-64 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Desbuquois syndrome 0.066 38 1.92e-45 9.70e-44 ✓ sig.
Desbuquois syndrome Osteoporosis-pseudoglioma syndrome 0.066 38 1.92e-45 9.70e-44 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Larsen syndrome 0.155 9 3.66e-19 7.02e-18 ✓ sig.
Larsen syndrome Osteoporosis-pseudoglioma syndrome 0.155 9 3.66e-19 7.02e-18 ✓ sig.
Osteoporosis Osteoporosis-pseudoglioma syndrome 0.059 11 8.14e-13 1.05e-11 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Osteoporosis 0.059 11 8.14e-13 1.05e-11 ✓ sig.
Osteogenesis imperfecta Osteoporosis 0.057 10 2.16e-12 2.64e-11 ✓ sig.
Cole-carpenter syndrome Osteogenesis imperfecta 0.075 3 1.50e-8 1.25e-7 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness Cole-carpenter syndrome 0.060 3 3.03e-8 2.42e-7 ✓ sig.
Cole-carpenter syndrome Osteoporosis-pseudoglioma syndrome 0.060 3 3.03e-8 2.42e-7 ✓ sig.
Larsen syndrome skeletal dysplasia, mild, with joint laxity and advanced bone age 0.056 1 1.10e-3 1.81e-3 ✓ sig.
ehlers-danlos syndrome, spondylodysplastic type, 1 Larsen syndrome 0.056 1 1.10e-3 1.81e-3 ✓ sig.
ehlers-danlos syndrome, spondylodysplastic type, 1 Osteoporosis-pseudoglioma syndrome 0.020 1 3.18e-3 4.16e-3 ✓ sig.
Bone fragility with contractures, arterial rupture, and deafness ehlers-danlos syndrome, spondylodysplastic type, 1 0.020 1 3.18e-3 4.16e-3 ✓ sig.
Desbuquois syndrome neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities 0.002 1 3.68e-2 3.87e-2 ✓ sig.