Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 242

7 diseases · 11 shared-gene connections
7 Diseases
154 Unique genes
0.057 Avg. similarity score
Hereditary spastic paraplegia Most-connected disease (6 links)
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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.

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

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Hereditary spastic paraplegia 6 6 101
Spastic paraplegia 6 6 120
Allan-herndon-dudley syndrome 2 2 1
complex hereditary spastic paraplegia 2 2 7
hereditary spastic paraplegia 11 2 2 1
hereditary spastic paraplegia 18 2 2 1
hereditary spastic paraplegia 62 2 2 1

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

Gene ⇵ Member diseases ⇵ Linked diseases
B4GALNT1 3 / 7 complex hereditary spastic paraplegia, Hereditary spastic paraplegia, Spastic paraplegia
DSTYK 3 / 7 complex hereditary spastic paraplegia, Hereditary spastic paraplegia, Spastic paraplegia
ENTPD1 3 / 7 complex hereditary spastic paraplegia, Hereditary spastic paraplegia, Spastic paraplegia
ERLIN1 3 / 7 Hereditary spastic paraplegia, hereditary spastic paraplegia 62, Spastic paraplegia
ERLIN2 3 / 7 Hereditary spastic paraplegia, hereditary spastic paraplegia 18, Spastic paraplegia
GBA2 3 / 7 complex hereditary spastic paraplegia, Hereditary spastic paraplegia, Spastic paraplegia
MAG 3 / 7 complex hereditary spastic paraplegia, Hereditary spastic paraplegia, Spastic paraplegia
NT5C2 3 / 7 complex hereditary spastic paraplegia, Hereditary spastic paraplegia, Spastic paraplegia
SLC16A2 3 / 7 Allan-herndon-dudley syndrome, Hereditary spastic paraplegia, Spastic paraplegia
SPG11 3 / 7 Hereditary spastic paraplegia, hereditary spastic paraplegia 11, Spastic paraplegia
VPS37A 3 / 7 complex hereditary spastic paraplegia, Hereditary spastic paraplegia, Spastic paraplegia
ABCD1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ABHD16A 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ALDH18A1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ALS2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
AMPD2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
AP4B1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
AP4E1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
AP4M1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
AP4S1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
AP5Z1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ARHGAP9 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ARL6IP1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ARSI 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ATL1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
BICD2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
BSCL2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
C19ORF12 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
CNNM2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
CPT1C 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
CYP2U1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
CYP7B1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
DCLRE1B 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
DDHD1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
DDHD2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
FA2H 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
FARS2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
GJC2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
HSPD1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
KIF1A 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
KIF1C 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
KIF5A 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
L1CAM 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
MARS1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
MTRFR 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
NIPA1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
PGAP1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
PLP1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
PNPLA6 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
REEP1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
REEP2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
RTN2 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SACS 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SETX 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SLC33A1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SPART 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SPAST 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SPG21 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SPG7 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
SPTAN1 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
