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Coexpression cluster:C2862: Difference between revisions

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|full_id=C2862_lung_bronchioalveolar_epidermoid_prostate_mucinous_bile_squamous
|full_id=C2862_lung_bronchioalveolar_epidermoid_prostate_mucinous_bile_squamous
|id=C2862
|id=C2862
|ontology_enrichment_celltype=CL:0002076!7.55e-29!43;CL:0000066!1.55e-27!254;CL:0000223!7.32e-22!59;CL:0002251!2.29e-13!21;CL:0002368!8.22e-12!13;CL:0002202!1.95e-08!9;CL:0002632!1.95e-08!9;CL:0002159!4.14e-08!13;CL:1000507!6.24e-07!12;CL:1000494!6.24e-07!12;CL:0000082!7.48e-07!19
|ontology_enrichment_celltype=CL:0002076!1.89e-32!42;CL:0000066!1.89e-27!253;CL:0000223!7.27e-24!58;CL:0002251!5.93e-17!20;CL:0002368!2.53e-12!13;CL:0002159!7.15e-09!14;CL:0002202!2.39e-08!9;CL:0002632!2.39e-08!9;CL:1000507!5.82e-07!10;CL:1000494!5.82e-07!10;CL:0002327!6.92e-07!4
|ontology_enrichment_disease=DOID:305!4.90e-19!106;DOID:1749!1.78e-16!14;DOID:299!5.77e-14!25;DOID:0050687!5.21e-10!143
|ontology_enrichment_disease=DOID:1749!2.90e-17!14;DOID:305!4.11e-17!106;DOID:299!4.63e-14!25;DOID:0050687!2.03e-09!143
|ontology_enrichment_uberon=UBERON:0004119!6.95e-28!169;UBERON:0000925!6.95e-28!169;UBERON:0006595!6.95e-28!169;UBERON:0001007!1.17e-22!155;UBERON:0001555!1.17e-22!155;UBERON:0007026!1.17e-22!155;UBERON:0001004!2.04e-19!72;UBERON:0000464!4.14e-18!104;UBERON:0000466!1.57e-15!126;UBERON:0005911!1.68e-15!82;UBERON:0004921!1.94e-15!129;UBERON:0004185!1.94e-15!129;UBERON:0000077!8.15e-15!130;UBERON:0000161!4.38e-14!35;UBERON:0000065!3.38e-13!53;UBERON:0005153!3.52e-13!37;UBERON:0005181!6.88e-13!35;UBERON:0005178!2.76e-12!34;UBERON:0002224!2.76e-12!34;UBERON:0000062!3.87e-12!511;UBERON:0001008!8.29e-12!45;UBERON:0005177!2.22e-11!107;UBERON:0001041!2.90e-11!98;UBERON:0006554!4.88e-11!44;UBERON:0000166!6.00e-11!21;UBERON:0005157!3.65e-10!51;UBERON:0005156!9.64e-10!59;UBERON:0000990!9.64e-10!59;UBERON:0002048!4.56e-09!22;UBERON:0000117!4.56e-09!22;UBERON:0000171!4.56e-09!22;UBERON:0000170!4.56e-09!22;UBERON:0005597!4.56e-09!22;UBERON:0000118!4.56e-09!22;UBERON:0008947!7.23e-09!38;UBERON:0003258!7.23e-09!38;UBERON:0003104!8.39e-09!238;UBERON:0009142!8.39e-09!238;UBERON:0000072!9.29e-09!46;UBERON:0003100!1.00e-08!41;UBERON:0000058!1.09e-08!26;UBERON:0000915!1.16e-08!52;UBERON:0004807!1.72e-08!28;UBERON:0000467!1.75e-08!625;UBERON:0003133!1.85e-08!48;UBERON:0000480!2.08e-08!626;UBERON:0003064!2.42e-08!37;UBERON:0009569!2.44e-08!113;UBERON:0000165!2.97e-08!28;UBERON:0000930!2.97e-08!28;UBERON:0002553!4.40e-08!70;UBERON:0000481!6.13e-08!347;UBERON:0007196!8.17e-08!14;UBERON:0001558!8.17e-08!14;UBERON:0000922!1.51e-07!612;UBERON:0004175!1.55e-07!25;UBERON:0000344!2.52e-07!12;UBERON:0000923!2.87e-07!604;UBERON:0005291!2.87e-07!604;UBERON:0006598!2.87e-07!604;UBERON:0002532!2.87e-07!604;UBERON:0002050!3.38e-07!605;UBERON:0005423!3.38e-07!605;UBERON:0002294!4.33e-07!7;UBERON:0001173!4.33e-07!7;UBERON:0004912!4.33e-07!7;UBERON:0000468!5.85e-07!659;UBERON:0009773!6.24e-07!12;UBERON:0001231!6.24e-07!12;UBERON:0004810!6.24e-07!12;UBERON:0000489!6.29e-07!32;UBERON:0004802!7.48e-07!19;UBERON:0000115!7.48e-07!19;UBERON:0003102!7.57e-07!95
|ontology_enrichment_uberon=UBERON:0004119!1.10e-26!160;UBERON:0000925!1.10e-26!160;UBERON:0006595!1.10e-26!160;UBERON:0001007!8.20e-22!145;UBERON:0001555!8.20e-22!145;UBERON:0007026!8.20e-22!145;UBERON:0001004!8.33e-17!74;UBERON:0005911!8.79e-16!82;UBERON:0004921!4.39e-15!118;UBERON:0000161!2.90e-14!36;UBERON:0005153!4.07e-14!37;UBERON:0005178!5.31e-13!34;UBERON:0002224!5.31e-13!34;UBERON:0000065!9.67e-13!54;UBERON:0005181!1.84e-12!35;UBERON:0005157!5.40e-12!47;UBERON:0001008!7.78e-12!48;UBERON:0000464!1.19e-11!95;UBERON:0005177!2.08e-11!101;UBERON:0001041!3.92e-11!87;UBERON:0006554!5.32e-11!47;UBERON:0000475!3.26e-10!264;UBERON:0000166!7.05e-10!22;UBERON:0000062!7.11e-10!503;UBERON:0000466!8.17e-10!117;UBERON:0005156!7.67e-09!59;UBERON:0000990!7.67e-09!59;UBERON:0000344!1.10e-08!20;UBERON:0002048!1.19e-08!22;UBERON:0000117!1.19e-08!22;UBERON:0000171!1.19e-08!22;UBERON:0000170!1.19e-08!22;UBERON:0005597!1.19e-08!22;UBERON:0000118!1.19e-08!22;UBERON:0008947!1.40e-08!38;UBERON:0003258!1.40e-08!38;UBERON:0003100!1.64e-08!41;UBERON:0000072!5.97e-08!47;UBERON:0003102!7.56e-08!99;UBERON:0000165!8.10e-08!29;UBERON:0000930!8.10e-08!29;UBERON:0000365!1.06e-07!5;UBERON:0008814!1.14e-07!18;UBERON:0004807!1.31e-07!28;UBERON:0007196!1.78e-07!15;UBERON:0001558!1.78e-07!15;UBERON:0000915!2.18e-07!52;UBERON:0000481!4.59e-07!342;UBERON:0009569!4.73e-07!112;UBERON:0003133!4.83e-07!48;UBERON:0000922!4.98e-07!592;UBERON:0004810!5.82e-07!10;UBERON:0001911!6.92e-07!4;UBERON:0005333!6.92e-07!4;UBERON:0008425!6.92e-07!4;UBERON:0005311!6.92e-07!4;UBERON:0000467!6.97e-07!624;UBERON:0000480!7.96e-07!625;UBERON:0005423!8.15e-07!581
|tf_chipseq_enrich=ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.6160097634588e-05!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.79158429709588e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444459201067435!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123496056984481
|tf_chipseq_enrich=ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.6160097634588e-05!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.79158429709588e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444459201067435!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123496056984481
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}}
}}

