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Coexpression cluster:C4385: Difference between revisions

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|ontology_enrichment_disease=DOID:305!5.07e-23!106;DOID:0050687!4.71e-14!143;DOID:1749!1.21e-10!14;DOID:299!1.21e-08!25;DOID:162!1.86e-08!235;DOID:14566!3.96e-08!239
|ontology_enrichment_disease=DOID:305!5.07e-23!106;DOID:0050687!4.71e-14!143;DOID:1749!1.21e-10!14;DOID:299!1.21e-08!25;DOID:162!1.86e-08!235;DOID:14566!3.96e-08!239
|ontology_enrichment_uberon=UBERON:0004119!1.38e-26!169;UBERON:0000925!1.38e-26!169;UBERON:0006595!1.38e-26!169;UBERON:0001004!3.63e-22!72;UBERON:0001007!3.76e-20!155;UBERON:0001555!3.76e-20!155;UBERON:0007026!3.76e-20!155;UBERON:0000065!1.81e-18!53;UBERON:0000077!4.02e-17!130;UBERON:0008947!5.01e-16!38;UBERON:0003258!5.01e-16!38;UBERON:0004921!6.39e-16!129;UBERON:0004185!6.39e-16!129;UBERON:0000072!8.09e-15!46;UBERON:0005911!4.24e-12!82;UBERON:0001041!1.13e-11!98;UBERON:0000464!2.05e-11!104;UBERON:0000161!1.61e-10!35;UBERON:0005153!1.84e-10!37;UBERON:0000063!6.96e-10!97;UBERON:0005178!1.51e-09!34;UBERON:0002224!1.51e-09!34;UBERON:0000064!1.80e-09!219;UBERON:0005181!4.88e-09!35;UBERON:0000466!6.20e-09!126;UBERON:0000344!1.71e-08!12;UBERON:0001737!1.72e-08!9;UBERON:0003100!2.94e-08!41;UBERON:0003104!3.69e-08!238;UBERON:0009142!3.69e-08!238;UBERON:0000062!3.70e-08!511;UBERON:0005157!4.19e-08!51;UBERON:0001557!5.45e-08!19;UBERON:0001008!6.91e-08!45;UBERON:0005156!8.17e-08!59;UBERON:0000990!8.17e-08!59;UBERON:0001048!1.00e-07!168;UBERON:0000166!1.08e-07!21;UBERON:0006554!1.47e-07!44;UBERON:0002048!1.54e-07!22;UBERON:0000117!1.54e-07!22;UBERON:0000171!1.54e-07!22;UBERON:0000170!1.54e-07!22;UBERON:0005597!1.54e-07!22;UBERON:0000118!1.54e-07!22;UBERON:0004807!4.49e-07!28;UBERON:0005795!5.21e-07!22;UBERON:0003134!6.43e-07!37;UBERON:0000474!6.43e-07!37;UBERON:0000481!6.71e-07!347;UBERON:0003975!8.44e-07!22
|ontology_enrichment_uberon=UBERON:0004119!1.38e-26!169;UBERON:0000925!1.38e-26!169;UBERON:0006595!1.38e-26!169;UBERON:0001004!3.63e-22!72;UBERON:0001007!3.76e-20!155;UBERON:0001555!3.76e-20!155;UBERON:0007026!3.76e-20!155;UBERON:0000065!1.81e-18!53;UBERON:0000077!4.02e-17!130;UBERON:0008947!5.01e-16!38;UBERON:0003258!5.01e-16!38;UBERON:0004921!6.39e-16!129;UBERON:0004185!6.39e-16!129;UBERON:0000072!8.09e-15!46;UBERON:0005911!4.24e-12!82;UBERON:0001041!1.13e-11!98;UBERON:0000464!2.05e-11!104;UBERON:0000161!1.61e-10!35;UBERON:0005153!1.84e-10!37;UBERON:0000063!6.96e-10!97;UBERON:0005178!1.51e-09!34;UBERON:0002224!1.51e-09!34;UBERON:0000064!1.80e-09!219;UBERON:0005181!4.88e-09!35;UBERON:0000466!6.20e-09!126;UBERON:0000344!1.71e-08!12;UBERON:0001737!1.72e-08!9;UBERON:0003100!2.94e-08!41;UBERON:0003104!3.69e-08!238;UBERON:0009142!3.69e-08!238;UBERON:0000062!3.70e-08!511;UBERON:0005157!4.19e-08!51;UBERON:0001557!5.45e-08!19;UBERON:0001008!6.91e-08!45;UBERON:0005156!8.17e-08!59;UBERON:0000990!8.17e-08!59;UBERON:0001048!1.00e-07!168;UBERON:0000166!1.08e-07!21;UBERON:0006554!1.47e-07!44;UBERON:0002048!1.54e-07!22;UBERON:0000117!1.54e-07!22;UBERON:0000171!1.54e-07!22;UBERON:0000170!1.54e-07!22;UBERON:0005597!1.54e-07!22;UBERON:0000118!1.54e-07!22;UBERON:0004807!4.49e-07!28;UBERON:0005795!5.21e-07!22;UBERON:0003134!6.43e-07!37;UBERON:0000474!6.43e-07!37;UBERON:0000481!6.71e-07!347;UBERON:0003975!8.44e-07!22
|tf_chipseq_enrich=PRDM1#639;2:87.8873038516405:0.000171624884802908:0.00209225298750215
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}}
}}

