Disease Clusters | GeDiPNet

← Back to all clusters

Cluster 626

5 diseases · 6 shared-gene connections

5 Diseases

5 Unique genes

0.311 Avg. similarity score

T-cell immunodeficiency Most-connected disease (4 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.

T-cell immunodeficiency Hemifacial microsomia T-cell immunodeficiency, congenital alopecia, and nail dystrophy T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant Thymic hypoplasia

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
T-cell immunodeficiency	4	4	2
Hemifacial microsomia	2	2	4
T-cell immunodeficiency, congenital alopecia, and nail dystrophy	2	2	1
T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant	2	2	1
Thymic hypoplasia	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
FOXI3	3 / 5	Hemifacial microsomia, T-cell immunodeficiency, Thymic hypoplasia
FOXN1	3 / 5	T-cell immunodeficiency, T-cell immunodeficiency, congenital alopecia, and nail dystrophy, T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant

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)

None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.

Pathway ⇵	Source ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
mRNA Splicing - Minor Pathway SF3B2	Reactome	1 / 52	46.2×	2.15e-2	8.93e-2
Regulation of PTEN stability and activity FRK	Reactome	1 / 69	34.8×	2.84e-2	1.05e-1
Spliceosome SF3B2	KEGG	1 / 162	14.8×	6.57e-2	1.69e-1
mRNA Splicing - Major Pathway SF3B2	Reactome	1 / 183	13.1×	7.39e-2	1.81e-1
Neutrophil degranulation FRK	Reactome	1 / 480	5.0×	1.85e-1	3.15e-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 ⇵
hair follicle development FOXI3, FOXN1	GO:0001942	2 / 48	156×	6.43e-5	2.23e-3 ✓ sig.
thymus development FOXI3, FOXN1	GO:0048538	2 / 50	149×	6.98e-5	2.37e-3 ✓ sig.
symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway FRK	GO:0039537	1 / 1	3,737×	2.68e-4	6.25e-3 ✓ sig.
otic placode development FOXI3	GO:1905040	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
lymphoid lineage cell migration into thymus FOXN1	GO:0097535	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
regulation of positive thymic T cell selection FOXN1	GO:1902232	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
thymus epithelium morphogenesis FOXN1	GO:0097536	1 / 2	1,869×	5.35e-4	9.88e-3 ✓ sig.
epidermal cell fate specification FOXI3	GO:0009957	1 / 5	747×	1.34e-3	1.71e-2 ✓ sig.
T cell lineage commitment FOXN1	GO:0002360	1 / 6	623×	1.60e-3	1.88e-2 ✓ sig.
cell differentiation FOXI3, FRK, FOXN1	GO:0030154	3 / 1,051	10.7×	1.63e-3	1.91e-2 ✓ sig.
regulation of T cell differentiation in thymus FOXN1	GO:0033081	1 / 7	534×	1.87e-3	2.05e-2 ✓ sig.
positive regulation of hair follicle development FOXN1	GO:0051798	1 / 7	534×	1.87e-3	2.05e-2 ✓ sig.
parathyroid gland development FOXI3	GO:0060017	1 / 7	534×	1.87e-3	2.05e-2 ✓ sig.
nail development FOXN1	GO:0035878	1 / 7	534×	1.87e-3	2.05e-2 ✓ sig.
positive regulation of epithelial cell differentiation FOXN1	GO:0030858	1 / 12	311×	3.21e-3	2.69e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
T-cell immunodeficiency, congenital alopecia, and nail dystrophy	T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant	0.500	1	6.46e-5	1.98e-4 ✓ sig.
T-cell immunodeficiency	T-cell immunodeficiency, congenital alopecia, and nail dystrophy	0.333	1	1.29e-4	3.27e-4 ✓ sig.
T-cell immunodeficiency	T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant	0.333	1	1.29e-4	3.27e-4 ✓ sig.
T-cell immunodeficiency	Thymic hypoplasia	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Hemifacial microsomia	Thymic hypoplasia	0.200	1	2.58e-4	5.38e-4 ✓ sig.
Hemifacial microsomia	T-cell immunodeficiency	0.167	1	5.16e-4	9.13e-4 ✓ sig.

Disease Clusters?