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Cluster 277

7 diseases · 20 shared-gene connections

7 Diseases

3 Unique genes

0.438 Avg. similarity score

Masa syndrome Most-connected disease (6 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.

Masa syndrome Partial corpus callosum agenesis, x-linked X-linked complicated corpus callosum dysgenesis X-linked complicated spastic paraplegia X-linked hydrocephalus with stenosis of the aqueduct of sylvius L1 syndrome

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

Disease ⇵	Connections in cluster ⇵	Significant partners ⇵	Curated genes ⇵
Masa syndrome	6	6	1
Partial corpus callosum agenesis, x-linked	6	6	1
X-linked complicated corpus callosum dysgenesis	6	6	1
X-linked complicated spastic paraplegia	6	6	1
X-linked hydrocephalus with stenosis of the aqueduct of sylvius	6	6	1
L1 syndrome	5	5	1
X-linked hydrocephalus syndrome	5	5	3

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

Gene ⇵	Member diseases ⇵	Linked diseases
L1CAM	7 / 7	L1 syndrome, Masa syndrome, Partial corpus callosum agenesis, x-linked, X-linked complicated corpus callosum dysgenesis and 3 more

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 ⇵
Recycling pathway of L1 L1CAM, TUBB3	Reactome	2 / 40	200×	3.24e-5	8.90e-4 ✓ sig.
L1CAM interactions L1CAM	Reactome	1 / 4	1,001×	9.99e-4	1.35e-2 ✓ sig.
Interaction between L1 and Ankyrins L1CAM	Reactome	1 / 13	308×	3.24e-3	3.26e-2 ✓ sig.
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane TUBB3	Reactome	1 / 18	222×	4.49e-3	4.08e-2 ✓ sig.
Cilium Assembly TUBB3	Reactome	1 / 19	211×	4.74e-3	4.23e-2 ✓ sig.
Signal transduction by L1 L1CAM	Reactome	1 / 21	191×	5.24e-3	4.50e-2 ✓ sig.
Basigin interactions L1CAM	Reactome	1 / 25	160×	6.23e-3	5.06e-2
Carboxyterminal post-translational modifications of tubulin TUBB3	Reactome	1 / 27	148×	6.73e-3	5.32e-2
Sealing of the nuclear envelope (NE) by ESCRT-III TUBB3	Reactome	1 / 31	129×	7.72e-3	5.83e-2
RHO GTPases activate IQGAPs TUBB3	Reactome	1 / 32	125×	7.97e-3	5.96e-2
Aggrephagy TUBB3	Reactome	1 / 40	100×	9.96e-3	6.82e-2
COPI-independent Golgi-to-ER retrograde traffic TUBB3	Reactome	1 / 51	78.5×	1.27e-2	7.88e-2
Intraflagellar transport TUBB3	Reactome	1 / 54	74.1×	1.34e-2	8.14e-2
HSP90 chaperone cycle for steroid hormone receptors (SHR) TUBB3	Reactome	1 / 55	72.8×	1.37e-2	8.23e-2
Hedgehog 'off' state TUBB3	Reactome	1 / 56	71.5×	1.39e-2	8.32e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵	GO ID ⇵	Overlap genes ⇵	Fold enrichment ⇵	P-value ⇵	FDR q-value ⇵
axon guidance L1CAM, TUBB3	GO:0007411	2 / 192	64.9×	3.13e-4	6.93e-3 ✓ sig.
cell killing ATN1	GO:0001906	1 / 2	3,115×	3.21e-4	7.03e-3 ✓ sig.
cell migration L1CAM, ATN1	GO:0016477	2 / 303	41.1×	7.78e-4	1.28e-2 ✓ sig.
dorsal root ganglion development TUBB3	GO:1990791	1 / 5	1,246×	8.03e-4	1.30e-2 ✓ sig.
maintenance of cell polarity ATN1	GO:0030011	1 / 7	890×	1.12e-3	1.62e-2 ✓ sig.
netrin-activated signaling pathway TUBB3	GO:0038007	1 / 9	692×	1.44e-3	1.87e-2 ✓ sig.
positive regulation of axon extension L1CAM	GO:0045773	1 / 31	201×	4.97e-3	3.66e-2 ✓ sig.
response to food ATN1	GO:0032094	1 / 33	189×	5.29e-3	3.78e-2 ✓ sig.
determination of adult lifespan ATN1	GO:0008340	1 / 38	164×	6.09e-3	4.05e-2 ✓ sig.
axon development L1CAM	GO:0061564	1 / 40	156×	6.41e-3	4.15e-2 ✓ sig.
microtubule-based process TUBB3	GO:0007017	1 / 46	135×	7.37e-3	4.44e-2 ✓ sig.
synapse organization L1CAM	GO:0050808	1 / 72	86.5×	1.15e-2	5.51e-2
post-embryonic development ATN1	GO:0009791	1 / 82	76.0×	1.31e-2	5.86e-2
neuron apoptotic process ATN1	GO:0051402	1 / 98	63.6×	1.57e-2	6.37e-2
cell-matrix adhesion L1CAM	GO:0007160	1 / 105	59.3×	1.68e-2	6.58e-2

