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Coexpression cluster:C4430: Difference between revisions

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|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
|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 16:44, 26 November 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 cell6.16e-28433
multi fate stem cell1.43e-27427
stem cell2.32e-27441
myeloid leukocyte5.69e-2672
myeloid cell1.10e-24108
common myeloid progenitor1.10e-24108
classical monocyte2.10e-2442
CD14-positive, CD16-negative classical monocyte2.10e-2442
hematopoietic stem cell5.47e-24168
angioblastic mesenchymal cell5.47e-24168
granulocyte monocyte progenitor cell9.31e-2367
leukocyte1.29e-22136
hematopoietic oligopotent progenitor cell1.76e-22161
hematopoietic multipotent progenitor cell1.76e-22161
hematopoietic cell2.56e-22177
monopoietic cell1.22e-2159
monocyte1.22e-2159
monoblast1.22e-2159
promonocyte1.22e-2159
defensive cell1.48e-2148
phagocyte1.48e-2148
myeloid lineage restricted progenitor cell4.48e-2166
connective tissue cell6.17e-21361
macrophage dendritic cell progenitor6.98e-2161
mesenchymal cell8.20e-21354
nongranular leukocyte1.18e-17115
hematopoietic lineage restricted progenitor cell1.70e-17120
motile cell7.25e-15386
somatic cell2.78e-13588
vascular associated smooth muscle cell3.60e-1032
stuff accumulating cell2.20e-0987
smooth muscle cell1.28e-0843
smooth muscle myoblast1.28e-0843
muscle cell3.64e-0855
muscle precursor cell4.38e-0858
myoblast4.38e-0858
multi-potent skeletal muscle stem cell4.38e-0858
contractile cell4.93e-0859
native cell9.16e-07722
Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.05e-21167
connective tissue3.01e-20371
mesoderm5.48e-20315
mesoderm-derived structure5.48e-20315
presumptive mesoderm5.48e-20315
bone marrow1.61e-1976
hematopoietic system1.80e-1998
blood island1.80e-1998
bone element5.57e-1882
skeletal element1.49e-1790
lateral plate mesoderm7.85e-17203
hemolymphoid system2.99e-16108
immune system2.44e-1593
skeletal system7.84e-15100
muscle tissue1.18e-0764
musculature1.18e-0764
musculature of body1.18e-0764
skeletal muscle tissue2.72e-0762
striated muscle tissue2.72e-0762
myotome2.72e-0762
artery7.02e-0742
arterial blood vessel7.02e-0742
arterial system7.02e-0742


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.