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Cluster 386

5 diseases · 6 shared-gene connections

5 Diseases

10 Unique genes

0.173 Avg. similarity score

Bone marrow failure syndromes Most-connected disease (4 links)

Significant edges only (q < 0.05) Spacing Colour by

Disease Searched: Bone marrow failure syndromes 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.

Bone marrow failure syndromes Congenital bone marrow failure syndrome Aplasia and myelodysplasia Growth hormone insensitivity syndrome with immune dysregulation Congenital progressive bone marrow failure-b-cell immunodeficiency-skeletal dysplasia syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Bone marrow failure syndromes	4	4	9
Congenital bone marrow failure syndrome	3	3	3
Aplasia and myelodysplasia	2	2	1
Growth hormone insensitivity syndrome with immune dysregulation	2	2	2
Congenital progressive bone marrow failure-b-cell immunodeficiency-skeletal dysplasia syndrome	1	1	1

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

Gene ⇵	Member diseases ⇵	Linked diseases
ERCC6L2	3 / 5	Bone marrow failure syndromes, Congenital bone marrow failure syndrome, Growth hormone insensitivity syndrome with immune dysregulation
SRP72	3 / 5	Aplasia and myelodysplasia, Bone marrow failure syndromes, Congenital bone marrow failure syndrome
DNAJC21	2 / 5	Bone marrow failure syndromes, Congenital bone marrow failure syndrome
MYSM1	2 / 5	Bone marrow failure syndromes, Congenital progressive bone marrow failure-b-cell immunodeficiency-skeletal dysplasia 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 ⇵
Stabilization of p53 TP53, MDM4	Reactome	2 / 11	218×	3.42e-5	9.46e-4 ✓ sig.
Regulation of TP53 Activity through Methylation TP53, MDM4	Reactome	2 / 19	126×	1.06e-4	2.38e-3 ✓ sig.
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain NPM1, TP53	Reactome	2 / 20	120×	1.18e-4	2.58e-3 ✓ sig.
Interleukin-3, Interleukin-5 and GM-CSF signaling CSF2, STAT5B	Reactome	2 / 23	104×	1.56e-4	3.24e-3 ✓ sig.
Oncogene Induced Senescence TP53, MDM4	Reactome	2 / 33	72.8×	3.25e-4	5.80e-3 ✓ sig.
Regulation of TP53 Degradation TP53, MDM4	Reactome	2 / 36	66.7×	3.87e-4	6.66e-3 ✓ sig.
Human T-cell leukemia virus 1 infection CSF2, TP53, STAT5B	KEGG	3 / 224	16.1×	6.97e-4	1.05e-2 ✓ sig.
Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) GCK	Reactome	1 / 1	1,201×	8.33e-4	1.21e-2 ✓ sig.
Acute myeloid leukemia CSF2, STAT5B	KEGG	2 / 68	35.3×	1.38e-3	1.78e-2 ✓ sig.
Prolactin signaling pathway GCK, STAT5B	KEGG	2 / 71	33.8×	1.50e-3	1.89e-2 ✓ sig.
Central carbon metabolism in cancer GCK, TP53	KEGG	2 / 71	33.8×	1.50e-3	1.89e-2 ✓ sig.
Non-small cell lung cancer TP53, STAT5B	KEGG	2 / 73	32.9×	1.59e-3	1.97e-2 ✓ sig.
Regulation of TP53 Expression TP53	Reactome	1 / 2	601×	1.66e-3	2.04e-2 ✓ sig.
Signaling by Leptin STAT5B	Reactome	1 / 2	601×	1.66e-3	2.04e-2 ✓ sig.
p53 signaling pathway TP53, MDM4	KEGG	2 / 75	32.0×	1.68e-3	2.05e-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 ⇵
regulation of cell population proliferation CSF2, NPM1, TP53, MDM4, STAT5B	GO:0042127	5 / 201	46.5×	3.30e-8	4.75e-6 ✓ sig.
regulation of DNA damage response, signal transduction by p53 class mediator NPM1, TP53	GO:0043516	2 / 7	534×	5.40e-6	3.26e-4 ✓ sig.
regulation of hemopoiesis MYSM1, STAT5B	GO:1903706	2 / 16	234×	3.08e-5	1.26e-3 ✓ sig.
macrophage differentiation CSF2, NPM1	GO:0030225	2 / 37	101×	1.70e-4	4.59e-3 ✓ sig.
T cell differentiation in thymus TP53, STAT5B	GO:0033077	2 / 41	91.2×	2.09e-4	5.32e-3 ✓ sig.
protein stabilization NPM1, TP53, MDM4	GO:0050821	3 / 248	22.6×	2.59e-4	6.16e-3 ✓ sig.
DNA damage response, signal transduction by p53 class mediator TP53, MDM4	GO:0030330	2 / 48	77.9×	2.87e-4	6.62e-3 ✓ sig.
regulation of cell cycle NPM1, TP53, MDM4	GO:0051726	3 / 262	21.4×	3.04e-4	6.93e-3 ✓ sig.
cell population proliferation CSF2, TP53, STAT5B	GO:0008283	3 / 263	21.3×	3.07e-4	6.98e-3 ✓ sig.
cellular response to UV NPM1, TP53	GO:0034644	2 / 55	68.0×	3.77e-4	8.05e-3 ✓ sig.
cellular senescence NPM1, TP53	GO:0090398	2 / 57	65.6×	4.05e-4	8.46e-3 ✓ sig.
negative regulation of helicase activity TP53	GO:0051097	1 / 1	1,869×	5.35e-4	1.02e-2 ✓ sig.
regulation of intrinsic apoptotic signaling pathway by p53 class mediator TP53	GO:1902253	1 / 1	1,869×	5.35e-4	1.02e-2 ✓ sig.
negative regulation of G1 to G0 transition TP53	GO:1903451	1 / 1	1,869×	5.35e-4	1.02e-2 ✓ sig.
regulation of endoribonuclease activity NPM1	GO:0060699	1 / 1	1,869×	5.35e-4	1.02e-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	1.36e-9 ✓ sig.
Aplasia and myelodysplasia	Congenital bone marrow failure syndrome	0.250	1	1.95e-4	5.32e-4 ✓ sig.
Congenital bone marrow failure syndrome	Growth hormone insensitivity syndrome with immune dysregulation	0.200	1	3.90e-4	8.64e-4 ✓ sig.
Aplasia and myelodysplasia	Bone marrow failure syndromes	0.100	1	5.84e-4	1.15e-3 ✓ sig.
Bone marrow failure syndromes	Congenital progressive bone marrow failure-b-cell immunodeficiency-skeletal dysplasia syndrome	0.100	1	5.84e-4	1.15e-3 ✓ sig.
Bone marrow failure syndromes	Growth hormone insensitivity syndrome with immune dysregulation	0.091	1	1.17e-3	1.89e-3 ✓ sig.

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