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Coexpression cluster:C4274

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Full id: C4274_neuroectodermal_neuroepithelioma_neuroblastoma_Astrocyte_peripheral_Neural_parietal



Phase1 CAGE Peaks

  Short description
Hg19::chr3:122746538..122746562,- p2@SEMA5B
Hg19::chr3:122746566..122746623,- p1@SEMA5B
Hg19::chr3:122746628..122746635,- p8@SEMA5B


Enriched pathways on this co-expression clusterSummary:
Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary:To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
neuronal stem cell1.90e-118
neural cell3.61e-0925
neuron7.52e-096
neuroblast7.52e-096
electrically signaling cell7.52e-096
neurectodermal cell1.23e-0759
embryonic stem cell1.65e-075
Uber Anatomy
Ontology termp-valuen
nervous system1.10e-4389
central nervous system2.30e-4181
telencephalon2.60e-3634
brain grey matter1.39e-3534
gray matter1.39e-3534
cerebral hemisphere1.26e-3432
neural tube2.96e-3456
neural rod2.96e-3456
future spinal cord2.96e-3456
neural keel2.96e-3456
regional part of telencephalon4.16e-3432
regional part of nervous system3.91e-3353
regional part of brain3.91e-3353
regional part of forebrain2.72e-3241
forebrain2.72e-3241
anterior neural tube2.72e-3241
future forebrain2.72e-3241
adult organism8.14e-30114
brain1.86e-2968
future brain1.86e-2968
ectoderm-derived structure5.09e-28171
ectoderm5.09e-28171
presumptive ectoderm5.09e-28171
cerebral cortex2.04e-2725
pallium2.04e-2725
neurectoderm8.50e-2786
neocortex1.79e-2420
regional part of cerebral cortex7.06e-2422
neural plate2.99e-2382
presumptive neural plate2.99e-2382
organ system subdivision6.36e-23223
pre-chordal neural plate3.48e-2061
ecto-epithelium1.36e-19104
structure with developmental contribution from neural crest2.49e-16132
anatomical cluster7.19e-13373
embryo1.20e-12592
basal ganglion3.77e-109
nuclear complex of neuraxis3.77e-109
aggregate regional part of brain3.77e-109
collection of basal ganglia3.77e-109
cerebral subcortex3.77e-109
multi-cellular organism8.00e-10656
developing anatomical structure1.39e-09581
neural nucleus1.54e-099
nucleus of brain1.54e-099
temporal lobe4.12e-096
embryonic structure4.54e-09564
germ layer7.31e-09560
germ layer / neural crest7.31e-09560
embryonic tissue7.31e-09560
presumptive structure7.31e-09560
germ layer / neural crest derived structure7.31e-09560
epiblast (generic)7.31e-09560
tube2.94e-08192
telencephalic nucleus4.08e-087
gyrus1.05e-076
occipital lobe2.79e-075
sympathetic nervous system4.33e-075
autonomic nervous system4.33e-075
parietal lobe4.56e-075
Disease
Ontology termp-valuen
germ cell and embryonal cancer4.13e-1122
germ cell cancer4.13e-1122
neuroectodermal tumor4.30e-1010


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary:The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.29.48295
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488362.71700033932814.049570681927e-060.000130053232610631
CTCF#1066435.360256373075030.0064925092527670.0280368482054883
CTCFL#140690319.74647435897440.0001298372005551160.00172103914059853
E2F6#187635.017155731697390.00791769806886330.0323342640421527
RAD21#5885310.35503389545630.0009004912073565420.00666192542361053
ZBTB7A#5134137.35190930787590.002516255860282270.0140592363466734



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.