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Coexpression cluster:C3802: Difference between revisions

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|tf_chipseq_enrich=ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000676294044472096!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00762124014982982!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156762855449604!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294466045944238!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239695464266649!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613643823231355!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390135858083911!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140164939885871!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388958921560602
|tf_chipseq_enrich=ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000676294044472096!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00762124014982982!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156762855449604!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294466045944238!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239695464266649!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613643823231355!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390135858083911!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140164939885871!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388958921560602
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}}
}}

Revision as of 16:21, 26 November 2012


Full id: C3802_Sebocyte_Urothelial_Corneal_Mammary_large_salivary_Bronchial



Phase1 CAGE Peaks

Hg19::chr19:45908278..45908282,-p5@PPP1R13L
Hg19::chr19:45908286..45908291,-p3@PPP1R13L
Hg19::chr19:45908292..45908374,-p1@PPP1R13L


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 cell3.89e-37253
endo-epithelial cell1.73e-1842
endodermal cell4.15e-1358
squamous epithelial cell2.89e-1163
epithelial cell of alimentary canal1.03e-0920
respiratory epithelial cell1.61e-0913
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.59e-13160
endoderm2.59e-13160
presumptive endoderm2.59e-13160
respiratory system6.92e-1274
respiratory tract2.60e-0954
anatomical space2.73e-0995
digestive system3.65e-09145
digestive tract3.65e-09145
primitive gut3.65e-09145
foregut7.85e-0887
female organism1.41e-0741
organism subdivision1.55e-07264
thoracic segment of trunk1.79e-0752
immaterial anatomical entity1.81e-07117
orifice2.60e-0736
subdivision of digestive tract2.68e-07118
respiratory primordium6.45e-0738
endoderm of foregut6.45e-0738
Disease
Ontology termp-valuen
carcinoma8.75e-14106
cell type cancer6.95e-12143
squamous cell carcinoma2.20e-0914
cancer3.15e-08235
disease of cellular proliferation1.60e-07239


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
ESR1#2099330.76860329615453.43136389821584e-050.000676294044472096
ETS1#211339.728760922202340.001085840092584840.00762124014982982
JUND#372736.994663941871030.002921845042734990.0156762855449604
MYC#460935.22228187160940.007020843755740150.0294466045944238
SIX5#147912317.0867153554590.0002004060546325010.00239695464266649
TCF7L2#6934310.77017656313730.0008003181298398380.00613643823231355
TFAP2A#7020211.01242291536330.01054990655215560.0390135858083911
ZBTB7A#5134137.35190930787590.002516255860282270.0140164939885871
ZNF143#7702313.50087655222790.0004062804962997170.00388958921560602



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.