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Coexpression cluster:C4664: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!1.75e-07!22;DOID:2994!1.75e-07!22
|ontology_enrichment_disease=DOID:3095!1.75e-07!22;DOID:2994!1.75e-07!22
|ontology_enrichment_uberon=UBERON:0001017!1.12e-29!82;UBERON:0005743!3.92e-29!86;UBERON:0000073!1.64e-27!94;UBERON:0001016!1.64e-27!94;UBERON:0007023!7.60e-22!115;UBERON:0001049!8.40e-22!57;UBERON:0005068!8.40e-22!57;UBERON:0006241!8.40e-22!57;UBERON:0007135!8.40e-22!57;UBERON:0000955!9.47e-22!69;UBERON:0006238!9.47e-22!69;UBERON:0000153!1.17e-20!129;UBERON:0007811!1.17e-20!129;UBERON:0002346!1.49e-20!90;UBERON:0000924!3.19e-20!173;UBERON:0006601!3.19e-20!173;UBERON:0002616!7.10e-20!59;UBERON:0003075!1.04e-19!86;UBERON:0007284!1.04e-19!86;UBERON:0004121!2.35e-19!169;UBERON:0000033!3.31e-19!123;UBERON:0002780!2.75e-18!41;UBERON:0001890!2.75e-18!41;UBERON:0006240!2.75e-18!41;UBERON:0003056!1.15e-17!61;UBERON:0003080!1.67e-17!42;UBERON:0001869!1.40e-16!32;UBERON:0002020!2.69e-16!34;UBERON:0003528!2.69e-16!34;UBERON:0001893!4.58e-16!34;UBERON:0002791!1.33e-15!33;UBERON:0000956!9.11e-13!25;UBERON:0000203!9.11e-13!25;UBERON:0002619!6.46e-11!22;UBERON:0001950!6.58e-10!20;UBERON:0000064!1.33e-07!219;UBERON:0004111!1.33e-07!241;UBERON:0000922!1.70e-07!612;UBERON:0000475!2.11e-07!365
|ontology_enrichment_uberon=UBERON:0001017!1.12e-29!82;UBERON:0005743!3.92e-29!86;UBERON:0000073!1.64e-27!94;UBERON:0001016!1.64e-27!94;UBERON:0007023!7.60e-22!115;UBERON:0001049!8.40e-22!57;UBERON:0005068!8.40e-22!57;UBERON:0006241!8.40e-22!57;UBERON:0007135!8.40e-22!57;UBERON:0000955!9.47e-22!69;UBERON:0006238!9.47e-22!69;UBERON:0000153!1.17e-20!129;UBERON:0007811!1.17e-20!129;UBERON:0002346!1.49e-20!90;UBERON:0000924!3.19e-20!173;UBERON:0006601!3.19e-20!173;UBERON:0002616!7.10e-20!59;UBERON:0003075!1.04e-19!86;UBERON:0007284!1.04e-19!86;UBERON:0004121!2.35e-19!169;UBERON:0000033!3.31e-19!123;UBERON:0002780!2.75e-18!41;UBERON:0001890!2.75e-18!41;UBERON:0006240!2.75e-18!41;UBERON:0003056!1.15e-17!61;UBERON:0003080!1.67e-17!42;UBERON:0001869!1.40e-16!32;UBERON:0002020!2.69e-16!34;UBERON:0003528!2.69e-16!34;UBERON:0001893!4.58e-16!34;UBERON:0002791!1.33e-15!33;UBERON:0000956!9.11e-13!25;UBERON:0000203!9.11e-13!25;UBERON:0002619!6.46e-11!22;UBERON:0001950!6.58e-10!20;UBERON:0000064!1.33e-07!219;UBERON:0004111!1.33e-07!241;UBERON:0000922!1.70e-07!612;UBERON:0000475!2.11e-07!365
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130494635127977!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327607922248298!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168438675699559!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.0039350043661482!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157645593024849!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295999475619952!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486795581484262!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247852294850519!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054561605186041!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617223638770808!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00198078836465192!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331173567650769!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243744268704346
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}}
}}

Revision as of 14:13, 5 September 2012


Full id: C4664_teratocarcinoma_iPS_HES3GFP_Neural_H9_Lens_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr7:148036524..148036538,+p7@CNTNAP2
Hg19::chr7:148036546..148036559,+p4@CNTNAP2
Hg19::chr7:148036562..148036609,+p3@CNTNAP2


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>disease_data<br>


Cell Type
Ontology termp-valuen
neuronal stem cell3.02e-088
neural cell6.54e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.12e-2982
regional part of nervous system1.64e-2794
nervous system1.64e-2794
adult organism7.60e-22115
neural tube8.40e-2257
neural rod8.40e-2257
future spinal cord8.40e-2257
neural keel8.40e-2257
brain9.47e-2269
future brain9.47e-2269
anterior region of body1.17e-20129
craniocervical region1.17e-20129
neurectoderm1.49e-2090
ectoderm3.19e-20173
presumptive ectoderm3.19e-20173
regional part of brain7.10e-2059
neural plate1.04e-1986
presumptive neural plate1.04e-1986
ectoderm-derived structure2.35e-19169
head3.31e-19123
regional part of forebrain2.75e-1841
forebrain2.75e-1841
future forebrain2.75e-1841
pre-chordal neural plate1.15e-1761
anterior neural tube1.67e-1742
cerebral hemisphere1.40e-1632
gray matter2.69e-1634
brain grey matter2.69e-1634
telencephalon4.58e-1634
regional part of telencephalon1.33e-1533
cerebral cortex9.11e-1325
pallium9.11e-1325
regional part of cerebral cortex6.46e-1122
neocortex6.58e-1020
organ part1.33e-07219
anatomical conduit1.33e-07241
embryo1.70e-07612
organism subdivision2.11e-07365
Disease
Ontology termp-valuen
germ cell and embryonal cancer1.75e-0722
germ cell cancer1.75e-0722


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
CTBP2#1488362.71700033932814.049570681927e-060.000130494635127977
E2F1#186934.907389214879320.008460985347239390.0327607922248298
EP300#203336.77394172622320.003216880500103790.0168438675699559
HDAC2#3066313.41562023662630.0004140761399857210.0039350043661482
JUND#372736.994663941871030.002921845042734990.0157645593024849
MYC#460935.22228187160940.007020843755740150.0295999475619952
RFX5#5993312.04791082719510.0005717246050312580.00486795581484262
SP1#666735.69838137814090.005403962701712170.0247852294850519
TAF7#6879311.43306940492390.0006690181981945830.0054561605186041
TCF7L2#6934310.77017656313730.0008003181298398380.00617223638770808
TRIM28#10155318.59052504526250.0001555969297255280.00198078836465192
YY1#752834.911170749853860.008441455341808260.0331173567650769
ZEB1#6935316.88843201754390.0002075486917327580.00243744268704346



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.