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Cluster 319

6 diseases · 8 shared-gene connections

6 Diseases

15 Unique genes

0.169 Avg. similarity score

Congenital bone marrow failure 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.

Congenital bone marrow failure syndrome Bone marrow failure syndromes Shwachman-diamond syndrome bone marrow failure syndrome 3 Aplasia and myelodysplasia shwachman-diamond syndrome 2

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Congenital bone marrow failure syndrome	4	4	3
Bone marrow failure syndromes	3	3	9
Shwachman-diamond syndrome	3	3	7
bone marrow failure syndrome 3	3	3	1
Aplasia and myelodysplasia	2	2	1
shwachman-diamond syndrome 2	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
DNAJC21	4 / 6	bone marrow failure syndrome 3, Bone marrow failure syndromes, Congenital bone marrow failure syndrome, Shwachman-diamond syndrome
SRP72	3 / 6	Aplasia and myelodysplasia, Bone marrow failure syndromes, Congenital bone marrow failure syndrome
EFL1	2 / 6	Shwachman-diamond syndrome, shwachman-diamond syndrome 2
ERCC6L2	2 / 6	Bone marrow failure syndromes, Congenital bone marrow failure 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 ⇵
Protein export SRP72, SRP54, SRPRA, SRP19	KEGG	4 / 31	103×	4.86e-8	3.48e-6 ✓ sig.
Stabilization of p53 TP53, MDM4	Reactome	2 / 11	146×	7.96e-5	1.86e-3 ✓ sig.
SRP-dependent cotranslational protein targeting to membrane SRP72, SRP54, SRP19	Reactome	3 / 93	25.8×	1.91e-4	3.77e-3 ✓ sig.
Regulation of TP53 Activity through Methylation TP53, MDM4	Reactome	2 / 19	84.3×	2.46e-4	4.59e-3 ✓ sig.
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain NPM1, TP53	Reactome	2 / 20	80.1×	2.73e-4	4.98e-3 ✓ sig.
Ribosome biogenesis in eukaryotes EFL1, EIF6, SBDS	KEGG	3 / 125	19.2×	4.57e-4	7.43e-3 ✓ sig.
Oncogene Induced Senescence TP53, MDM4	Reactome	2 / 33	48.5×	7.52e-4	1.10e-2 ✓ sig.
Regulation of TP53 Degradation TP53, MDM4	Reactome	2 / 36	44.5×	8.95e-4	1.25e-2 ✓ sig.
Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) GCK	Reactome	1 / 1	801×	1.25e-3	1.60e-2 ✓ sig.
Regulation of TP53 Expression TP53	Reactome	1 / 2	400×	2.50e-3	2.69e-2 ✓ sig.
Central carbon metabolism in cancer GCK, TP53	KEGG	2 / 71	22.6×	3.44e-3	3.40e-2 ✓ sig.
p53 signaling pathway TP53, MDM4	KEGG	2 / 75	21.4×	3.83e-3	3.66e-2 ✓ sig.
Transcriptional activation of cell cycle inhibitor p21 TP53	Reactome	1 / 4	200×	4.99e-3	4.37e-2 ✓ sig.
Nuclear import of Rev protein NPM1	Reactome	1 / 4	200×	4.99e-3	4.37e-2 ✓ sig.
Regulation of TP53 Activity through Phosphorylation TP53, MDM4	Reactome	2 / 92	17.4×	5.71e-3	4.79e-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 ⇵
SRP-dependent cotranslational protein targeting to membrane SRP72, SRP54, SRPRA, SRP19	GO:0006614	4 / 10	498×	5.63e-11	1.72e-8 ✓ sig.
cytosolic ribosome assembly EFL1, EIF6, SBDS	GO:0042256	3 / 5	747×	4.18e-9	7.95e-7 ✓ sig.
SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition SRP54, SRPRA, SRP19	GO:0006617	3 / 14	267×	1.52e-7	1.72e-5 ✓ sig.
ribosome biogenesis NPM1, EFL1, EIF6, SBDS	GO:0042254	4 / 122	40.8×	2.23e-6	1.57e-4 ✓ sig.
regulation of DNA damage response, signal transduction by p53 class mediator NPM1, TP53	GO:0043516	2 / 7	356×	1.26e-5	6.25e-4 ✓ sig.
regulation of cell population proliferation CSF2, NPM1, TP53, MDM4	GO:0042127	4 / 201	24.8×	1.62e-5	7.62e-4 ✓ sig.
bone marrow development TP53, SBDS	GO:0048539	2 / 9	277×	2.16e-5	9.54e-4 ✓ sig.
cotranslational protein targeting to membrane SRPRA, SRP19	GO:0006613	2 / 10	249×	2.70e-5	1.13e-3 ✓ sig.
regulation of glycolytic process GCK, EIF6	GO:0006110	2 / 13	192×	4.67e-5	1.71e-3 ✓ sig.
protein targeting to ER SRP54, SRPRA	GO:0045047	2 / 15	166×	6.28e-5	2.13e-3 ✓ sig.
macrophage differentiation CSF2, NPM1	GO:0030225	2 / 37	67.3×	3.94e-4	8.11e-3 ✓ sig.
ribosomal large subunit biogenesis NPM1, EIF6	GO:0042273	2 / 39	63.9×	4.38e-4	8.72e-3 ✓ sig.
DNA damage response, signal transduction by p53 class mediator TP53, MDM4	GO:0030330	2 / 48	51.9×	6.64e-4	1.15e-2 ✓ sig.
negative regulation of helicase activity TP53	GO:0051097	1 / 1	1,246×	8.03e-4	1.30e-2 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator TP53	GO:1902253	1 / 1	1,246×	8.03e-4	1.30e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
Bone marrow failure syndromes	Congenital bone marrow failure syndrome	0.300	3	1.38e-10	1.43e-9 ✓ sig.
Aplasia and myelodysplasia	Congenital bone marrow failure syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
bone marrow failure syndrome 3	Congenital bone marrow failure syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
bone marrow failure syndrome 3	Shwachman-diamond syndrome	0.125	1	4.55e-4	9.55e-4 ✓ sig.
Shwachman-diamond syndrome	shwachman-diamond syndrome 2	0.125	1	4.55e-4	9.55e-4 ✓ sig.
Aplasia and myelodysplasia	Bone marrow failure syndromes	0.100	1	5.84e-4	1.14e-3 ✓ sig.
bone marrow failure syndrome 3	Bone marrow failure syndromes	0.100	1	5.84e-4	1.14e-3 ✓ sig.
Congenital bone marrow failure syndrome	Shwachman-diamond syndrome	0.100	1	1.36e-3	2.13e-3 ✓ sig.

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