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Coexpression cluster:C2506: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512211908782586!CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00440939425310586!E2F4#1874;3:9.50104523646333:0.00185075103472827:0.0109283986722443!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466221995448671!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284916129926644!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.00079391510599531!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.043494736779617!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172684301252579!SETDB1#9869;3:30.2400196335079:5.98509618524166e-05:0.000984684090249612!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765709201612016!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346600895032292!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.0097666125485081
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512211908782586!CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00440939425310586!E2F4#1874;3:9.50104523646333:0.00185075103472827:0.0109283986722443!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466221995448671!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284916129926644!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.00079391510599531!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.043494736779617!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172684301252579!SETDB1#9869;3:30.2400196335079:5.98509618524166e-05:0.000984684090249612!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765709201612016!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346600895032292!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.0097666125485081
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}}
}}

Revision as of 15:32, 26 November 2012


Full id: C2506_putamen_caudate_nucleus_temporal_amygdala_insula_frontal



Phase1 CAGE Peaks

Hg19::chr19:7989858..7989889,-p2@CTXN1
Hg19::chr19:7990008..7990044,-p4@CTXN1
Hg19::chr19:7990260..7990308,+p@chr19:7990260..7990308
+
Hg19::chr19:7990991..7991059,-p1@CTXN1


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
embryonic cell4.76e-15250
epithelial cell1.55e-14253
neurectodermal cell2.19e-1159
lining cell1.18e-0958
barrier cell1.18e-0958
ectodermal cell3.43e-0972
mesodermal cell1.80e-08121
neural cell6.60e-0825
squamous epithelial cell6.56e-0763
Uber Anatomy
Ontology termp-valuen
anatomical cluster1.67e-24373
central nervous system1.24e-2381
nervous system2.41e-2389
pre-chordal neural plate3.54e-1961
brain3.88e-1968
future brain3.88e-1968
cerebral hemisphere5.79e-1932
brain grey matter7.83e-1934
gray matter7.83e-1934
telencephalon9.07e-1934
neurectoderm1.09e-1886
regional part of telencephalon3.11e-1832
regional part of nervous system4.58e-1853
regional part of brain4.58e-1853
neural plate7.85e-1882
presumptive neural plate7.85e-1882
regional part of forebrain8.27e-1841
forebrain8.27e-1841
anterior neural tube8.27e-1841
future forebrain8.27e-1841
neural tube1.83e-1756
neural rod1.83e-1756
future spinal cord1.83e-1756
neural keel1.83e-1756
tube3.87e-16192
cell layer9.12e-16309
epithelium1.45e-15306
anatomical conduit7.95e-15240
cerebral cortex1.36e-1425
pallium1.36e-1425
ectoderm-derived structure1.52e-14171
ectoderm1.52e-14171
presumptive ectoderm1.52e-14171
ecto-epithelium6.51e-14104
organ system subdivision1.06e-13223
regional part of cerebral cortex2.83e-1322
structure with developmental contribution from neural crest7.32e-13132
multi-tissue structure1.92e-12342
neocortex5.11e-1220
embryo3.86e-09592
multi-cellular organism1.28e-08656
organ part3.44e-08218
developing anatomical structure1.49e-07581


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#90546.336201576962630.0006203100587215640.00512211908782586
CTCFL#140690314.80985576923080.0004996291767563340.00440939425310586
E2F4#187439.501045236463330.001850751034728270.0109283986722443
MAX#414934.839416631755340.01315737137836840.0466221995448671
NANOG#79923214.62238924050630.006698757715363760.0284916129926644
NRF1#4899412.21027944771094.49717228915276e-050.00079391510599531
PAX5#507935.002174148383370.01196533174786410.043494736779617
RAD21#588537.766275421592250.0033411193858720.0172684301252579
SETDB1#9869330.24001963350795.98509618524166e-050.000984684090249612
SMC3#9126311.28369963369960.001115802366868050.00765709201612016
ZBTB7A#5134147.35190930787590.000342223540015990.00346600895032292
ZNF143#7702310.12565741417090.001534861610688180.0097666125485081



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.