Disease Clusters | GeDiPNet

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Cluster 600

5 diseases · 8 shared-gene connections

5 Diseases

3 Unique genes

0.344 Avg. similarity score

Elejalde syndrome 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.

Elejalde syndrome Griscelli syndrome Cerebellar cortical atrophy Griscelli syndrome type 1 Griscelli syndrome type 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Elejalde syndrome	4	4	2
Griscelli syndrome	4	4	3
Cerebellar cortical atrophy	3	3	1
Griscelli syndrome type 1	3	3	1
Griscelli syndrome type 2	2	2	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
MYO5A	4 / 5	Cerebellar cortical atrophy, Elejalde syndrome, Griscelli syndrome, Griscelli syndrome type 1
RAB27A	3 / 5	Elejalde syndrome, Griscelli syndrome, Griscelli syndrome type 2

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 ⇵
FCGR3A-mediated phagocytosis MYO5A	Reactome	1 / 59	67.9×	1.47e-2	7.17e-2
Regulation of actin dynamics for phagocytic cup formation MYO5A	Reactome	1 / 60	66.7×	1.49e-2	7.22e-2
RAB geranylgeranylation RAB27A	Reactome	1 / 65	61.6×	1.62e-2	7.58e-2
RAB GEFs exchange GTP for GDP on RABs RAB27A	Reactome	1 / 90	44.5×	2.23e-2	9.12e-2
Motor proteins MYO5A	KEGG	1 / 194	20.6×	4.77e-2	1.41e-1
Pathogenic Escherichia coli infection MYO5A	KEGG	1 / 200	20.0×	4.91e-2	1.43e-1
Neutrophil degranulation RAB27A	Reactome	1 / 480	8.3×	1.15e-1	2.35e-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 ⇵
melanosome transport MYO5A, RAB27A, MLPH	GO:0032402	3 / 22	849×	1.42e-9	3.17e-7 ✓ sig.
multivesicular body organization RAB27A	GO:0036257	1 / 1	6,229×	1.61e-4	4.34e-3 ✓ sig.
cytotoxic T cell degranulation RAB27A	GO:0043316	1 / 1	6,229×	1.61e-4	4.34e-3 ✓ sig.
positive regulation of constitutive secretory pathway RAB27A	GO:1903435	1 / 1	6,229×	1.61e-4	4.34e-3 ✓ sig.
pigment granule localization RAB27A	GO:0051875	1 / 2	3,115×	3.21e-4	7.04e-3 ✓ sig.
pigment granule transport RAB27A	GO:0051904	1 / 2	3,115×	3.21e-4	7.04e-3 ✓ sig.
complement-dependent cytotoxicity RAB27A	GO:0097278	1 / 3	2,076×	4.82e-4	9.24e-3 ✓ sig.
exosomal secretion RAB27A	GO:1990182	1 / 4	1,557×	6.42e-4	1.11e-2 ✓ sig.
positive regulation of regulated secretory pathway RAB27A	GO:1903307	1 / 5	1,246×	8.03e-4	1.28e-2 ✓ sig.
melanosome localization RAB27A	GO:0032400	1 / 5	1,246×	8.03e-4	1.28e-2 ✓ sig.
vesicle-mediated transport MYO5A, RAB27A	GO:0016192	2 / 326	38.2×	9.00e-4	1.38e-2 ✓ sig.
vesicle transport along actin filament MYO5A	GO:0030050	1 / 6	1,038×	9.63e-4	1.42e-2 ✓ sig.
natural killer cell degranulation RAB27A	GO:0043320	1 / 8	779×	1.28e-3	1.67e-2 ✓ sig.
regulation of Golgi organization MYO5A	GO:1903358	1 / 13	479×	2.09e-3	2.17e-2 ✓ sig.
post-Golgi vesicle-mediated transport MYO5A	GO:0006892	1 / 16	389×	2.57e-3	2.40e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Elejalde syndrome	Griscelli syndrome	0.500	2	2.50e-8	1.87e-7 ✓ sig.
Cerebellar cortical atrophy	Griscelli syndrome type 1	0.500	1	6.46e-5	1.98e-4 ✓ sig.
Cerebellar cortical atrophy	Elejalde syndrome	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Elejalde syndrome	Griscelli syndrome type 2	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Elejalde syndrome	Griscelli syndrome type 1	0.333	1	1.29e-4	3.27e-4 ✓ sig.
Cerebellar cortical atrophy	Griscelli syndrome	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Griscelli syndrome	Griscelli syndrome type 2	0.250	1	1.94e-4	4.41e-4 ✓ sig.
Griscelli syndrome	Griscelli syndrome type 1	0.250	1	1.94e-4	4.41e-4 ✓ sig.

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