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Coexpression cluster:C257: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!3.81e-42!94;UBERON:0001016!3.81e-42!94;UBERON:0005743!1.51e-41!86;UBERON:0001017!9.40e-41!82;UBERON:0007023!6.81e-34!115;UBERON:0000955!1.17e-33!69;UBERON:0006238!1.17e-33!69;UBERON:0001049!1.30e-33!57;UBERON:0005068!1.30e-33!57;UBERON:0006241!1.30e-33!57;UBERON:0007135!1.30e-33!57;UBERON:0002346!4.40e-32!90;UBERON:0003075!9.50e-32!86;UBERON:0007284!9.50e-32!86;UBERON:0002616!2.01e-29!59;UBERON:0002780!4.98e-27!41;UBERON:0001890!4.98e-27!41;UBERON:0006240!4.98e-27!41;UBERON:0003080!8.38e-27!42;UBERON:0000924!1.52e-25!173;UBERON:0006601!1.52e-25!173;UBERON:0004121!6.29e-25!169;UBERON:0001893!1.15e-22!34;UBERON:0002020!1.17e-22!34;UBERON:0003528!1.17e-22!34;UBERON:0003056!1.38e-22!61;UBERON:0000033!2.32e-22!123;UBERON:0000475!5.59e-22!365;UBERON:0002791!5.62e-22!33;UBERON:0000153!9.72e-22!129;UBERON:0007811!9.72e-22!129;UBERON:0001869!1.32e-21!32;UBERON:0000956!2.68e-17!25;UBERON:0000203!2.68e-17!25;UBERON:0000025!8.95e-17!194;UBERON:0002619!4.98e-16!22;UBERON:0001950!8.35e-15!20;UBERON:0000483!3.38e-14!309;UBERON:0000119!1.10e-13!312;UBERON:0000481!1.83e-13!347;UBERON:0004111!2.06e-12!241;UBERON:0000468!9.98e-11!659;UBERON:0000477!1.03e-09!286;UBERON:0003076!5.44e-08!15;UBERON:0003057!5.44e-08!15;UBERON:0000922!1.27e-07!612;UBERON:0000480!4.20e-07!626;UBERON:0000467!4.23e-07!625;UBERON:0004732!7.07e-07!13;UBERON:0002420!7.16e-07!9;UBERON:0007245!7.16e-07!9;UBERON:0010009!7.16e-07!9;UBERON:0010011!7.16e-07!9;UBERON:0000454!7.16e-07!9;UBERON:0002308!8.32e-07!9;UBERON:0000125!8.32e-07!9
|ontology_enrichment_uberon=UBERON:0000073!3.81e-42!94;UBERON:0001016!3.81e-42!94;UBERON:0005743!1.51e-41!86;UBERON:0001017!9.40e-41!82;UBERON:0007023!6.81e-34!115;UBERON:0000955!1.17e-33!69;UBERON:0006238!1.17e-33!69;UBERON:0001049!1.30e-33!57;UBERON:0005068!1.30e-33!57;UBERON:0006241!1.30e-33!57;UBERON:0007135!1.30e-33!57;UBERON:0002346!4.40e-32!90;UBERON:0003075!9.50e-32!86;UBERON:0007284!9.50e-32!86;UBERON:0002616!2.01e-29!59;UBERON:0002780!4.98e-27!41;UBERON:0001890!4.98e-27!41;UBERON:0006240!4.98e-27!41;UBERON:0003080!8.38e-27!42;UBERON:0000924!1.52e-25!173;UBERON:0006601!1.52e-25!173;UBERON:0004121!6.29e-25!169;UBERON:0001893!1.15e-22!34;UBERON:0002020!1.17e-22!34;UBERON:0003528!1.17e-22!34;UBERON:0003056!1.38e-22!61;UBERON:0000033!2.32e-22!123;UBERON:0000475!5.59e-22!365;UBERON:0002791!5.62e-22!33;UBERON:0000153!9.72e-22!129;UBERON:0007811!9.72e-22!129;UBERON:0001869!1.32e-21!32;UBERON:0000956!2.68e-17!25;UBERON:0000203!2.68e-17!25;UBERON:0000025!8.95e-17!194;UBERON:0002619!4.98e-16!22;UBERON:0001950!8.35e-15!20;UBERON:0000483!3.38e-14!309;UBERON:0000119!1.10e-13!312;UBERON:0000481!1.83e-13!347;UBERON:0004111!2.06e-12!241;UBERON:0000468!9.98e-11!659;UBERON:0000477!1.03e-09!286;UBERON:0003076!5.44e-08!15;UBERON:0003057!5.44e-08!15;UBERON:0000922!1.27e-07!612;UBERON:0000480!4.20e-07!626;UBERON:0000467!4.23e-07!625;UBERON:0004732!7.07e-07!13;UBERON:0002420!7.16e-07!9;UBERON:0007245!7.16e-07!9;UBERON:0010009!7.16e-07!9;UBERON:0010011!7.16e-07!9;UBERON:0000454!7.16e-07!9;UBERON:0002308!8.32e-07!9;UBERON:0000125!8.32e-07!9
|tf_chipseq_enrich=CTBP2#1488;4:4.91898041877083:0.00889265822188434:0.0337343479000174!RAD21#5885;11:2.23343868333372:0.00845143374874908:0.0328004195200894
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}}

