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Coexpression cluster:C4430: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.43e-22!375;UBERON:0002204!1.18e-19!167;UBERON:0002390!3.33e-18!102;UBERON:0003061!3.33e-18!102;UBERON:0003081!1.40e-17!216;UBERON:0002371!2.88e-16!80;UBERON:0002193!8.36e-16!112;UBERON:0001474!1.58e-14!86;UBERON:0004765!3.90e-13!101;UBERON:0001434!3.90e-13!101;UBERON:0002405!9.25e-09!115;UBERON:0001637!2.44e-07!42;UBERON:0003509!2.44e-07!42;UBERON:0004572!2.44e-07!42;UBERON:0002385!2.74e-07!63;UBERON:0001015!2.74e-07!63;UBERON:0000383!2.74e-07!63;UBERON:0001134!5.82e-07!61;UBERON:0002036!5.82e-07!61;UBERON:0003082!5.82e-07!61;UBERON:0000486!8.90e-07!82
|ontology_enrichment_uberon=UBERON:0002384!1.43e-22!375;UBERON:0002204!1.18e-19!167;UBERON:0002390!3.33e-18!102;UBERON:0003061!3.33e-18!102;UBERON:0003081!1.40e-17!216;UBERON:0002371!2.88e-16!80;UBERON:0002193!8.36e-16!112;UBERON:0001474!1.58e-14!86;UBERON:0004765!3.90e-13!101;UBERON:0001434!3.90e-13!101;UBERON:0002405!9.25e-09!115;UBERON:0001637!2.44e-07!42;UBERON:0003509!2.44e-07!42;UBERON:0004572!2.44e-07!42;UBERON:0002385!2.74e-07!63;UBERON:0001015!2.74e-07!63;UBERON:0000383!2.74e-07!63;UBERON:0001134!5.82e-07!61;UBERON:0002036!5.82e-07!61;UBERON:0003082!5.82e-07!61;UBERON:0000486!8.90e-07!82
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190781486655474!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323747736517897!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321948178526952!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464245773315126!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168093151823855!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900561987258733!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000372124752884391!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438296006176308!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109017790789656!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128562361302428!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157361063540738!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722155946530975!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.0047279673045675!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667043061246257!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770114765805558!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277836934290177!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247526187712871!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109323317401194!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249138783042972!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617996184785919!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197669234200272
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}}
}}

Revision as of 13:33, 5 September 2012


Full id: C4430_CD14_Neutrophils_mesenchymal_Smooth_Mast_Whole_large



Phase1 CAGE Peaks

Hg19::chr4:80994351..80994402,-p1@ANTXR2
Hg19::chr4:80994415..80994426,-p11@ANTXR2
Hg19::chr4:80994471..80994485,-p7@ANTXR2


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
somatic stem cell2.42e-30436
multi fate stem cell6.64e-30430
stem cell2.21e-29444
connective tissue cell3.37e-23365
mesenchymal cell3.57e-23358
hematopoietic stem cell4.33e-23172
angioblastic mesenchymal cell4.33e-23172
CD14-positive, CD16-negative classical monocyte9.39e-2342
leukocyte1.36e-22140
myeloid leukocyte3.81e-2276
hematopoietic oligopotent progenitor cell1.47e-21165
hematopoietic multipotent progenitor cell1.47e-21165
myeloid cell4.03e-21112
common myeloid progenitor4.03e-21112
hematopoietic cell1.19e-20182
granulocyte monocyte progenitor cell7.46e-1971
classical monocyte1.86e-1845
myeloid lineage restricted progenitor cell2.36e-1770
somatic cell2.56e-17591
monopoietic cell3.45e-1763
monocyte3.45e-1763
monoblast3.45e-1763
promonocyte3.45e-1763
nongranular leukocyte4.61e-17119
hematopoietic lineage restricted progenitor cell8.45e-17124
motile cell8.88e-17390
macrophage dendritic cell progenitor9.46e-1765
native cell2.42e-09722
vascular associated smooth muscle cell4.95e-0932
smooth muscle cell4.08e-0842
smooth muscle myoblast4.08e-0842
muscle cell6.09e-0854
muscle precursor cell7.23e-0857
myoblast7.23e-0857
multi-potent skeletal muscle stem cell7.23e-0857
contractile cell3.39e-0759
Uber Anatomy
Ontology termp-valuen
connective tissue1.43e-22375
musculoskeletal system1.18e-19167
hematopoietic system3.33e-18102
blood island3.33e-18102
lateral plate mesoderm1.40e-17216
bone marrow2.88e-1680
hemolymphoid system8.36e-16112
bone element1.58e-1486
skeletal element3.90e-13101
skeletal system3.90e-13101
immune system9.25e-09115
artery2.44e-0742
arterial blood vessel2.44e-0742
arterial system2.44e-0742
muscle tissue2.74e-0763
musculature2.74e-0763
musculature of body2.74e-0763
skeletal muscle tissue5.82e-0761
striated muscle tissue5.82e-0761
myotome5.82e-0761
multilaminar epithelium8.90e-0782


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#90536.336201576962630.003930750035764890.0190781486655474
E2F6#187635.017155731697390.00791769806886330.0323747736517897
EGR1#195834.988179094810140.008056488137383440.0321948178526952
ELF1#199734.258097958807540.01295179875054610.0464245773315126
EP300#203336.77394172622320.003216880500103790.0168093151823855
FOS#235338.99795530889440.001372499272417130.00900561987258733
FOSL1#8061339.7135797163731.59554825631833e-050.000372124752884391
GATA2#2624312.7449317335540.0004829527704283790.00438296006176308
HMGN3#932438.178547723350590.001827766942164210.0109017790789656
IRF1#365937.63716375356390.002244692747297240.0128562361302428
JUND#372736.994663941871030.002921845042734990.0157361063540738
MXI1#460139.96157162875930.001011470541259020.00722155946530975
NRF1#4899312.21027944771090.0005492172401020010.0047279673045675
RAD21#5885310.35503389545630.0009004912073565420.00667043061246257
REST#597839.650028716128020.001112636247114590.00770114765805558
SIN3A#2594235.408884726815140.006318961977991520.0277836934290177
SP1#666735.69838137814090.005403962701712170.0247526187712871
SPI1#668838.204323508522730.001810593189410520.0109323317401194
TFAP2A#7020316.5186343730450.0002218033880766340.00249138783042972
TFAP2C#7022310.80922860986020.0007916746575753130.00617996184785919
TRIM28#10155318.59052504526250.0001555969297255280.00197669234200272



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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