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Coexpression cluster:C1094: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;8:5.36025637307503:1.46631949289063e-06:5.66768843515931e-05!E2F1#1869;5:3.06711825929958:0.0112973236497416:0.0414458755323648!ELF1#1997;8:4.25809795880754:9.24826870984006e-06:0.000246586657081181!FOXA1#3169;8:11.0814197493855:4.39110036332964e-09:3.56334212001387e-07!GTF2F1#2962;8:12.7396608767577:1.43868108630934e-09:1.28422576045351e-07!HEY1#23462;8:4.04011104310571:1.4081650274634e-05:0.0003393339808566!IRF1#3659;8:7.6371637535639:8.63190100943299e-08:5.13386736631077e-06!MXI1#4601;8:9.9615716287593:1.02988186499756e-08:7.78291115039651e-07!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127273022807142!RFX5#5993;8:12.0479108271951:2.24894609348582e-09:1.92050434225319e-07!SIN3A#25942;8:5.40888472681514:1.36410592556506e-06:5.35787359007481e-05!SIX5#147912;8:17.086715355459:1.37300676536722e-10:1.46471351959333e-08!SP1#6667;8:5.6983813781409:8.98832477855329e-07:3.86786836237053e-05!SRF#6722;8:13.7971782621678:7.60038632817713e-10:7.190006772903e-08!TAF1#6872;8:3.34304628574529:6.40776711117462e-05:0.00104402619239308!TBP#6908;8:3.70677068709639:2.80450451364125e-05:0.000592554414121339!THAP1#55145;8:31.3691446028513:1.06164581143752e-12:1.49229107537985e-10!USF1#7391;8:6.36149927720796:3.72538670743375e-07:1.83439727646239e-05!YY1#7528;8:4.91117074985386:2.95299276601526e-06:0.000101084107338534!ZNF263#10127;8:8.22184163701068:4.78378813558924e-08:3.10705254410948e-06
|tf_chipseq_enrich=CTCF#10664;8:5.36025637307503:1.46631949289063e-06:5.66768843515931e-05!E2F1#1869;5:3.06711825929958:0.0112973236497416:0.0414458755323648!ELF1#1997;8:4.25809795880754:9.24826870984006e-06:0.000246586657081181!FOXA1#3169;8:11.0814197493855:4.39110036332964e-09:3.56334212001387e-07!GTF2F1#2962;8:12.7396608767577:1.43868108630934e-09:1.28422576045351e-07!HEY1#23462;8:4.04011104310571:1.4081650274634e-05:0.0003393339808566!IRF1#3659;8:7.6371637535639:8.63190100943299e-08:5.13386736631077e-06!MXI1#4601;8:9.9615716287593:1.02988186499756e-08:7.78291115039651e-07!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127273022807142!RFX5#5993;8:12.0479108271951:2.24894609348582e-09:1.92050434225319e-07!SIN3A#25942;8:5.40888472681514:1.36410592556506e-06:5.35787359007481e-05!SIX5#147912;8:17.086715355459:1.37300676536722e-10:1.46471351959333e-08!SP1#6667;8:5.6983813781409:8.98832477855329e-07:3.86786836237053e-05!SRF#6722;8:13.7971782621678:7.60038632817713e-10:7.190006772903e-08!TAF1#6872;8:3.34304628574529:6.40776711117462e-05:0.00104402619239308!TBP#6908;8:3.70677068709639:2.80450451364125e-05:0.000592554414121339!THAP1#55145;8:31.3691446028513:1.06164581143752e-12:1.49229107537985e-10!USF1#7391;8:6.36149927720796:3.72538670743375e-07:1.83439727646239e-05!YY1#7528;8:4.91117074985386:2.95299276601526e-06:0.000101084107338534!ZNF263#10127;8:8.22184163701068:4.78378813558924e-08:3.10705254410948e-06
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}}
}}

Revision as of 14:40, 26 November 2012


Full id: C1094_salivary_submaxillary_thyroid_parotid_skeletal_Preadipocyte_Adipocyte



Phase1 CAGE Peaks

Hg19::chr8:120885918..120885931,+p8@DEPTOR
Hg19::chr8:120885933..120885947,+p4@DEPTOR
Hg19::chr8:120885949..120885976,+p1@DEPTOR
Hg19::chr8:120885982..120885993,+p6@DEPTOR
Hg19::chr8:120886006..120886025,+p2@DEPTOR
Hg19::chr8:120886031..120886042,+p5@DEPTOR
Hg19::chr8:120886054..120886078,+p3@DEPTOR
Hg19::chr8:120886102..120886125,+p7@DEPTOR


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.49e-30114
neural tube4.46e-1656
neural rod4.46e-1656
future spinal cord4.46e-1656
neural keel4.46e-1656
regional part of nervous system1.03e-1453
regional part of brain1.03e-1453
central nervous system1.28e-1481
brain4.96e-1468
future brain4.96e-1468
nervous system3.24e-1389
regional part of forebrain1.03e-1241
forebrain1.03e-1241
anterior neural tube1.03e-1241
future forebrain1.03e-1241
organ system subdivision3.15e-12223
telencephalon6.63e-1034
brain grey matter8.66e-1034
gray matter8.66e-1034
regional part of cerebral cortex2.43e-0922
regional part of telencephalon5.39e-0932
cerebral hemisphere5.57e-0932
structure with developmental contribution from neural crest5.80e-09132
neocortex1.14e-0820
neural plate3.13e-0882
presumptive neural plate3.13e-0882
tube2.22e-07192
neurectoderm2.25e-0786
organ4.41e-07503


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#1066485.360256373075031.46631949289063e-065.66768843515931e-05
E2F1#186953.067118259299580.01129732364974160.0414458755323648
ELF1#199784.258097958807549.24826870984006e-060.000246586657081181
FOXA1#3169811.08141974938554.39110036332964e-093.56334212001387e-07
GTF2F1#2962812.73966087675771.43868108630934e-091.28422576045351e-07
HEY1#2346284.040111043105711.4081650274634e-050.0003393339808566
IRF1#365987.63716375356398.63190100943299e-085.13386736631077e-06
MXI1#460189.96157162875931.02988186499756e-087.78291115039651e-07
POLR2A#543082.147453176558070.002210725788971910.0127273022807142
RFX5#5993812.04791082719512.24894609348582e-091.92050434225319e-07
SIN3A#2594285.408884726815141.36410592556506e-065.35787359007481e-05
SIX5#147912817.0867153554591.37300676536722e-101.46471351959333e-08
SP1#666785.69838137814098.98832477855329e-073.86786836237053e-05
SRF#6722813.79717826216787.60038632817713e-107.190006772903e-08
TAF1#687283.343046285745296.40776711117462e-050.00104402619239308
TBP#690883.706770687096392.80450451364125e-050.000592554414121339
THAP1#55145831.36914460285131.06164581143752e-121.49229107537985e-10
USF1#739186.361499277207963.72538670743375e-071.83439727646239e-05
YY1#752884.911170749853862.95299276601526e-060.000101084107338534
ZNF263#1012788.221841637010684.78378813558924e-083.10705254410948e-06



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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