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Coexpression cluster:C1060

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Full id: C1060_Mesenchymal_Pericytes_Fibroblast_occipital_Renal_temporal_Nucleus



Phase1 CAGE Peaks

  Short description
Hg19::chr19:1885483..1885507,- p1@FAM108A1
Hg19::chr19:2015699..2015748,- p1@BTBD2
Hg19::chr19:40854559..40854625,+ p2@PLD3
Hg19::chr19:50270219..50270319,+ p1@AP2A1
Hg19::chr19:7580944..7581031,+ p1@ZNF358
Hg19::chr1:201857992..201858055,+ p1@SHISA4
Hg19::chr4:102268904..102268948,+ p1@FLJ20021
Hg19::chrX:48455870..48455905,+ p1@WDR13


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


GO IDGO nameFDR corrected p-value
GO:0030128clathrin coat of endocytic vesicle0.022949948668774
GO:0030669clathrin-coated endocytic vesicle membrane0.022949948668774
GO:0030122AP-2 adaptor complex0.022949948668774
GO:0030666endocytic vesicle membrane0.022949948668774
GO:0004630phospholipase D activity0.022949948668774
GO:0006895Golgi to endosome transport0.022949948668774
GO:0045334clathrin-coated endocytic vesicle0.022949948668774
GO:0030132clathrin coat of coated pit0.0372772031699452
GO:0030130clathrin coat of trans-Golgi network vesicle0.0376591196280217
GO:0012510trans-Golgi network transport vesicle membrane0.0376591196280217
GO:0006892post-Golgi vesicle-mediated transport0.0376591196280217
GO:0030125clathrin vesicle coat0.0376591196280217
GO:0030139endocytic vesicle0.0376591196280217
GO:0030665clathrin coated vesicle membrane0.0376591196280217
GO:0030140trans-Golgi network transport vesicle0.0431205011761095
GO:0030658transport vesicle membrane0.0431205011761095
GO:0030660Golgi-associated vesicle membrane0.0431205011761095



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
epithelium3.07e-28306
cell layer3.92e-28309
anatomical cluster1.41e-23373
multi-cellular organism4.48e-23656
multi-tissue structure1.83e-22342
anatomical conduit2.16e-22240
tube3.30e-21192
anatomical system8.18e-21624
anatomical group1.62e-20625
structure with developmental contribution from neural crest1.30e-18132
ectoderm-derived structure3.41e-17171
ectoderm3.41e-17171
presumptive ectoderm3.41e-17171
neural plate5.12e-1782
presumptive neural plate5.12e-1782
developing anatomical structure1.22e-16581
neurectoderm3.72e-1686
epithelial vesicle4.30e-1678
germ layer9.57e-16560
germ layer / neural crest9.57e-16560
embryonic tissue9.57e-16560
presumptive structure9.57e-16560
germ layer / neural crest derived structure9.57e-16560
epiblast (generic)9.57e-16560
embryo2.32e-15592
embryonic structure2.33e-15564
ecto-epithelium2.85e-15104
brain4.23e-1568
future brain4.23e-1568
dense mesenchyme tissue1.80e-1473
neural tube2.11e-1456
neural rod2.11e-1456
future spinal cord2.11e-1456
neural keel2.11e-1456
regional part of nervous system3.27e-1453
regional part of brain3.27e-1453
paraxial mesoderm3.36e-1472
presumptive paraxial mesoderm3.36e-1472
mesenchyme5.36e-14160
entire embryonic mesenchyme5.36e-14160
pre-chordal neural plate6.60e-1461
somite9.84e-1471
presomitic mesoderm9.84e-1471
presumptive segmental plate9.84e-1471
dermomyotome9.84e-1471
trunk paraxial mesoderm9.84e-1471
multilaminar epithelium1.24e-1383
vasculature2.21e-1378
vascular system2.21e-1378
central nervous system2.81e-1381
skeletal muscle tissue7.65e-1362
striated muscle tissue7.65e-1362
myotome7.65e-1362
organ part9.03e-13218
muscle tissue1.14e-1264
musculature1.14e-1264
musculature of body1.14e-1264
adult organism1.18e-12114
circulatory system1.23e-12112
splanchnic layer of lateral plate mesoderm1.34e-1283
nervous system1.77e-1289
cerebral hemisphere3.49e-1232
telencephalon3.84e-1234
cardiovascular system5.79e-12109
regional part of forebrain5.82e-1241
forebrain5.82e-1241
anterior neural tube5.82e-1241
future forebrain5.82e-1241
brain grey matter6.63e-1234
gray matter6.63e-1234
regional part of telencephalon1.73e-1132
trunk mesenchyme1.74e-11122
epithelial tube1.92e-11117
organism subdivision4.70e-11264
vessel6.93e-1168
unilaminar epithelium8.98e-11148
regional part of cerebral cortex1.99e-1022
epithelial tube open at both ends2.30e-1059
blood vessel2.30e-1059
blood vasculature2.30e-1059
vascular cord2.30e-1059
cerebral cortex5.92e-1025
pallium5.92e-1025
neocortex2.31e-0920
trunk3.63e-09199
artery1.21e-0842
arterial blood vessel1.21e-0842


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)
MA0003.13.24424
MA0004.11.15451
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.12.6969
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.11.52958
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.110.4631
MA0058.11.69448
MA0059.10.361075
MA0060.11.67203
MA0061.10.497495
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.11.57731
MA0074.10.552456
MA0076.10.985027
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.13.41003
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.11.48478
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.11.28413
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.11.25866
MA0146.11.63914
MA0147.10.243042
MA0148.10.480298
MA0149.121.9828
MA0062.21.50503
MA0035.20.515566
MA0039.24.9691
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.21.69642
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.11.16939
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.13.77262
MA0163.11.42814
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.226.3195
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
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
EGR1#195884.988179094810142.607361705472e-069.15328568597615e-05
IRF1#365943.818581876781950.01326136316826170.0469063402286073
POLR2A#543082.147453176558070.002210725788971910.0127216921414093
SP2#666839.807573935191740.002707184665085610.0148870924198018
TAF1#687272.925165500027130.001265325357915740.00849234079142485
YY1#752853.069481718658660.0112591365358360.0413304615186173
ZBTB7A#5134154.594943317422430.001819435193540470.010900642047853



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.