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Coexpression cluster:C1998

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Full id: C1998_liver_chorionic_placenta_tubular_Hepatocyte_lung_hepatocellular



Phase1 CAGE Peaks

Hg19::chr7:45928057..45928065,+p8@IGFBP1
Hg19::chr7:45928079..45928095,+p1@IGFBP1
Hg19::chr7:45928116..45928125,+p5@IGFBP1
Hg19::chr7:45928178..45928184,+p10@IGFBP1
Hg19::chr7:45928188..45928195,+p6@IGFBP1


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
anatomical cluster8.89e-12286
multi-tissue structure2.56e-11347
immaterial anatomical entity1.54e-10126
excretory tube2.32e-1017
mesonephric epithelium2.32e-1017
mesonephric tubule2.32e-1017
nephric duct2.32e-1017
kidney epithelium2.32e-1017
renal duct2.32e-1017
mesonephric duct2.32e-1017
pronephric duct2.32e-1017
nephron epithelium4.01e-1016
nephron4.01e-1016
uriniferous tubule4.01e-1016
metanephric mesenchyme4.01e-1016
nephrogenic mesenchyme4.01e-1016
abdomen element8.16e-1055
abdominal segment element8.16e-1055
tube1.63e-09194
mesonephros1.72e-0918
pronephros1.72e-0918
nephrogenic cord1.72e-0918
pronephric mesoderm1.72e-0918
rostral part of nephrogenic cord1.72e-0918
presumptive pronephric mesoderm1.72e-0918
body cavity precursor2.54e-0963
duct4.75e-0926
trunk region element4.85e-09107
renal tubule6.08e-0912
nephron tubule6.08e-0912
nephron tubule epithelium6.08e-0912
intraembryonic coelom1.15e-0821
mesenchyme1.72e-08238
entire embryonic mesenchyme1.72e-08238
anatomical cavity1.74e-0870
abdominal segment of trunk1.78e-0861
abdomen1.78e-0861
urogenital ridge4.93e-0820
cortex of kidney4.97e-0813
renal parenchyma4.97e-0813
cell layer7.57e-08312
epithelial tube9.10e-08118
foregut1.24e-0798
digestive tract diverticulum1.91e-0723
primordium2.60e-07168
larynx2.66e-079
cavitated compound organ3.07e-0732
epithelium of foregut-midgut junction3.37e-0725
anatomical boundary3.37e-0725
hepatobiliary system3.37e-0725
foregut-midgut junction3.37e-0725
septum transversum3.37e-0725
kidney3.38e-0727
kidney mesenchyme3.38e-0727
kidney rudiment3.38e-0727
kidney field3.38e-0727
hepatic diverticulum4.12e-0722
liver primordium4.12e-0722
epithelium5.68e-07309
mixed endoderm/mesoderm-derived structure9.73e-07130


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
E2F1#186954.907389214879320.0003512818099256460.00353512439264064
EP300#203356.77394172622327.00901578206049e-050.00111045904014353
FOXA1#3169511.08141974938555.98116883436141e-060.000179296008005704
FOXA2#3170524.63046375266521.10174651693954e-076.41032336950688e-06
HEY1#2346254.040111043105710.0009288852205177990.00675005869368622
HNF4A#3172523.13229036295371.50794906621644e-078.48538214044065e-06
MAFF#23764556.31535648994521.76021388477016e-091.54094700680227e-07
NR3C1#2908514.9730233311731.32777388277837e-065.25867942902882e-05
SIN3A#2594255.408884726815140.0002159522671657270.00248362942743325
SP1#666755.69838137814090.000166391843712550.00204540934151307
TBP#690853.706770687096390.001428755106721120.00920472238546957
TCF7L2#6934510.77017656313736.89693748574565e-060.000200197124534127
USF2#7392410.39375790805570.0001646179728687530.0020279000316631



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.