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Coexpression cluster:C4531

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Full id: C4531_temporal_duodenum_Mesenchymal_occipital_parietal_Neurons_glioblastoma



Phase1 CAGE Peaks

  Short description
Hg19::chr5:92919068..92919082,+ p5@NR2F1
Hg19::chr5:92919100..92919135,+ p3@NR2F1
Hg19::chr5:92919375..92919438,+ p6@NR2F1


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
anatomical cluster1.31e-29373
neural plate1.95e-2682
presumptive neural plate1.95e-2682
neurectoderm6.54e-2686
central nervous system4.31e-2581
neural tube1.39e-2456
neural rod1.39e-2456
future spinal cord1.39e-2456
neural keel1.39e-2456
multi-tissue structure1.75e-23342
regional part of nervous system1.37e-2253
regional part of brain1.37e-2253
brain2.63e-2268
future brain2.63e-2268
nervous system3.03e-2289
structure with developmental contribution from neural crest6.96e-22132
cell layer1.45e-21309
organ system subdivision5.78e-21223
anatomical conduit6.71e-21240
epithelium1.64e-20306
adult organism6.52e-19114
pre-chordal neural plate1.48e-1861
tube2.98e-18192
ecto-epithelium3.56e-18104
regional part of forebrain1.38e-1641
forebrain1.38e-1641
anterior neural tube1.38e-1641
future forebrain1.38e-1641
ectoderm-derived structure9.45e-16171
ectoderm9.45e-16171
presumptive ectoderm9.45e-16171
multi-cellular organism1.87e-15656
brain grey matter2.37e-1534
gray matter2.37e-1534
telencephalon2.81e-1534
cerebral hemisphere1.67e-1432
regional part of telencephalon2.01e-1432
cerebral cortex1.45e-1225
pallium1.45e-1225
organ part2.27e-12218
regional part of cerebral cortex1.32e-1122
anatomical system1.81e-11624
anatomical group2.90e-11625
embryo3.07e-11592
germ layer4.46e-11560
germ layer / neural crest4.46e-11560
embryonic tissue4.46e-11560
presumptive structure4.46e-11560
germ layer / neural crest derived structure4.46e-11560
epiblast (generic)4.46e-11560
embryonic structure8.44e-11564
neocortex9.07e-1120
developing anatomical structure1.15e-10581
organ4.16e-10503
posterior neural tube2.37e-0915
chordal neural plate2.37e-0915
organism subdivision3.04e-08264
organ segment5.05e-0898
segmental subdivision of nervous system1.93e-0713
mesenchyme2.13e-07160
entire embryonic mesenchyme2.13e-07160
segmental subdivision of hindbrain2.18e-0712
hindbrain2.18e-0712
presumptive hindbrain2.18e-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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.12.96495
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
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
MA0140.12.07172
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
HDAC2#3066313.41562023662630.0004140761399857210.00393071241446725
HNF4A#3172215.42152690863580.005444210486686610.0246879379540212
HNF4G#3174219.16894835096450.003543986611284220.0179797152285977
JUND#372736.994663941871030.002921845042734990.0157491006615504
MXI1#460139.96157162875930.001011470541259020.00722699403834925
TAL1#6886219.91241111829350.003287176608740550.017020795133379
TRIM28#10155212.39368336350830.008368344129438470.0329406562842765
ZNF263#1012738.221841637010680.001799043925565870.0109973865111018
ZZZ3#260093239.4132124352337.25894005043406e-084.38724791624585e-06



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.