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Coexpression cluster:C4354: Difference between revisions

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|full_id=C4354_Small_Prostate_Mallassezderived_Urothelial_Sebocyte_Keratinocyte_Macrophage
|full_id=C4354_Small_Prostate_Mallassezderived_Urothelial_Sebocyte_Keratinocyte_Macrophage
|id=C4354
|id=C4354
|ontology_enrichment_celltype=CL:0002194!3.09e-21!63;CL:0000576!3.09e-21!63;CL:0000040!3.09e-21!63;CL:0000559!3.09e-21!63;CL:0002009!1.71e-20!65;CL:0000557!3.03e-18!71;CL:0002057!6.50e-17!42;CL:0000839!8.40e-17!70;CL:0000766!7.52e-16!76;CL:0000860!4.43e-14!45;CL:0000763!9.39e-13!112;CL:0000049!9.39e-13!112;CL:0002076!2.80e-07!43;CL:0000223!3.40e-07!59
|ontology_enrichment_celltype=CL:0002194!3.99e-24!59;CL:0000576!3.99e-24!59;CL:0000040!3.99e-24!59;CL:0000559!3.99e-24!59;CL:0002009!2.44e-23!61;CL:0000473!1.51e-20!48;CL:0000234!1.51e-20!48;CL:0000557!1.56e-20!67;CL:0000839!6.55e-19!66;CL:0000766!9.70e-18!72;CL:0000860!9.74e-17!42;CL:0002057!9.74e-17!42;CL:0000763!4.39e-14!108;CL:0000049!4.39e-14!108;CL:0000325!5.56e-09!87;CL:0002076!2.30e-07!42
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002405!1.17e-16!115;UBERON:0002193!1.03e-14!112;UBERON:0002371!1.82e-14!80;UBERON:0002390!3.90e-14!102;UBERON:0003061!3.90e-14!102;UBERON:0002204!7.85e-13!167;UBERON:0000467!3.34e-12!625;UBERON:0000480!5.86e-12!626;UBERON:0001474!1.15e-11!86;UBERON:0004765!1.95e-11!101;UBERON:0001434!1.95e-11!101;UBERON:0000468!2.61e-10!659;UBERON:0003081!2.30e-09!216;UBERON:0000923!1.39e-08!604;UBERON:0005291!1.39e-08!604;UBERON:0006598!1.39e-08!604;UBERON:0002532!1.39e-08!604;UBERON:0002050!1.50e-08!605;UBERON:0005423!1.50e-08!605;UBERON:0000062!7.83e-08!511;UBERON:0000922!8.48e-08!612;UBERON:0002365!6.42e-07!31;UBERON:0002330!6.42e-07!31
|ontology_enrichment_uberon=UBERON:0002371!3.00e-16!76;UBERON:0002193!1.29e-15!108;UBERON:0002390!1.50e-15!98;UBERON:0003061!1.50e-15!98;UBERON:0002405!4.45e-15!93;UBERON:0002204!5.55e-14!167;UBERON:0000467!3.29e-13!624;UBERON:0004765!4.38e-13!90;UBERON:0001474!4.85e-13!82;UBERON:0000480!5.84e-13!625;UBERON:0001434!1.62e-12!100;UBERON:0002050!4.96e-12!564;UBERON:0005423!8.29e-12!581;UBERON:0000468!1.36e-11!656;UBERON:0000923!5.43e-11!560;UBERON:0010316!5.43e-11!560;UBERON:0005291!5.43e-11!560;UBERON:0006598!5.43e-11!560;UBERON:0010317!5.43e-11!560;UBERON:0002532!5.43e-11!560;UBERON:0000922!4.16e-10!592;UBERON:0003081!8.87e-10!203;UBERON:0000926!9.67e-09!315;UBERON:0004120!9.67e-09!315;UBERON:0006603!9.67e-09!315;UBERON:0000062!2.62e-08!503;UBERON:0000479!1.60e-07!773;UBERON:0007023!8.42e-07!114
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115566460325812!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464022815583782!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168000691344304!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123200897845118!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000759093087922567!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165714486209442!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247406830003558!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644429485037388
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115566460325812!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464022815583782!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168000691344304!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123200897845118!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000759093087922567!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165714486209442!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247406830003558!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644429485037388
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}}
}}

Revision as of 15:53, 19 October 2012


Full id: C4354_Small_Prostate_Mallassezderived_Urothelial_Sebocyte_Keratinocyte_Macrophage



Phase1 CAGE Peaks

Hg19::chr4:10023095..10023109,-p3@SLC2A9
Hg19::chr4:10023114..10023128,-p1@SLC2A9
Hg19::chr4:10023130..10023156,-p2@SLC2A9


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><br>


Uber Anatomy
Ontology termp-valuen
bone marrow3.00e-1676
hemolymphoid system1.29e-15108
hematopoietic system1.50e-1598
blood island1.50e-1598
immune system4.45e-1593
musculoskeletal system5.55e-14167
anatomical system3.29e-13624
skeletal element4.38e-1390
bone element4.85e-1382
anatomical group5.84e-13625
skeletal system1.62e-12100
embryonic structure4.96e-12564
developing anatomical structure8.29e-12581
multi-cellular organism1.36e-11656
germ layer5.43e-11560
germ layer / neural crest5.43e-11560
embryonic tissue5.43e-11560
presumptive structure5.43e-11560
germ layer / neural crest derived structure5.43e-11560
epiblast (generic)5.43e-11560
embryo4.16e-10592
lateral plate mesoderm8.87e-10203
mesoderm9.67e-09315
mesoderm-derived structure9.67e-09315
presumptive mesoderm9.67e-09315
organ2.62e-08503
tissue1.60e-07773
adult organism8.42e-07114


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
CEBPB#105137.971147625824820.001974187055288560.0115566460325812
ELF1#199734.258097958807540.01295179875054610.0464022815583782
EP300#203336.77394172622320.003216880500103790.0168000691344304
HNF4A#3172323.13229036295378.07584663437677e-050.00123200897845118
HNF4G#3174328.75342252644684.20470658818262e-050.000759093087922567
RXRA#6256320.07461713913330.0001235730348432220.00165714486209442
SP1#666735.69838137814090.005403962701712170.0247406830003558
STAT3#6774310.51946499715420.0008589184530415310.00644429485037388



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.