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Coexpression cluster:C3004

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Full id: C3004_smooth_putamen_bladder_vagina_neuroectodermal_caudate_salivary



Phase1 CAGE Peaks

  Short description
Hg19::chr10:18429301..18429338,+ p1@CACNB2
Hg19::chr10:18429342..18429359,+ p3@CACNB2
Hg19::chr10:18429658..18429670,+ p14@CACNB2


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


uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism2.50e-62114
neural tube2.20e-4256
neural rod2.20e-4256
future spinal cord2.20e-4256
neural keel2.20e-4256
regional part of nervous system1.67e-4053
regional part of brain1.67e-4053
central nervous system1.63e-3781
neurectoderm3.69e-3786
nervous system9.88e-3789
regional part of forebrain2.48e-3541
forebrain2.48e-3541
anterior neural tube2.48e-3541
future forebrain2.48e-3541
neural plate6.42e-3582
presumptive neural plate6.42e-3582
brain3.11e-3368
future brain3.11e-3368
telencephalon3.70e-3034
brain grey matter4.08e-3034
gray matter4.08e-3034
cerebral hemisphere3.21e-2932
regional part of telencephalon1.48e-2832
organ system subdivision1.39e-27223
ectoderm-derived structure4.54e-27171
ectoderm4.54e-27171
presumptive ectoderm4.54e-27171
pre-chordal neural plate8.78e-2761
structure with developmental contribution from neural crest4.56e-26132
ecto-epithelium2.83e-24104
cerebral cortex1.65e-2225
pallium1.65e-2225
regional part of cerebral cortex8.15e-2122
neocortex5.16e-1920
anatomical cluster2.09e-18373
multi-tissue structure1.76e-17342
multi-cellular organism1.18e-13656
embryo1.44e-11592
organ part4.45e-11218
organ1.95e-10503
anatomical conduit3.73e-10240
embryonic structure4.19e-10564
germ layer4.99e-10560
germ layer / neural crest4.99e-10560
embryonic tissue4.99e-10560
presumptive structure4.99e-10560
germ layer / neural crest derived structure4.99e-10560
epiblast (generic)4.99e-10560
developing anatomical structure7.72e-10581
basal ganglion3.68e-099
nuclear complex of neuraxis3.68e-099
aggregate regional part of brain3.68e-099
collection of basal ganglia3.68e-099
cerebral subcortex3.68e-099
neural nucleus5.31e-099
nucleus of brain5.31e-099
tube5.42e-09192
large intestine1.02e-0811
anatomical system1.59e-08624
posterior neural tube1.78e-0815
chordal neural plate1.78e-0815
epithelium1.83e-08306
anatomical group1.97e-08625
cell layer3.95e-08309
intestine1.02e-0717
temporal lobe1.16e-076
telencephalic nucleus1.68e-077
colon2.79e-079
segmental subdivision of hindbrain9.27e-0712
hindbrain9.27e-0712
presumptive hindbrain9.27e-0712


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0048.12.45333
MA0050.10.81185
MA0051.12.15619
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0105.11.5295
MA0106.10.986396
MA0107.11.36919
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.707589
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
MA0102.21.88331
MA0258.11.29138
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
CTCF#1066435.360256373075030.0064925092527670.0278160222279088



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.