Personal tools

Coexpression cluster:C454

From FANTOM5_SSTAR

Jump to: navigation, search


Full id: C454_Placental_Amniotic_Smooth_Mesenchymal_Lens_Renal_bile



Phase1 CAGE Peaks

  Short description
Hg19::chr20:36757631..36757652,- -
p@chr20:36757631..36757652
Hg19::chr20:36757658..36757727,- p@chr20:36757658..36757727
-
Hg19::chr20:36758336..36758366,- p5@TGM2
Hg19::chr20:36758421..36758453,- p9@TGM2
Hg19::chr20:36758577..36758603,- p16@TGM2
Hg19::chr20:36758636..36758676,- p10@TGM2
Hg19::chr20:36766606..36766630,- p7@TGM2
Hg19::chr20:36766683..36766700,- p14@TGM2
Hg19::chr20:36766747..36766778,- p3@TGM2
Hg19::chr20:36767838..36767854,- p@chr20:36767838..36767854
-
Hg19::chr20:36767860..36767871,- -
p@chr20:36767860..36767871
Hg19::chr20:36767877..36767891,- p@chr20:36767877..36767891
-
Hg19::chr20:36767914..36767938,- p@chr20:36767914..36767938
-
Hg19::chr20:36768004..36768016,- p@chr20:36768004..36768016
-
Hg19::chr20:36768047..36768061,- p@chr20:36768047..36768061
-
Hg19::chr20:36770579..36770603,- -
p@chr20:36770579..36770603
Hg19::chr20:36776392..36776431,- p@chr20:36776392..36776431
-
Hg19::chr20:36779386..36779404,- p@chr20:36779386..36779404
-
Hg19::chr20:36784334..36784364,- p@chr20:36784334..36784364
-
Hg19::chr20:36784443..36784469,- p@chr20:36784443..36784469
-
Hg19::chr20:36793649..36793659,- p2@TGM2
Hg19::chr20:36793663..36793735,- p1@TGM2


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
epithelial tube7.66e-32117
vasculature1.72e-3178
vascular system1.72e-3178
vessel2.54e-2968
splanchnic layer of lateral plate mesoderm2.61e-2883
epithelial tube open at both ends3.98e-2759
blood vessel3.98e-2759
blood vasculature3.98e-2759
vascular cord3.98e-2759
circulatory system3.74e-24112
cardiovascular system1.62e-22109
unilaminar epithelium5.68e-19148
artery6.16e-1942
arterial blood vessel6.16e-1942
arterial system6.16e-1942
anatomical conduit1.53e-18240
mesenchyme3.88e-17160
entire embryonic mesenchyme3.88e-17160
cell layer4.26e-17309
epithelium2.03e-16306
trunk mesenchyme3.62e-16122
anatomical cluster7.92e-16373
tube3.21e-15192
systemic artery3.84e-1533
systemic arterial system3.84e-1533
trunk4.65e-15199
multi-cellular organism4.55e-13656
mesoderm1.26e-12315
mesoderm-derived structure1.26e-12315
presumptive mesoderm1.26e-12315
organism subdivision1.56e-12264
epithelial vesicle3.46e-1278
anatomical system8.26e-12624
anatomical group1.15e-11625
multi-tissue structure2.64e-11342
muscle tissue2.01e-1064
musculature2.01e-1064
musculature of body2.01e-1064
urinary system structure3.40e-1047
extraembryonic membrane3.53e-1014
membranous layer3.53e-1014
skeletal muscle tissue6.87e-1062
striated muscle tissue6.87e-1062
myotome6.87e-1062
renal system1.01e-0948
aorta1.14e-0921
aortic system1.14e-0921
multilaminar epithelium1.96e-0983
dense mesenchyme tissue4.22e-0973
somite4.24e-0971
presomitic mesoderm4.24e-0971
presumptive segmental plate4.24e-0971
dermomyotome4.24e-0971
trunk paraxial mesoderm4.24e-0971
developing anatomical structure4.72e-09581
blood vessel endothelium4.84e-0918
endothelium4.84e-0918
cardiovascular system endothelium4.84e-0918
smooth muscle tissue4.99e-0915
paraxial mesoderm9.09e-0972
presumptive paraxial mesoderm9.09e-0972
embryo9.34e-09592
simple squamous epithelium2.13e-0822
parenchyma3.14e-0815
embryonic structure3.85e-08564
compound organ5.09e-0868
organ component layer1.06e-0766
lateral plate mesoderm1.21e-07203
germ layer1.41e-07560
germ layer / neural crest1.41e-07560
embryonic tissue1.41e-07560
presumptive structure1.41e-07560
germ layer / neural crest derived structure1.41e-07560
epiblast (generic)1.41e-07560
extraembryonic structure1.47e-0724
squamous epithelium1.57e-0725
intermediate mesoderm3.29e-0728


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)
MA0003.10.0441973
MA0004.10.478761
MA0006.10.244486
MA0007.11.41691
MA0009.10.526253
MA0014.10.587217
MA0017.11.53695
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.265828
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.11.21054
MA0040.10.456051
MA0041.10.170492
MA0042.10.457543
MA0043.10.526535
MA0046.10.516541
MA0048.10.00505311
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.114719
MA0056.10
MA0057.10.0257204
MA0058.11.66036
MA0059.13.6347
MA0060.10.496174
MA0061.10.0189504
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.0112936
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.10.0207841
MA0074.10.225345
MA0076.10.356648
MA0077.10.49237
MA0078.10.30111
MA0081.10.331815
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.61755
MA0089.10
MA0090.10.759616
MA0091.10.482932
MA0092.10.136418
MA0093.10.248476
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.0724124
MA0103.10.501795
MA0105.10.447321
MA0106.10.259598
MA0107.10.041912
MA0108.20.383574
MA0109.10
MA0111.10.398557
MA0113.10.272101
MA0114.10.0401034
MA0115.10.747865
MA0116.11.04256
MA0117.11.37693
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.11.52938
MA0132.10
MA0133.10
MA0135.11.36313
MA0136.10.234116
MA0139.11.69892
MA0140.10.199454
MA0141.11.11836
MA0142.10.359701
MA0143.10.272236
MA0144.11.34149
MA0145.10.699444
MA0146.11.44705
MA0147.10.684477
MA0148.10.174705
MA0149.10.192747
MA0062.20.396181
MA0035.20.57743
MA0039.20.0101604
MA0138.20.816468
MA0002.20.24323
MA0137.20.578057
MA0104.20.792272
MA0047.20.250458
MA0112.20.0833569
MA0065.20.0401599
MA0150.10.369323
MA0151.10
MA0152.10.589582
MA0153.10.615584
MA0154.10.908866
MA0155.10.0746593
MA0156.10.277694
MA0157.10.337287
MA0158.10
MA0159.10.686643
MA0160.11.03867
MA0161.10
MA0162.10.0975101
MA0163.10.472083
MA0164.10.28168
MA0080.20.531199
MA0018.20.260646
MA0099.20.59018
MA0079.20.00567359
MA0102.21.03595
MA0258.10.564645
MA0259.10.403807
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
GATA2#262463.475890472787450.005791119096792690.026038345417166
GATA3#262544.952093883128370.007815040484215180.0321020654132134



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.