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Coexpression cluster:C3665: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279190996767708!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171624697997416!MEF2C#4208;2:27.5409029950827:0.00172911993836969:0.0106478512525585!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174451287978262!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324706551419654!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381229352927632!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663466675168323!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329829464871413!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457379262353819!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390094420393196!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378092263487783
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279190996767708!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171624697997416!MEF2C#4208;2:27.5409029950827:0.00172911993836969:0.0106478512525585!NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174451287978262!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324706551419654!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381229352927632!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663466675168323!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329829464871413!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457379262353819!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390094420393196!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378092263487783
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}}
}}

Revision as of 16:16, 26 November 2012


Full id: C3665_pineal_eye_retina_caudate_migratory_globus_putamen



Phase1 CAGE Peaks

Hg19::chr17:63133467..63133494,+p2@RGS9
Hg19::chr17:63133526..63133562,+p1@RGS9
Hg19::chr17:63215686..63215697,+p@chr17:63215686..63215697
+


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
adult organism1.26e-35114
central nervous system5.38e-2681
nervous system3.60e-2589
neural tube1.16e-2456
neural rod1.16e-2456
future spinal cord1.16e-2456
neural keel1.16e-2456
regional part of nervous system9.63e-2353
regional part of brain9.63e-2353
brain6.32e-2268
future brain6.32e-2268
regional part of forebrain4.55e-2041
forebrain4.55e-2041
anterior neural tube4.55e-2041
future forebrain4.55e-2041
neural plate3.03e-1782
presumptive neural plate3.03e-1782
neurectoderm2.00e-1586
brain grey matter9.17e-1534
gray matter9.17e-1534
telencephalon1.05e-1434
pre-chordal neural plate3.64e-1461
cerebral hemisphere7.87e-1432
regional part of telencephalon1.35e-1332
organ system subdivision1.77e-12223
regional part of cerebral cortex1.92e-1022
ecto-epithelium3.15e-10104
ectoderm-derived structure7.91e-10171
ectoderm7.91e-10171
presumptive ectoderm7.91e-10171
structure with developmental contribution from neural crest2.05e-09132
neocortex4.64e-0920
cerebral cortex5.35e-0925
pallium5.35e-0925
neural nucleus7.32e-089
nucleus of brain7.32e-089
diencephalon2.59e-077
future diencephalon2.59e-077


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
CTCF#1066435.360256373075030.0064925092527670.0279190996767708
CTCFL#140690319.74647435897440.0001298372005551160.00171624697997416
MEF2C#4208227.54090299508270.001729119938369690.0106478512525585
NANOG#79923219.49651898734180.003427255648501020.0174451287978262
NFYA#4800212.28372046655370.008516011403724430.0324706551419654
NFYB#4801211.17319550235760.01025467135054530.0381229352927632
RAD21#5885310.35503389545630.0009004912073565420.00663466675168323
SMARCB1#6598212.16847718743830.008675002221921740.0329829464871413
SMC3#9126210.02995522995520.0126656379767470.0457379262353819
TFAP2A#7020211.01242291536330.01054990655215560.0390094420393196
ZEB1#6935211.25895467836260.01010222676646330.0378092263487783



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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