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Coexpression cluster:C4732: Difference between revisions

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|full_id=C4732_Hepatocyte_Neutrophils_CD14_granulocyte_small_Eosinophils_duodenum
|full_id=C4732_Hepatocyte_Neutrophils_CD14_granulocyte_small_Eosinophils_duodenum
|id=C4732
|id=C4732
|ontology_enrichment_celltype=CL:0000763!6.54e-24!112;CL:0000049!6.54e-24!112;CL:0000766!7.99e-24!76;CL:0000557!1.81e-21!71;CL:0002057!1.58e-20!42;CL:0000839!2.01e-20!70;CL:0002009!3.84e-20!65;CL:0002194!7.65e-20!63;CL:0000576!7.65e-20!63;CL:0000040!7.65e-20!63;CL:0000559!7.65e-20!63;CL:0000860!4.04e-19!45;CL:0000037!5.05e-19!172;CL:0000566!5.05e-19!172;CL:0002032!1.39e-18!165;CL:0000837!1.39e-18!165;CL:0000738!8.71e-17!140;CL:0000988!1.04e-15!182;CL:0002031!2.25e-14!124;CL:0002087!1.79e-13!119;CL:0002320!5.31e-07!365;CL:0000134!5.92e-07!358
|ontology_enrichment_celltype=CL:0000766!9.92e-21!72;CL:0000763!5.52e-20!108;CL:0000049!5.52e-20!108;CL:0000557!5.78e-18!67;CL:0000839!3.04e-17!66;CL:0002194!3.98e-17!59;CL:0000576!3.98e-17!59;CL:0000040!3.98e-17!59;CL:0000559!3.98e-17!59;CL:0002009!5.68e-17!61;CL:0000473!1.21e-16!48;CL:0000234!1.21e-16!48;CL:0000860!1.72e-16!42;CL:0002057!1.72e-16!42;CL:0000037!2.87e-15!168;CL:0000566!2.87e-15!168;CL:0002032!6.55e-15!161;CL:0000837!6.55e-15!161;CL:0000738!1.47e-13!136;CL:0000988!3.55e-12!177;CL:0002031!4.04e-11!120;CL:0002087!5.91e-11!115;CL:0000325!4.62e-09!87
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002405!3.35e-22!115;UBERON:0002371!1.51e-21!80;UBERON:0002390!2.50e-18!102;UBERON:0003061!2.50e-18!102;UBERON:0002193!1.83e-17!112;UBERON:0001474!3.21e-17!86;UBERON:0004765!3.38e-14!101;UBERON:0001434!3.38e-14!101;UBERON:0007023!1.44e-08!115;UBERON:0002204!2.38e-08!167;UBERON:0002384!6.93e-07!375
|ontology_enrichment_uberon=UBERON:0002371!5.26e-18!76;UBERON:0002405!1.11e-17!93;UBERON:0002390!1.15e-14!98;UBERON:0003061!1.15e-14!98;UBERON:0001474!4.22e-14!82;UBERON:0002193!7.62e-14!108;UBERON:0004765!3.43e-13!90;UBERON:0001434!5.50e-12!100;UBERON:0007023!8.45e-09!114;UBERON:0002204!1.99e-07!167
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191243642497554!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281427398460087!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465123756862762!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154865693860613!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123435291474854!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.00076040753482806!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128767145905183!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000606504434998874!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310340149297329!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00166012917236832!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024796118826243!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109443536351919!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155408384499105!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645867840141151!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00632148621778459!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331372732359749!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243881388567479
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191243642497554!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281427398460087!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465123756862762!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154865693860613!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123435291474854!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.00076040753482806!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128767145905183!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000606504434998874!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310340149297329!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00166012917236832!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024796118826243!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109443536351919!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155408384499105!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645867840141151!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00632148621778459!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331372732359749!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243881388567479
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}}
}}

Revision as of 16:12, 19 October 2012


Full id: C4732_Hepatocyte_Neutrophils_CD14_granulocyte_small_Eosinophils_duodenum



Phase1 CAGE Peaks

Hg19::chr8:144635648..144635661,-p@chr8:144635648..144635661
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Hg19::chr8:144635664..144635703,-p@chr8:144635664..144635703
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Hg19::chr8:144635740..144635767,-p@chr8:144635740..144635767
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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>


Cell Type
Ontology termp-valuen
myeloid leukocyte9.92e-2172
myeloid cell5.52e-20108
common myeloid progenitor5.52e-20108
granulocyte monocyte progenitor cell5.78e-1867
myeloid lineage restricted progenitor cell3.04e-1766
monopoietic cell3.98e-1759
monocyte3.98e-1759
monoblast3.98e-1759
promonocyte3.98e-1759
macrophage dendritic cell progenitor5.68e-1761
defensive cell1.21e-1648
phagocyte1.21e-1648
classical monocyte1.72e-1642
CD14-positive, CD16-negative classical monocyte1.72e-1642
hematopoietic stem cell2.87e-15168
angioblastic mesenchymal cell2.87e-15168
hematopoietic oligopotent progenitor cell6.55e-15161
hematopoietic multipotent progenitor cell6.55e-15161
leukocyte1.47e-13136
hematopoietic cell3.55e-12177
hematopoietic lineage restricted progenitor cell4.04e-11120
nongranular leukocyte5.91e-11115
stuff accumulating cell4.62e-0987
Uber Anatomy
Ontology termp-valuen
bone marrow5.26e-1876
immune system1.11e-1793
hematopoietic system1.15e-1498
blood island1.15e-1498
bone element4.22e-1482
hemolymphoid system7.62e-14108
skeletal element3.43e-1390
skeletal system5.50e-12100
adult organism8.45e-09114
musculoskeletal system1.99e-07167


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
CCNT2#90536.336201576962630.003930750035764890.0191243642497554
CTCF#1066435.360256373075030.0064925092527670.0281427398460087
ELF1#199734.258097958807540.01295179875054610.0465123756862762
GABPB1#255337.067683836182170.002832212825417420.0154865693860613
HNF4A#3172323.13229036295378.07584663437677e-050.00123435291474854
HNF4G#3174328.75342252644684.20470658818262e-050.00076040753482806
IRF1#365937.63716375356390.002244692747297240.0128767145905183
NR2C2#7182332.61461090524092.88098172333076e-050.000606504434998874
NR3C1#2908314.9730233311730.0002978331194675480.00310340149297329
RXRA#6256320.07461713913330.0001235730348432220.00166012917236832
SP1#666735.69838137814090.005403962701712170.024796118826243
SPI1#668838.204323508522730.001810593189410520.0109443536351919
STAT1#6772320.70658749719920.0001125992441046670.00155408384499105
STAT3#6774310.51946499715420.0008589184530415310.00645867840141151
TCF12#6938310.63446490218640.0008313523990202070.00632148621778459
YY1#752834.911170749853860.008441455341808260.0331372732359749
ZEB1#6935316.88843201754390.0002075486917327580.00243881388567479



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.