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Coexpression cluster:C4794

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Full id: C4794_placenta_Smooth_Fibroblast_neuroectodermal_Lens_mesenchymal_chorionic



Phase1 CAGE Peaks

  Short description
Hg19::chr9:118915849..118915859,+ p16@PAPPA
Hg19::chr9:118915863..118915909,+ p4@PAPPA
Hg19::chr9:118915915..118915930,+ p12@PAPPA


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


Uber Anatomy
Ontology termp-valuen
somite6.18e-2471
presomitic mesoderm6.18e-2471
presumptive segmental plate6.18e-2471
dermomyotome6.18e-2471
trunk paraxial mesoderm6.18e-2471
paraxial mesoderm2.60e-2372
presumptive paraxial mesoderm2.60e-2372
dense mesenchyme tissue1.05e-2273
skeletal muscle tissue1.52e-2162
striated muscle tissue1.52e-2162
myotome1.52e-2162
multilaminar epithelium1.24e-2083
muscle tissue2.69e-2064
musculature2.69e-2064
musculature of body2.69e-2064
epithelial vesicle6.12e-2078
trunk mesenchyme3.33e-14122
mesenchyme2.16e-12160
entire embryonic mesenchyme2.16e-12160
splanchnic layer of lateral plate mesoderm1.13e-1083
artery1.48e-1042
arterial blood vessel1.48e-1042
arterial system1.48e-1042
integument3.29e-1046
integumental system3.29e-1046
unilaminar epithelium3.78e-10148
organism subdivision1.83e-09264
systemic artery2.39e-0933
systemic arterial system2.39e-0933
trunk2.48e-09199
cardiovascular system3.56e-09109
vasculature4.50e-0978
vascular system4.50e-0978
skin of body9.66e-0941
circulatory system1.64e-08112
surface structure2.35e-0899
heart7.09e-0824
primitive heart tube7.09e-0824
primary heart field7.09e-0824
anterior lateral plate mesoderm7.09e-0824
heart tube7.09e-0824
heart primordium7.09e-0824
cardiac mesoderm7.09e-0824
cardiogenic plate7.09e-0824
heart rudiment7.09e-0824
epithelial tube open at both ends1.48e-0759
blood vessel1.48e-0759
blood vasculature1.48e-0759
vascular cord1.48e-0759
epithelial tube2.68e-07117
smooth muscle tissue4.69e-0715
blood vessel smooth muscle5.55e-0710
arterial system smooth muscle5.55e-0710
artery smooth muscle tissue5.55e-0710
aorta smooth muscle tissue5.55e-0710


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
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.12.74347
MA0031.12.60497
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
MA0057.12.4146
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
MA0070.12.89432
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.14.28695
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
MA0116.11.3784
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
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.13.29283
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.23.66129
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
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
FOXA1#3169311.08141974938550.000734755275698670.0058475277176479
NR3C1#2908314.9730233311730.0002978331194675480.00310526037377172
REST#597839.650028716128020.001112636247114590.00771956533663726



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.