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Coexpression cluster:C2480: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.043653766909256!CCNT2#905;3:4.75215118272197:0.0138620699668949:0.048722512124673!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160894437808148!ESR1#2099;2:15.3843016480772:0.00606557262969351:0.026839060283547!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.019205075301579!FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.0150366378521107!FOXA2#3170;3:18.4728478144989:0.000259448418743726:0.00278198494919671!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378590935438872!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186056111335629!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485424896881311!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186350233679666!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00887754213929114!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284892925452977!NR2C2#7182;3:24.4609581789307:0.000112590606343803:0.00155581507487966!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119618059242819!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443823954151944!SETDB1#9869;2:20.1600130890052:0.0035690868540764:0.0180859709826728!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796362635150267!SREBF1#6720;2:23.5029247202441:0.00263845490076824:0.0145836248415631!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584470166319661!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322235185707597!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244226412909295!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158638925380907!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342435075919933
|tf_chipseq_enrich=BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.043653766909256!CCNT2#905;3:4.75215118272197:0.0138620699668949:0.048722512124673!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160894437808148!ESR1#2099;2:15.3843016480772:0.00606557262969351:0.026839060283547!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.019205075301579!FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.0150366378521107!FOXA2#3170;3:18.4728478144989:0.000259448418743726:0.00278198494919671!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378590935438872!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186056111335629!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485424896881311!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186350233679666!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00887754213929114!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284892925452977!NR2C2#7182;3:24.4609581789307:0.000112590606343803:0.00155581507487966!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119618059242819!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443823954151944!SETDB1#9869;2:20.1600130890052:0.0035690868540764:0.0180859709826728!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796362635150267!SREBF1#6720;2:23.5029247202441:0.00263845490076824:0.0145836248415631!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584470166319661!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322235185707597!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244226412909295!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158638925380907!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342435075919933
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}}
}}

Revision as of 15:31, 26 November 2012


Full id: C2480_Mesenchymal_liposarcoma_skeletal_Alveolar_heart_left_Osteoblast



Phase1 CAGE Peaks

Hg19::chr19:1605424..1605474,-p1@UQCR11
Hg19::chr19:5680503..5680541,-p1@C19orf70
Hg19::chr19:5680543..5680554,-p2@C19orf70
Hg19::chr2:110970096..110970134,-p1@LINC00116


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
epithelial vesicle1.95e-2478
multilaminar epithelium1.73e-2183
somite3.79e-2171
presomitic mesoderm3.79e-2171
presumptive segmental plate3.79e-2171
dermomyotome3.79e-2171
trunk paraxial mesoderm3.79e-2171
dense mesenchyme tissue7.75e-2173
paraxial mesoderm9.91e-2172
presumptive paraxial mesoderm9.91e-2172
mesenchyme2.14e-20160
entire embryonic mesenchyme2.14e-20160
skeletal muscle tissue1.20e-1962
striated muscle tissue1.20e-1962
myotome1.20e-1962
muscle tissue1.10e-1864
musculature1.10e-1864
musculature of body1.10e-1864
trunk mesenchyme4.29e-18122
trunk1.81e-16199
unilaminar epithelium3.02e-16148
organism subdivision3.18e-16264
epithelial tube6.20e-14117
vasculature8.37e-1378
vascular system8.37e-1378
splanchnic layer of lateral plate mesoderm1.43e-1283
multi-tissue structure4.76e-12342
epithelium7.58e-12306
cell layer1.21e-11309
vessel1.42e-1168
epithelial tube open at both ends3.07e-1159
blood vessel3.07e-1159
blood vasculature3.07e-1159
vascular cord3.07e-1159
compound organ1.41e-1068
artery1.72e-0942
arterial blood vessel1.72e-0942
arterial system1.72e-0942
circulatory system4.60e-09112
cardiovascular system4.69e-08109
primary circulatory organ7.64e-0827
systemic artery4.58e-0733
systemic arterial system4.58e-0733


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
BCLAF1#9774210.82632380506090.01202203816432580.043653766909256
CCNT2#90534.752151182721970.01386206996689490.048722512124673
ELF1#199744.258097958807540.003041525565781240.0160894437808148
ESR1#2099215.38430164807720.006065572629693510.026839060283547
ETS1#211337.296570691651750.00400857377511390.019205075301579
FOXA1#316938.311064812039090.002740138182109850.0150366378521107
FOXA2#3170318.47284781449890.0002594484187437260.00278198494919671
GABPB1#255335.300762877136630.01012678824234270.0378590935438872
HEY1#2346244.040111043105710.00375304636917980.0186056111335629
MAX#414946.452555509007120.0005767613195645490.00485424896881311
MXI1#460137.471178721569470.003741314738550960.0186350233679666
MYC#460945.22228187160940.001344309395272740.00887754213929114
NANOG#79923214.62238924050630.006698757715363760.0284892925452977
NR2C2#7182324.46095817893070.0001125906063438030.00155581507487966
NRF1#489939.157709585783180.002061953791733420.0119618059242819
PAX5#507946.669565531177830.0005052774169483260.00443823954151944
SETDB1#9869220.16001308900520.00356908685407640.0180859709826728
SIN3A#2594245.408884726815140.001168172384885160.00796362635150267
SREBF1#6720223.50292472024410.002638454900768240.0145836248415631
SRF#6722413.79717826216782.75840773062708e-050.000584470166319661
TAF1#687243.343046285745290.008005664898701650.0322235185707597
TBP#690843.706770687096390.005296377814784350.0244226412909295
TCF7L2#693438.077632422353010.002978381685834620.0158638925380907
ZBTB7A#5134135.513931980906920.009038352821081090.0342435075919933



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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