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Coexpression cluster:C1159: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;4:12.8360997291479:0.000123233863882769:0.00165834576859329!CCNT2#905;6:5.43102992311083:9.35028339706757e-05:0.00135799506008391!CHD2#1106;5:7.3885877386549:0.000149868960082067:0.00193188895606159!CTCF#10664;7:5.36025637307503:7.86114662284756e-06:0.000222315270009092!E2F1#1869;6:4.20633361275371:0.000413523201700764:0.00393691428098688!ELF1#1997;5:3.04149854200538:0.00971956226937075:0.0365631006681847!EP300#2033;5:4.83852980444514:0.00113270819078547:0.00775679697970256!FOSL2#2355;4:9.67440034546382:0.000368369688968872:0.00366785794129279!GATA3#2625;5:19.4546545408614:1.31487982230667e-06:5.21156484864844e-05!HDAC2#3066;5:9.58258588330447:4.24859153994197e-05:0.00075992233574242!HEY1#23462;6:3.46295232266204:0.00126789009587212:0.00850463543498965!HMGN3#9324;6:7.01018376287194:2.09275278497296e-05:0.000461594526103044!JUND#3727;5:4.99618852990788:0.000973430860007092:0.00699636264457234!MAX#4149;4:3.6871745765755:0.0136057064395334:0.0480153536135172!NR3C1#2908;5:10.6950166651236:2.48694675006425e-05:0.000538644196661054!RAD21#5885;6:8.87574333896257:5.20411262905738e-06:0.000159434531788244!RXRA#6256;5:14.339012242238:5.91222266390468e-06:0.000177432937584925!SMC3#9126;6:12.8956567242282:5.68588239295796e-07:2.62291462561014e-05!SPI1#6688;6:7.03227729301948:2.05436318006376e-05:0.000454952578801269!TBP#6908;6:3.17723201751119:0.00207411205185266:0.0120176526259883!TCF7L2#6934;5:7.69298325938382:0.000123319885015426:0.00165886211632226!USF1#7391;5:4.54392805514854:0.00152278835596876:0.00970338579066633!USF2#7392;5:9.28014098933542:4.96618200858162e-05:0.000850546216454995!ZBTB7A#51341;5:5.25136379133993:0.000768769248321446:0.00603045602564545
|tf_chipseq_enrich=ATF3#467;4:12.8360997291479:0.000123233863882769:0.00165834576859329!CCNT2#905;6:5.43102992311083:9.35028339706757e-05:0.00135799506008391!CHD2#1106;5:7.3885877386549:0.000149868960082067:0.00193188895606159!CTCF#10664;7:5.36025637307503:7.86114662284756e-06:0.000222315270009092!E2F1#1869;6:4.20633361275371:0.000413523201700764:0.00393691428098688!ELF1#1997;5:3.04149854200538:0.00971956226937075:0.0365631006681847!EP300#2033;5:4.83852980444514:0.00113270819078547:0.00775679697970256!FOSL2#2355;4:9.67440034546382:0.000368369688968872:0.00366785794129279!GATA3#2625;5:19.4546545408614:1.31487982230667e-06:5.21156484864844e-05!HDAC2#3066;5:9.58258588330447:4.24859153994197e-05:0.00075992233574242!HEY1#23462;6:3.46295232266204:0.00126789009587212:0.00850463543498965!HMGN3#9324;6:7.01018376287194:2.09275278497296e-05:0.000461594526103044!JUND#3727;5:4.99618852990788:0.000973430860007092:0.00699636264457234!MAX#4149;4:3.6871745765755:0.0136057064395334:0.0480153536135172!NR3C1#2908;5:10.6950166651236:2.48694675006425e-05:0.000538644196661054!RAD21#5885;6:8.87574333896257:5.20411262905738e-06:0.000159434531788244!RXRA#6256;5:14.339012242238:5.91222266390468e-06:0.000177432937584925!SMC3#9126;6:12.8956567242282:5.68588239295796e-07:2.62291462561014e-05!SPI1#6688;6:7.03227729301948:2.05436318006376e-05:0.000454952578801269!TBP#6908;6:3.17723201751119:0.00207411205185266:0.0120176526259883!TCF7L2#6934;5:7.69298325938382:0.000123319885015426:0.00165886211632226!USF1#7391;5:4.54392805514854:0.00152278835596876:0.00970338579066633!USF2#7392;5:9.28014098933542:4.96618200858162e-05:0.000850546216454995!ZBTB7A#51341;5:5.25136379133993:0.000768769248321446:0.00603045602564545
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}}
}}

