Disease Clusters | GeDiPNet

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Cluster 192

8 diseases · 18 shared-gene connections

8 Diseases

9 Unique genes

0.304 Avg. similarity score

Acrocallosal syndrome Most-connected disease (7 links)

Significant edges only (q < 0.05) Spacing Colour by

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.

Acrocallosal syndrome Cronkhite-canada syndrome Pilosebaceous disorder Tibial hemimelia White sutton syndrome greig cephalopolysyndactyly syndrome

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Acrocallosal syndrome	7	7	2
Cronkhite-canada syndrome	5	5	1
Pilosebaceous disorder	5	5	2
Tibial hemimelia	5	5	1
White sutton syndrome	5	5	3
greig cephalopolysyndactyly syndrome	5	5	1
Hydrolethalus syndrome	2	2	3
Male infertility testicular dysgenesis	2	2	3

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

Gene ⇵	Member diseases ⇵	Linked diseases
GLI3	6 / 8	Acrocallosal syndrome, Cronkhite-canada syndrome, greig cephalopolysyndactyly syndrome, Pilosebaceous disorder and 2 more
KIF7	3 / 8	Acrocallosal syndrome, Hydrolethalus syndrome, Male infertility testicular dysgenesis

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 ⇵
GLI proteins bind promoters of Hh responsive genes to promote transcription GLI3, GLI2	Reactome	2 / 3	890×	1.50e-6	6.92e-5 ✓ sig.
Hedgehog signaling pathway GLI3, KIF7, GLI2	KEGG	3 / 56	71.5×	7.91e-6	2.76e-4 ✓ sig.
Hedgehog 'off' state GLI3, KIF7, GLI2	Reactome	3 / 56	71.5×	7.91e-6	2.76e-4 ✓ sig.
Basal cell carcinoma GLI3, KIF7, GLI2	KEGG	3 / 63	63.5×	1.13e-5	3.71e-4 ✓ sig.
Hedgehog 'on' state GLI3, KIF7, GLI2	Reactome	3 / 70	57.2×	1.55e-5	4.85e-4 ✓ sig.
Pathways in cancer GLI3, KIF7, SOS2, GLI2	KEGG	4 / 533	10.0×	4.04e-4	6.76e-3 ✓ sig.
Interleukin-15 signaling SOS2	Reactome	1 / 13	103×	9.70e-3	6.74e-2
tRNA modification in the nucleus and cytosol PUS3	Reactome	1 / 19	70.2×	1.42e-2	8.41e-2
Synthesis of IP3 and IP4 in the cytosol PLCD1	Reactome	1 / 28	47.7×	2.08e-2	1.05e-1
Transcriptional Regulation by E2F6 CHEK1	Reactome	1 / 35	38.1×	2.59e-2	1.19e-1
Signaling by SCF-KIT CHEK1	Reactome	1 / 37	36.1×	2.74e-2	1.23e-1
Activation of ATR in response to replication stress CHEK1	Reactome	1 / 37	36.1×	2.74e-2	1.23e-1
Presynaptic phase of homologous DNA pairing and strand exchange CHEK1	Reactome	1 / 39	34.2×	2.89e-2	1.26e-1
Ubiquitin Mediated Degradation of Phosphorylated Cdc25A CHEK1	Reactome	1 / 52	25.7×	3.83e-2	1.48e-1
NRAGE signals death through JNK SOS2	Reactome	1 / 55	24.3×	4.05e-2	1.53e-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 ⇵
smoothened signaling pathway involved in ventral spinal cord interneuron specification GLI3, GLI2	GO:0021775	2 / 3	1,384×	6.18e-7	5.59e-5 ✓ sig.
hindgut morphogenesis GLI3, GLI2	GO:0007442	2 / 4	1,038×	1.24e-6	9.83e-5 ✓ sig.
spinal cord dorsal/ventral patterning GLI3, GLI2	GO:0021513	2 / 8	519×	5.76e-6	3.36e-4 ✓ sig.
tube development GLI3, GLI2	GO:0035295	2 / 13	319×	1.60e-5	7.57e-4 ✓ sig.
embryonic digestive tract development GLI3, GLI2	GO:0048566	2 / 19	219×	3.51e-5	1.38e-3 ✓ sig.
proximal/distal pattern formation GLI3, GLI2	GO:0009954	2 / 26	160×	6.66e-5	2.23e-3 ✓ sig.
branching morphogenesis of an epithelial tube GLI3, GLI2	GO:0048754	2 / 29	143×	8.32e-5	2.64e-3 ✓ sig.
developmental growth GLI3, GLI2	GO:0048589	2 / 30	138×	8.91e-5	2.78e-3 ✓ sig.
negative regulation of smoothened signaling pathway GLI3, KIF7	GO:0045879	2 / 35	119×	1.22e-4	3.51e-3 ✓ sig.
mammary gland development GLI3, GLI2	GO:0030879	2 / 37	112×	1.36e-4	3.80e-3 ✓ sig.
odontogenesis of dentin-containing tooth GLI3, GLI2	GO:0042475	2 / 56	74.2×	3.13e-4	6.93e-3 ✓ sig.
pattern specification process GLI3, GLI2	GO:0007389	2 / 60	69.2×	3.60e-4	7.59e-3 ✓ sig.
lateral ganglionic eminence cell proliferation GLI3	GO:0022018	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
lambdoid suture morphogenesis GLI3	GO:0060366	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.
sagittal suture morphogenesis GLI3	GO:0060367	1 / 1	2,076×	4.82e-4	9.31e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
greig cephalopolysyndactyly syndrome	Tibial hemimelia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Cronkhite-canada syndrome	Tibial hemimelia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Cronkhite-canada syndrome	greig cephalopolysyndactyly syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Acrocallosal syndrome	Cronkhite-canada syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Pilosebaceous disorder	Tibial hemimelia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
greig cephalopolysyndactyly syndrome	Pilosebaceous disorder	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Cronkhite-canada syndrome	Pilosebaceous disorder	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Acrocallosal syndrome	greig cephalopolysyndactyly syndrome	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Acrocallosal syndrome	Tibial hemimelia	0.333	1	1.30e-4	3.90e-4 ✓ sig.
Cronkhite-canada syndrome	White sutton syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
greig cephalopolysyndactyly syndrome	White sutton syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Tibial hemimelia	White sutton syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Acrocallosal syndrome	Pilosebaceous disorder	0.250	1	2.60e-4	6.40e-4 ✓ sig.
Acrocallosal syndrome	White sutton syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Acrocallosal syndrome	Hydrolethalus syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Acrocallosal syndrome	Male infertility testicular dysgenesis	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Pilosebaceous disorder	White sutton syndrome	0.200	1	3.90e-4	8.52e-4 ✓ sig.
Hydrolethalus syndrome	Male infertility testicular dysgenesis	0.167	1	5.84e-4	1.14e-3 ✓ sig.

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