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Coexpression cluster:C3573: Difference between revisions

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|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436626596180484!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000850504812247283!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276208960791636!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247912286465492!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00614733900092997
|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436626596180484!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000850504812247283!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276208960791636!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247912286465492!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00614733900092997
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}}
}}

Revision as of 16:12, 26 November 2012


Full id: C3573_liver_Bronchial_Mesenchymal_Fibroblast_Tracheal_Keratinocyte_Mammary



Phase1 CAGE Peaks

Hg19::chr16:56643233..56643256,+p@chr16:56643233..56643256
+
Hg19::chr16:56643260..56643307,+p@chr16:56643260..56643307
+
Hg19::chr16:56643282..56643333,-p@chr16:56643282..56643333
-


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

No GOStat results

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
cell layer2.26e-26309
epithelium3.06e-25306
multilaminar epithelium1.21e-1983
unilaminar epithelium1.48e-19148
epithelial vesicle1.71e-1978
epithelial tube4.12e-19117
organism subdivision5.64e-19264
multi-tissue structure1.38e-17342
vasculature2.13e-1778
vascular system2.13e-1778
trunk6.66e-17199
anatomical conduit6.70e-17240
somite1.10e-1671
presomitic mesoderm1.10e-1671
presumptive segmental plate1.10e-1671
dermomyotome1.10e-1671
trunk paraxial mesoderm1.10e-1671
dense mesenchyme tissue2.14e-1673
paraxial mesoderm3.41e-1672
presumptive paraxial mesoderm3.41e-1672
trunk mesenchyme7.10e-16122
vessel4.84e-1568
mesenchyme6.60e-15160
entire embryonic mesenchyme6.60e-15160
anatomical cluster5.93e-14373
tube6.15e-14192
artery7.91e-1442
arterial blood vessel7.91e-1442
arterial system7.91e-1442
skeletal muscle tissue1.12e-1362
striated muscle tissue1.12e-1362
myotome1.12e-1362
epithelial tube open at both ends2.90e-1359
blood vessel2.90e-1359
blood vasculature2.90e-1359
vascular cord2.90e-1359
muscle tissue7.37e-1364
musculature7.37e-1364
musculature of body7.37e-1364
anatomical system1.75e-11624
anatomical group2.91e-11625
circulatory system4.34e-11112
systemic artery5.20e-1133
systemic arterial system5.20e-1133
cardiovascular system6.24e-11109
splanchnic layer of lateral plate mesoderm9.20e-1183
multi-cellular organism6.37e-10656
developing anatomical structure3.08e-09581
embryo1.71e-08592
embryonic structure2.20e-08564
germ layer5.04e-08560
germ layer / neural crest5.04e-08560
embryonic tissue5.04e-08560
presumptive structure5.04e-08560
germ layer / neural crest derived structure5.04e-08560
epiblast (generic)5.04e-08560
nephron epithelium1.74e-0715
renal tubule1.74e-0715
nephron tubule1.74e-0715
nephron1.74e-0715
uriniferous tubule1.74e-0715
nephrogenic mesenchyme1.74e-0715
excretory tube3.89e-0716
kidney epithelium3.89e-0716
surface structure5.12e-0799


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
GATA2#2624312.7449317335540.0004829527704283790.00436626596180484
GATA3#2625327.2365163572064.94721007899563e-050.000850504812247283
SIN3A#2594235.408884726815140.006318961977991520.0276208960791636
TFAP2A#7020316.5186343730450.0002218033880766340.00247912286465492
TFAP2C#7022310.80922860986020.0007916746575753130.00614733900092997



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.

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