TFG 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
UCHL1 2 / 7 hereditary spastic paraplegia, Spastic paraplegia
USP8 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
WASHC5 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
WDR48 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ZFR 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
ZFYVE26 2 / 7 Hereditary spastic paraplegia, Spastic paraplegia
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 ⇵
Lysosome Vesicle Biogenesis
AP4B1, AP4E1, AP4M1, AP4S1, DNM2
 Reactome 5 / 35 11.1× 7.73e-5 1.82e-3 ✓ sig.
Mitophagy - animal
USP8, PRKN, VCP, TBK1, AMFR, SQSTM1
 KEGG 6 / 105 4.5× 2.29e-3 2.52e-2 ✓ sig.
Phosphonate and phosphinate metabolism
PCYT2, SELENOI
 KEGG 2 / 6 26.0× 2.37e-3 2.58e-2 ✓ sig.
Synthesis of PE
PCYT2, SELENOI
 Reactome 2 / 12 13.0× 9.91e-3 6.82e-2
Josephin domain DUBs
PRKN, VCP
 Reactome 2 / 12 13.0× 9.91e-3 6.82e-2
Downregulation of ERBB2:ERBB3 signaling
USP8, NRG1
 Reactome 2 / 13 12.0× 1.16e-2 7.51e-2
Interaction between L1 and Ankyrins
L1CAM, SPTAN1
 Reactome 2 / 13 12.0× 1.16e-2 7.51e-2
Defective CYP2U1 causes Spastic paraplegia 56, autosomal recessive (SPG56)
CYP2U1
 Reactome 1 / 1 78.0× 1.28e-2 7.92e-2
Defective ABCD1 causes adrenoleukodystrophy (ALD)
ABCD1
 Reactome 1 / 1 78.0× 1.28e-2 7.92e-2
Defective MUTYH substrate binding
MUTYH
 Reactome 1 / 1 78.0× 1.28e-2 7.92e-2
Defective SLC33A1 causes spastic paraplegia 42 (SPG42)
SLC33A1
 Reactome 1 / 1 78.0× 1.28e-2 7.92e-2
Defective CYP7B1 causes Spastic paraplegia 5A, autosomal recessive (SPG5A) and Congenital bile acid synthesis defect 3 (CBAS3)
CYP7B1
 Reactome 1 / 1 78.0× 1.28e-2 7.92e-2
Membrane binding and targetting of GAG proteins
UBAP1, VPS37A
 Reactome 2 / 14 11.1× 1.34e-2 8.14e-2
Fanconi Anemia Pathway
WDR48, DCLRE1B, FANCI
 Reactome 3 / 40 5.8× 1.44e-2 8.52e-2
Endocytosis
KIF5A, WASHC5, SPART, SPG21, VPS37A, USP8, ZFYVE27, DNM2
 KEGG 8 / 250 2.5× 1.52e-2 8.78e-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 ⇵
vesicle-mediated transport
KIF5A, AP5Z1, TFG, KIF1A, KIF1C, AP4B1, AP4E1, AP4M1, AP4S1, VAMP1, ZFYVE27, TRAPPC2
 GO:0016192 13 / 326 4.8× 3.15e-6 2.07e-4 ✓ sig.
retrograde neuronal dense core vesicle transport
KIF5A, KIF1A, KIF1C
 GO:1990049 3 / 5 72.8× 5.42e-6 3.20e-4 ✓ sig.
autophagosome organization
SPG11, ATP13A2, ZFYVE26
 GO:1905037 3 / 5 72.8× 5.42e-6 3.20e-4 ✓ sig.
lipid metabolic process
BSCL2, CPT1C, FAR1, SPART, B4GALNT1, DDHD1, FA2H, PNPLA6, GBA2, DDHD2, CYP2U1, CYP7B1
 GO:0006629 21 / 840 3.0× 5.63e-6 3.30e-4 ✓ sig.
endoplasmic reticulum tubular network formation
RTN2, ARL6IP1, ZFYVE27
 GO:0071787 3 / 6 60.7× 1.08e-5 5.52e-4 ✓ sig.
positive regulation of mitochondrial fission
DDHD1, DDHD2, PRKN, DNM1L
 GO:0090141 4 / 22 22.1× 2.89e-5 1.19e-3 ✓ sig.
regulation of mitochondrion organization
ATP13A2, PRKN, DNM1L, SQSTM1
 GO:0010821 4 / 22 22.1× 2.89e-5 1.19e-3 ✓ sig.
endoplasmic reticulum tubular network membrane organization
RTN2, ATL1, ARL6IP1
 GO:1990809 3 / 8 45.5× 2.98e-5 1.22e-3 ✓ sig.
endosome organization
WASHC5, USP8, ALS2, SQSTM1, USP50
 GO:0007032 5 / 45 13.5× 3.34e-5 1.33e-3 ✓ sig.
macroautophagy
VPS37A, RAB3GAP2, PRKN, VCP, TBK1, SQSTM1
 GO:0016236 6 / 77 9.5× 4.16e-5 1.57e-3 ✓ sig.
SREBP signaling pathway
ERLIN1, ERLIN2, SREBF2
 GO:0032933 3 / 9 40.4× 4.45e-5 1.65e-3 ✓ sig.
protein targeting
SORL1, AP4B1, AP4E1, AP4M1, AP4S1
 GO:0006605 5 / 49 12.4× 5.07e-5 1.82e-3 ✓ sig.
mitochondrial DNA replication
POLG, POLG2, TWNK
 GO:0006264 3 / 11 33.1× 8.63e-5 2.71e-3 ✓ sig.
autophagy
AP5Z1, ATP13A2, PRKN, VCP, SQSTM1, DNAJC16, DNM2, RETREG1, TECPR2
 GO:0006914 9 / 221 4.9× 9.24e-5 2.85e-3 ✓ sig.
protein transport
RTN2, UBAP1, KPNA3, WASHC5, AP5Z1, VPS37A, PGAP1, AP4B1, AP4E1, AP4M1, AP4S1, BICD2
 GO:0015031 16 / 667 2.9× 1.28e-4 3.64e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Hereditary spastic paraplegia Spastic paraplegia 0.432 67 3.88e-125 6.19e-123 ✓ sig.
complex hereditary spastic paraplegia Hereditary spastic paraplegia 0.069 7 4.23e-16 6.86e-15 ✓ sig.
complex hereditary spastic paraplegia Spastic paraplegia 0.058 7 1.46e-15 2.29e-14 ✓ sig.
Allan-herndon-dudley syndrome Hereditary spastic paraplegia 0.010 1 6.56e-3 7.82e-3 ✓ sig.
Hereditary spastic paraplegia hereditary spastic paraplegia 11 0.010 1 6.56e-3 7.82e-3 ✓ sig.
Hereditary spastic paraplegia hereditary spastic paraplegia 18 0.010 1 6.56e-3 7.82e-3 ✓ sig.
Hereditary spastic paraplegia hereditary spastic paraplegia 62 0.010 1 6.56e-3 7.82e-3 ✓ sig.
Allan-herndon-dudley syndrome Spastic paraplegia 0.008 1 7.79e-3 9.07e-3 ✓ sig.
hereditary spastic paraplegia 11 Spastic paraplegia 0.008 1 7.79e-3 9.07e-3 ✓ sig.
hereditary spastic paraplegia 18 Spastic paraplegia 0.008 1 7.79e-3 9.07e-3 ✓ sig.
hereditary spastic paraplegia 62 Spastic paraplegia 0.008 1 7.79e-3 9.07e-3 ✓ sig.