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Coexpression cluster:C1483: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!4.27e-08!143;DOID:305!6.29e-08!106;DOID:1749!1.32e-07!14
|ontology_enrichment_disease=DOID:0050687!4.27e-08!143;DOID:305!6.29e-08!106;DOID:1749!1.32e-07!14
|ontology_enrichment_uberon=UBERON:0000481!5.33e-18!347;UBERON:0004119!5.34e-15!169;UBERON:0000925!5.34e-15!169;UBERON:0006595!5.34e-15!169;UBERON:0000475!5.72e-15!365;UBERON:0000922!3.39e-12!612;UBERON:0000064!3.88e-12!219;UBERON:0003104!4.72e-12!238;UBERON:0009142!4.72e-12!238;UBERON:0000483!1.34e-11!309;UBERON:0002050!1.76e-11!605;UBERON:0005423!1.76e-11!605;UBERON:0000119!2.36e-11!312;UBERON:0000923!2.66e-11!604;UBERON:0005291!2.66e-11!604;UBERON:0006598!2.66e-11!604;UBERON:0002532!2.66e-11!604;UBERON:0000467!4.07e-11!625;UBERON:0001007!4.62e-11!155;UBERON:0001555!4.62e-11!155;UBERON:0007026!4.62e-11!155;UBERON:0000480!4.72e-11!626;UBERON:0000468!1.11e-10!659;UBERON:0001004!9.43e-10!72;UBERON:0000077!5.31e-09!130;UBERON:0004111!1.11e-08!241;UBERON:0000477!1.21e-08!286;UBERON:0004921!3.33e-08!129;UBERON:0004185!3.33e-08!129;UBERON:0000065!4.95e-08!53;UBERON:0002100!1.10e-07!216;UBERON:0000486!4.02e-07!82;UBERON:0000072!4.77e-07!46
|ontology_enrichment_uberon=UBERON:0000481!5.33e-18!347;UBERON:0004119!5.34e-15!169;UBERON:0000925!5.34e-15!169;UBERON:0006595!5.34e-15!169;UBERON:0000475!5.72e-15!365;UBERON:0000922!3.39e-12!612;UBERON:0000064!3.88e-12!219;UBERON:0003104!4.72e-12!238;UBERON:0009142!4.72e-12!238;UBERON:0000483!1.34e-11!309;UBERON:0002050!1.76e-11!605;UBERON:0005423!1.76e-11!605;UBERON:0000119!2.36e-11!312;UBERON:0000923!2.66e-11!604;UBERON:0005291!2.66e-11!604;UBERON:0006598!2.66e-11!604;UBERON:0002532!2.66e-11!604;UBERON:0000467!4.07e-11!625;UBERON:0001007!4.62e-11!155;UBERON:0001555!4.62e-11!155;UBERON:0007026!4.62e-11!155;UBERON:0000480!4.72e-11!626;UBERON:0000468!1.11e-10!659;UBERON:0001004!9.43e-10!72;UBERON:0000077!5.31e-09!130;UBERON:0004111!1.11e-08!241;UBERON:0000477!1.21e-08!286;UBERON:0004921!3.33e-08!129;UBERON:0004185!3.33e-08!129;UBERON:0000065!4.95e-08!53;UBERON:0002100!1.10e-07!216;UBERON:0000486!4.02e-07!82;UBERON:0000072!4.77e-07!46
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755613507103263!HDAC2#3066;5:11.1796835305219:1.29408913564529e-05:0.000317038177897392!HEY1#23462;6:4.04011104310571:0.000229896855580751:0.0025329884692476!HNF4A#3172;6:23.1322903629537:6.51490260560877e-09:5.13129647984295e-07!MXI1#4601;6:9.9615716287593:1.02262624227062e-06:4.3013315391261e-05!MYC#4609;6:5.2222818716094:4.92821127172503e-05:0.000854411449215954!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380500060447656!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573431699358421!TAF7#6879;6:11.4330694049239:4.47357982339933e-07:2.12660993707784e-05!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00377957849897037!TCF7L2#6934;6:10.7701765631373:6.40204410218762e-07:2.91339034417591e-05!TFAP2C#7022;6:10.8092286098602:6.2644941908553e-07:2.86577971440533e-05
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}}
}}

Revision as of 13:39, 5 September 2012


Full id: C1483_Gingival_Keratinocyte_Mammary_Prostate_Tracheal_Small_embryonic



Phase1 CAGE Peaks

Hg19::chr20:6103758..6103773,-p5@FERMT1
Hg19::chr20:6103778..6103792,-p4@FERMT1
Hg19::chr20:6103800..6103809,-p10@FERMT1
Hg19::chr20:6103830..6103851,-p6@FERMT1
Hg19::chr20:6103859..6103907,-p2@FERMT1
Hg19::chr20:6103918..6103923,-p15@FERMT1


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>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure5.33e-18347
endoderm-derived structure5.34e-15169
endoderm5.34e-15169
presumptive endoderm5.34e-15169
organism subdivision5.72e-15365
embryo3.39e-12612
organ part3.88e-12219
mesenchyme4.72e-12238
entire embryonic mesenchyme4.72e-12238
epithelium1.34e-11309
embryonic structure1.76e-11605
developing anatomical structure1.76e-11605
cell layer2.36e-11312
germ layer2.66e-11604
embryonic tissue2.66e-11604
presumptive structure2.66e-11604
epiblast (generic)2.66e-11604
anatomical system4.07e-11625
digestive system4.62e-11155
digestive tract4.62e-11155
primitive gut4.62e-11155
anatomical group4.72e-11626
multi-cellular organism1.11e-10659
respiratory system9.43e-1072
mixed endoderm/mesoderm-derived structure5.31e-09130
anatomical conduit1.11e-08241
anatomical cluster1.21e-08286
subdivision of digestive tract3.33e-08129
endodermal part of digestive tract3.33e-08129
respiratory tract4.95e-0853
trunk1.10e-07216
multilaminar epithelium4.02e-0782
segment of respiratory tract4.77e-0746
Disease
Ontology termp-valuen
cell type cancer4.27e-08143
carcinoma6.29e-08106
squamous cell carcinoma1.32e-0714


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
CTCF#1066465.360256373075034.21437267579784e-050.000755613507103263
HDAC2#3066511.17968353052191.29408913564529e-050.000317038177897392
HEY1#2346264.040111043105710.0002298968555807510.0025329884692476
HNF4A#3172623.13229036295376.51490260560877e-095.13129647984295e-07
MXI1#460169.96157162875931.02262624227062e-064.3013315391261e-05
MYC#460965.22228187160944.92821127172503e-050.000854411449215954
POLR2A#543062.147453176558070.01019570676818780.0380500060447656
TAF1#687263.343046285745290.0007162474284635620.00573431699358421
TAF7#6879611.43306940492394.47357982339933e-072.12660993707784e-05
TBP#690863.706770687096390.000385416472907960.00377957849897037
TCF7L2#6934610.77017656313736.40204410218762e-072.91339034417591e-05
TFAP2C#7022610.80922860986026.2644941908553e-072.86577971440533e-05



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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