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Coexpression cluster:C4701: Difference between revisions

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|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285853597184222!CTBP2#1488;2:41.8113335595521:0.000754340825991485:0.00593644800887082!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281322314172399!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327741580253814!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460819962945232!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330141951337421!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457822505331215!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390357007865295!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191197828711203
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285853597184222!CTBP2#1488;2:41.8113335595521:0.000754340825991485:0.00593644800887082!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281322314172399!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327741580253814!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460819962945232!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330141951337421!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457822505331215!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390357007865295!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191197828711203
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}}
}}

Revision as of 16:54, 26 November 2012


Full id: C4701_Mast_optic_mature_small_substantia_adrenal_serous



Phase1 CAGE Peaks

Hg19::chr7:79764112..79764209,+p1@GNAI1
Hg19::chr7:79764242..79764256,+p3@GNAI1
Hg19::chr7:79764393..79764437,+p2@GNAI1


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
central nervous system3.87e-2381
nervous system1.99e-2289
neural tube1.05e-2156
neural rod1.05e-2156
future spinal cord1.05e-2156
neural keel1.05e-2156
regional part of nervous system5.64e-2053
regional part of brain5.64e-2053
organ system subdivision6.11e-20223
brain1.08e-1968
future brain1.08e-1968
ectoderm-derived structure3.60e-18171
ectoderm3.60e-18171
presumptive ectoderm3.60e-18171
neural plate2.12e-1782
presumptive neural plate2.12e-1782
ecto-epithelium2.61e-17104
telencephalon4.11e-1734
brain grey matter4.35e-1734
gray matter4.35e-1734
regional part of forebrain6.23e-1741
forebrain6.23e-1741
anterior neural tube6.23e-1741
future forebrain6.23e-1741
neurectoderm7.56e-1686
regional part of telencephalon8.27e-1632
cerebral hemisphere8.85e-1632
structure with developmental contribution from neural crest3.13e-15132
pre-chordal neural plate4.67e-1461
multi-cellular organism4.75e-14656
regional part of cerebral cortex1.64e-1322
organ2.24e-13503
anatomical system2.32e-13624
anatomical group4.50e-13625
neocortex2.00e-1220
cerebral cortex4.09e-1225
pallium4.09e-1225
anatomical cluster1.94e-11373
adult organism3.28e-11114
organ part3.56e-10218
multi-tissue structure4.56e-09342
embryonic structure1.56e-07564
developing anatomical structure7.39e-07581
germ layer8.83e-07560
germ layer / neural crest8.83e-07560
embryonic tissue8.83e-07560
presumptive structure8.83e-07560
germ layer / neural crest derived structure8.83e-07560
epiblast (generic)8.83e-07560


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285853597184222
CTBP2#1488241.81133355955210.0007543408259914850.00593644800887082
CTCF#1066435.360256373075030.0064925092527670.0281322314172399
E2F1#186934.907389214879320.008460985347239390.0327741580253814
NR3C1#290829.982015554115360.01278474365547170.0460819962945232
SMARCB1#6598212.16847718743830.008675002221921740.0330141951337421
SMC3#9126210.02995522995520.0126656379767470.0457822505331215
TFAP2A#7020211.01242291536330.01054990655215560.0390357007865295
USF1#739136.361499277207960.00388404057290560.0191197828711203



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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