Pairs within this cluster, by significance

Disease A ⇵	Disease B ⇵	Similarity score ⇵	Shared genes ⇵	P-value ⇵	FDR q-value ⇵
L1 syndrome	Masa syndrome	0.500	1	6.49e-5	2.34e-4 ✓ sig.
X-linked complicated spastic paraplegia	X-linked hydrocephalus with stenosis of the aqueduct of sylvius	0.500	1	6.49e-5	2.34e-4 ✓ sig.
X-linked complicated corpus callosum dysgenesis	X-linked hydrocephalus with stenosis of the aqueduct of sylvius	0.500	1	6.49e-5	2.34e-4 ✓ sig.
X-linked complicated corpus callosum dysgenesis	X-linked complicated spastic paraplegia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Partial corpus callosum agenesis, x-linked	X-linked hydrocephalus with stenosis of the aqueduct of sylvius	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Partial corpus callosum agenesis, x-linked	X-linked complicated spastic paraplegia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Partial corpus callosum agenesis, x-linked	X-linked complicated corpus callosum dysgenesis	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Masa syndrome	X-linked hydrocephalus with stenosis of the aqueduct of sylvius	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Masa syndrome	X-linked complicated spastic paraplegia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Masa syndrome	X-linked complicated corpus callosum dysgenesis	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Masa syndrome	Partial corpus callosum agenesis, x-linked	0.500	1	6.49e-5	2.34e-4 ✓ sig.
L1 syndrome	X-linked hydrocephalus with stenosis of the aqueduct of sylvius	0.500	1	6.49e-5	2.34e-4 ✓ sig.
L1 syndrome	X-linked complicated spastic paraplegia	0.500	1	6.49e-5	2.34e-4 ✓ sig.
L1 syndrome	X-linked complicated corpus callosum dysgenesis	0.500	1	6.49e-5	2.34e-4 ✓ sig.
L1 syndrome	Partial corpus callosum agenesis, x-linked	0.500	1	6.49e-5	2.34e-4 ✓ sig.
Partial corpus callosum agenesis, x-linked	X-linked hydrocephalus syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
Masa syndrome	X-linked hydrocephalus syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
X-linked complicated corpus callosum dysgenesis	X-linked hydrocephalus syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
X-linked complicated spastic paraplegia	X-linked hydrocephalus syndrome	0.250	1	1.95e-4	5.28e-4 ✓ sig.
X-linked hydrocephalus syndrome	X-linked hydrocephalus with stenosis of the aqueduct of sylvius	0.250	1	1.95e-4	5.28e-4 ✓ sig.

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