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Coexpression cluster:C1060

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Full id: C1060_Mesenchymal_Pericytes_Fibroblast_occipital_Renal_temporal_Nucleus



Phase1 CAGE Peaks

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 cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>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 cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


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 cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>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 cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.