Revision as of 13:50, 5 September 2012


Full id: C4385_Keratinocyte_Tracheal_Bronchial_Mallassezderived_Gingival_Sebocyte_oral



Phase1 CAGE Peaks

Hg19::chr4:15937715..15937733,-p@chr4:15937715..15937733
-
Hg19::chr4:15939963..15939978,-p1@FGFBP1
Hg19::chr4:15939984..15939995,-p2@FGFBP1


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
endoderm-derived structure1.38e-26169
endoderm1.38e-26169
presumptive endoderm1.38e-26169
respiratory system3.63e-2272
digestive system3.76e-20155
digestive tract3.76e-20155
primitive gut3.76e-20155
respiratory tract1.81e-1853
mixed endoderm/mesoderm-derived structure4.02e-17130
respiratory primordium5.01e-1638
endoderm of foregut5.01e-1638
subdivision of digestive tract6.39e-16129
endodermal part of digestive tract6.39e-16129
segment of respiratory tract8.09e-1546
endo-epithelium4.24e-1282
foregut1.13e-1198
anatomical space2.05e-11104
orifice1.61e-1035
epithelial bud1.84e-1037
organ segment6.96e-1097
thoracic cavity element1.51e-0934
thoracic cavity1.51e-0934
organ part1.80e-09219
thoracic segment organ4.88e-0935
immaterial anatomical entity6.20e-09126
mucosa1.71e-0812
larynx1.72e-089
female organism2.94e-0841
mesenchyme3.69e-08238
entire embryonic mesenchyme3.69e-08238
organ3.70e-08511
epithelial fold4.19e-0851
upper respiratory tract5.45e-0819
renal system6.91e-0845
reproductive structure8.17e-0859
reproductive system8.17e-0859
primordium1.00e-07168
oral opening1.08e-0721
urinary system structure1.47e-0744
lung1.54e-0722
respiratory tube1.54e-0722
respiration organ1.54e-0722
pair of lungs1.54e-0722
lung primordium1.54e-0722
lung bud1.54e-0722
respiratory system epithelium4.49e-0728
embryonic uterus5.21e-0722
female reproductive organ6.43e-0737
female reproductive system6.43e-0737
multi-tissue structure6.71e-07347
internal female genitalia8.44e-0722
Disease
Ontology termp-valuen
carcinoma5.07e-23106
cell type cancer4.71e-14143
squamous cell carcinoma1.21e-1014
adenocarcinoma1.21e-0825
cancer1.86e-08235
disease of cellular proliferation3.96e-08239


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
PRDM1#639287.88730385164050.0001716248848029080.00209225298750215



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.