Revision as of 14:30, 19 October 2012


Full id: C2862_lung_bronchioalveolar_epidermoid_prostate_mucinous_bile_squamous



Phase1 CAGE Peaks

Hg19::chr6:47009992..47009993,-p4@GPR110
Hg19::chr6:47009996..47010035,-p2@GPR110
Hg19::chr6:47010042..47010053,-p3@GPR110
Hg19::chr6:47010061..47010104,-p1@GPR110


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 structure1.10e-26160
endoderm1.10e-26160
presumptive endoderm1.10e-26160
digestive system8.20e-22145
digestive tract8.20e-22145
primitive gut8.20e-22145
respiratory system8.33e-1774
endo-epithelium8.79e-1682
subdivision of digestive tract4.39e-15118
orifice2.90e-1436
epithelial bud4.07e-1437
thoracic cavity element5.31e-1334
thoracic cavity5.31e-1334
respiratory tract9.67e-1354
thoracic segment organ1.84e-1235
epithelial fold5.40e-1247
renal system7.78e-1248
anatomical space1.19e-1195
trunk region element2.08e-11101
foregut3.92e-1187
urinary system structure5.32e-1147
organism subdivision3.26e-10264
oral opening7.05e-1022
organ7.11e-10503
immaterial anatomical entity8.17e-10117
reproductive structure7.67e-0959
reproductive system7.67e-0959
mucosa1.10e-0820
lung1.19e-0822
respiratory tube1.19e-0822
respiration organ1.19e-0822
pair of lungs1.19e-0822
lung primordium1.19e-0822
lung bud1.19e-0822
respiratory primordium1.40e-0838
endoderm of foregut1.40e-0838
female organism1.64e-0841
segment of respiratory tract5.97e-0847
surface structure7.56e-0899
mouth8.10e-0829
stomodeum8.10e-0829
urothelium1.06e-075
pharyngeal arch system1.14e-0718
respiratory system epithelium1.31e-0728
tracheobronchial tree1.78e-0715
lower respiratory tract1.78e-0715
thoracic segment of trunk2.18e-0752
multi-tissue structure4.59e-07342
subdivision of trunk4.73e-07112
reproductive organ4.83e-0748
embryo4.98e-07592
nephron tubule epithelium5.82e-0710
mammary gland6.92e-074
mammary bud6.92e-074
mammary ridge6.92e-074
mammary placode6.92e-074
anatomical system6.97e-07624
anatomical group7.96e-07625
developing anatomical structure8.15e-07581
Disease
Ontology termp-valuen
squamous cell carcinoma2.90e-1714
carcinoma4.11e-17106
adenocarcinoma4.63e-1425
cell type cancer2.03e-09143


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#2099430.76860329615451.11467714392546e-064.6160097634588e-05
GATA3#2625427.2365163572061.81561517799785e-066.79158429709588e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000444459201067435
STAT3#6774410.51946499715428.16377768286615e-050.00123496056984481



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.