Revision as of 14:43, 26 November 2012


Full id: C1159_Mast_cerebellum_colon_choriocarcinoma_H9_Melanocyte_occipital



Phase1 CAGE Peaks

Hg19::chr12:108523388..108523427,+p2@WSCD2
Hg19::chr12:63327799..63327812,-p7@PPM1H
Hg19::chr12:63328619..63328637,-p4@PPM1H
Hg19::chr12:63328657..63328672,-p3@PPM1H
Hg19::chr12:63328853..63328870,-p2@PPM1H
Hg19::chr12:63328878..63328888,-p5@PPM1H
Hg19::chr12:63328897..63328942,-p1@PPM1H


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

GO IDGO nameFDR corrected p-value
GO:0015071protein phosphatase type 2C activity0.0369564026814861
GO:0008287protein serine/threonine phosphatase complex0.0369564026814861
GO:0004722protein serine/threonine phosphatase activity0.0369564026814861



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.23e-35114
neural tube3.00e-3356
neural rod3.00e-3356
future spinal cord3.00e-3356
neural keel3.00e-3356
regional part of nervous system3.98e-3153
regional part of brain3.98e-3153
central nervous system1.42e-2781
regional part of forebrain2.56e-2641
forebrain2.56e-2641
anterior neural tube2.56e-2641
future forebrain2.56e-2641
brain6.41e-2668
future brain6.41e-2668
telencephalon1.19e-2234
nervous system1.67e-2289
brain grey matter1.92e-2234
gray matter1.92e-2234
neural plate7.08e-2282
presumptive neural plate7.08e-2282
regional part of telencephalon8.07e-2132
cerebral hemisphere8.26e-2132
neurectoderm7.21e-2086
organ system subdivision2.85e-19223
regional part of cerebral cortex2.71e-1722
neocortex1.30e-1520
pre-chordal neural plate1.61e-1561
cerebral cortex2.55e-1525
pallium2.55e-1525
ecto-epithelium2.13e-14104
structure with developmental contribution from neural crest1.92e-13132
anatomical cluster5.35e-09373
tube8.04e-09192
basal ganglion8.53e-099
nuclear complex of neuraxis8.53e-099
aggregate regional part of brain8.53e-099
collection of basal ganglia8.53e-099
cerebral subcortex8.53e-099
neural nucleus9.27e-099
nucleus of brain9.27e-099
posterior neural tube4.10e-0815
chordal neural plate4.10e-0815
ectoderm-derived structure8.23e-08171
ectoderm8.23e-08171
presumptive ectoderm8.23e-08171
organ8.90e-08503
multi-tissue structure1.08e-07342
anatomical conduit2.92e-07240
telencephalic nucleus3.83e-077
gyrus4.07e-076


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
ATF3#467412.83609972914790.0001232338638827690.00165834576859329
CCNT2#90565.431029923110839.35028339706757e-050.00135799506008391
CHD2#110657.38858773865490.0001498689600820670.00193188895606159
CTCF#1066475.360256373075037.86114662284756e-060.000222315270009092
E2F1#186964.206333612753710.0004135232017007640.00393691428098688
ELF1#199753.041498542005380.009719562269370750.0365631006681847
EP300#203354.838529804445140.001132708190785470.00775679697970256
FOSL2#235549.674400345463820.0003683696889688720.00366785794129279
GATA3#2625519.45465454086141.31487982230667e-065.21156484864844e-05
HDAC2#306659.582585883304474.24859153994197e-050.00075992233574242
HEY1#2346263.462952322662040.001267890095872120.00850463543498965
HMGN3#932467.010183762871942.09275278497296e-050.000461594526103044
JUND#372754.996188529907880.0009734308600070920.00699636264457234
MAX#414943.68717457657550.01360570643953340.0480153536135172
NR3C1#2908510.69501666512362.48694675006425e-050.000538644196661054
RAD21#588568.875743338962575.20411262905738e-060.000159434531788244
RXRA#6256514.3390122422385.91222266390468e-060.000177432937584925
SMC3#9126612.89565672422825.68588239295796e-072.62291462561014e-05
SPI1#668867.032277293019482.05436318006376e-050.000454952578801269
TBP#690863.177232017511190.002074112051852660.0120176526259883
TCF7L2#693457.692983259383820.0001233198850154260.00165886211632226
USF1#739154.543928055148540.001522788355968760.00970338579066633
USF2#739259.280140989335424.96618200858162e-050.000850546216454995
ZBTB7A#5134155.251363791339930.0007687692483214460.00603045602564545



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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