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Difference between revisions of "Coexpression cluster:C1824"

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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C1824_Alveolar_nonsmall_brain_duodenum_Neurons_Renal_temporal
 
|full_id=C1824_Alveolar_nonsmall_brain_duodenum_Neurons_Renal_temporal
 
|id=C1824
 
|id=C1824

Revision as of 05:27, 12 September 2012


Full id: C1824_Alveolar_nonsmall_brain_duodenum_Neurons_Renal_temporal



Phase1 CAGE Peaks

Hg19::chr19:42806477..42806500,-p6@PAFAH1B3
Hg19::chr19:42806505..42806542,-p4@PAFAH1B3
Hg19::chr19:42806559..42806580,-p5@PAFAH1B3
Hg19::chr19:42806590..42806657,-p2@PAFAH1B3
Hg19::chr19:42806728..42806795,-p1@PAFAH1B3


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell3.61e-35254
embryonic cell9.72e-26248
ectodermal cell9.71e-1271
neurectodermal cell4.89e-1059
neural cell5.30e-1025
animal cell1.53e-09679
eukaryotic cell1.53e-09679
endodermal cell3.16e-0959
endo-epithelial cell2.18e-0843
migratory neural crest cell3.19e-0841
epithelial cell of nephron8.02e-0816
kidney cell1.78e-0718
kidney epithelial cell1.78e-0718
Uber Anatomy
Ontology termp-valuen
multi-tissue structure7.99e-12347
cell layer1.31e-10312
epithelium4.92e-10309
mesenchyme3.59e-09238
entire embryonic mesenchyme3.59e-09238
organ part4.07e-09219
organ segment8.00e-0997
segment of respiratory tract2.51e-0846
organism subdivision5.45e-08365
nephron epithelium8.02e-0816
nephron8.02e-0816
uriniferous tubule8.02e-0816
metanephric mesenchyme8.02e-0816
nephrogenic mesenchyme8.02e-0816
respiratory primordium9.48e-0838
endoderm of foregut9.48e-0838
trunk region element4.03e-07107
kidney4.11e-0727
kidney mesenchyme4.11e-0727
kidney rudiment4.11e-0727
kidney field4.11e-0727
respiratory tract5.86e-0753
excretory tube6.79e-0717
mesonephric epithelium6.79e-0717
mesonephric tubule6.79e-0717
nephric duct6.79e-0717
kidney epithelium6.79e-0717
renal duct6.79e-0717
mesonephric duct6.79e-0717
pronephric duct6.79e-0717
Disease
Ontology termp-valuen
cancer1.22e-21235
disease of cellular proliferation4.57e-21239
cell type cancer1.16e-15143
carcinoma7.39e-13106
organ system cancer7.08e-12137


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
CCNT2#90556.336201576962639.78880505817628e-050.00139092926730731
CHD2#1106510.34402283411698.43981772346334e-060.000230202696061841
E2F1#186954.907389214879320.0003512818099256460.00352934304442756
E2F4#1874512.66806031528443.06319883889696e-060.000103466178375019
E2F6#187655.017155731697390.0003144978599297790.00322840986762396
EGR1#195854.988179094810140.0003237398000590710.00330864673435457
ELF1#199754.258097958807540.0007142416939776840.00573364245021794
EP300#203356.77394172622327.00901578206049e-050.00110860911595126
HEY1#2346254.040111043105710.0009288852205177990.00674442738776824
HMGN3#932458.178547723350592.73180911341838e-050.000582141220151606
IRF1#365957.63716375356393.84754333311872e-050.000724546660958504
JUND#372756.994663941871035.97069468343598e-050.000984330516248413
NR3C1#2908514.9730233311731.32777388277837e-065.24674145075634e-05
PAX5#507956.669565531177837.57493746384605e-050.0011701211267366
SIN3A#2594255.408884726815140.0002159522671657270.00248144337446599
SIX5#147912517.0867153554596.86007756253503e-073.1015568855134e-05
SP1#666755.69838137814090.000166391843712550.00204372548106492
STAT3#6774510.51946499715427.759040745861e-060.000220442452790255
TAF1#687253.343046285745290.002394600090870310.0135417824826946
TBP#690853.706770687096390.001428755106721120.00919111515804418
TCF7L2#6934510.77017656313736.89693748574565e-060.000199863832983848
USF1#739156.361499277207969.59569864925045e-050.0013687041398922
USF2#7392512.99219738506962.69963551658264e-069.42652068593696e-05
ZNF263#1012758.221841637010682.6606316672286e-050.00057128641178801



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.