Revision as of 14:10, 5 September 2012


Full id: C257_pineal_insula_frontal_occipital_temporal_medial_paracentral



Phase1 CAGE Peaks

Hg19::chr11:107462012..107462019,+p5@ELMOD1
Hg19::chr11:73309049..73309054,-p5@FAM168A
Hg19::chr11:74952393..74952412,+p@chr11:74952393..74952412
+
Hg19::chr11:795358..795372,-p9@SLC25A22
Hg19::chr11:84148843..84148867,-p21@DLG2
Hg19::chr11:84148869..84148881,-p35@DLG2
Hg19::chr12:130303241..130303258,-p@chr12:130303241..130303258
-
Hg19::chr12:57735443..57735464,-p18@R3HDM2
Hg19::chr12:57735499..57735520,-p10@R3HDM2
Hg19::chr12:57736218..57736229,-p@chr12:57736218..57736229
-
Hg19::chr12:57736233..57736245,-p@chr12:57736233..57736245
-
Hg19::chr12:81992111..81992164,-p1@PPFIA2
Hg19::chr14:72399114..72399238,+p1@RGS6
Hg19::chr19:46580848..46580895,-p1@ENST00000366172
p1@uc002pdz.1
Hg19::chr1:110082487..110082535,+p1@GPR61
Hg19::chr1:177133980..177133992,-p7@ASTN1
Hg19::chr1:204640767..204640771,-p@chr1:204640767..204640771
-
Hg19::chr1:217262933..217262968,-p3@ESRRG
Hg19::chr1:217262969..217262995,-p7@ESRRG
Hg19::chr1:50489619..50489650,-p2@AGBL4
Hg19::chr1:77334255..77334267,+p7@ST6GALNAC5
Hg19::chr2:210444126..210444140,+p14@MAP2
Hg19::chr2:210444142..210444194,+p6@MAP2
Hg19::chr2:215275814..215275834,+p1@VWC2L
Hg19::chr2:219824420..219824431,+p3@CDK5R2
Hg19::chr2:220174072..220174149,-p1@PTPRN
Hg19::chr2:48667898..48667981,+p1@PPP1R21
Hg19::chr2:50574708..50574743,-p17@NRXN1
Hg19::chr3:118753716..118753731,-p7@IGSF11
Hg19::chr3:124103560..124103577,+p8@KALRN
Hg19::chr3:127347780..127347822,-p@chr3:127347780..127347822
-
Hg19::chr3:158991085..158991096,+p26@SCHIP1
Hg19::chr3:64211112..64211152,-p4@PRICKLE2
Hg19::chr3:64211156..64211179,-p11@PRICKLE2
Hg19::chr5:138210931..138210938,-p6@LRRTM2
Hg19::chr5:138210954..138210965,-p4@LRRTM2
Hg19::chr5:138210977..138210999,-p2@LRRTM2
Hg19::chr5:146435485..146435499,-p8@PPP2R2B
Hg19::chr5:146435501..146435530,-p3@PPP2R2B
Hg19::chr5:146435572..146435581,-p24@PPP2R2B
Hg19::chr5:161494848..161494859,+p9@GABRG2
Hg19::chr5:161494946..161494955,+p10@GABRG2
Hg19::chr5:161494956..161494967,+p8@GABRG2
Hg19::chr5:71403323..71403340,+p3@MAP1B
Hg19::chr5:74162339..74162405,-p2@FAM169A
Hg19::chr6:84418484..84418496,-p3@SNAP91
Hg19::chr7:14942830..14942867,-p4@DGKB
Hg19::chr7:14942923..14942941,-p6@DGKB
Hg19::chr7:31023427..31023491,+p1@GHRHR
Hg19::chr7:39125494..39125510,+p4@POU6F2
Hg19::chr7:39125511..39125560,+p1@POU6F2


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


GO IDGO nameFDR corrected p-value
GO:0031114regulation of microtubule depolymerization0.0132628609623142
GO:0007026negative regulation of microtubule depolymerization0.0132628609623142
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0132628609623142
GO:0007019microtubule depolymerization0.0132628609623142
GO:0031110regulation of microtubule polymerization or depolymerization0.015800510186969
GO:0031109microtubule polymerization or depolymerization0.015800510186969
GO:0044464cell part0.015800510186969
GO:0051261protein depolymerization0.0261605814414009
GO:0005515protein binding0.0261605814414009
GO:0051129negative regulation of cellular component organization and biogenesis0.0261605814414009
GO:0007402ganglion mother cell fate determination0.0261605814414009
GO:0016533cyclin-dependent protein kinase 5 activator complex0.0410943584387354
GO:0048664neuron fate determination0.0410943584387354
GO:0016534cyclin-dependent protein kinase 5 activator activity0.0410943584387354



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
non-terminally differentiated cell1.29e-11180
neural cell6.65e-0925
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.81e-4294
nervous system3.81e-4294
central nervous system9.40e-4182
adult organism6.81e-34115
brain1.17e-3369
future brain1.17e-3369
neural tube1.30e-3357
neural rod1.30e-3357
future spinal cord1.30e-3357
neural keel1.30e-3357
neurectoderm4.40e-3290
neural plate9.50e-3286
presumptive neural plate9.50e-3286
regional part of brain2.01e-2959
regional part of forebrain4.98e-2741
forebrain4.98e-2741
future forebrain4.98e-2741
anterior neural tube8.38e-2742
ectoderm1.52e-25173
presumptive ectoderm1.52e-25173
ectoderm-derived structure6.29e-25169
telencephalon1.15e-2234
gray matter1.17e-2234
brain grey matter1.17e-2234
pre-chordal neural plate1.38e-2261
head2.32e-22123
organism subdivision5.59e-22365
regional part of telencephalon5.62e-2233
anterior region of body9.72e-22129
craniocervical region9.72e-22129
cerebral hemisphere1.32e-2132
cerebral cortex2.68e-1725
pallium2.68e-1725
tube8.95e-17194
regional part of cerebral cortex4.98e-1622
neocortex8.35e-1520
epithelium3.38e-14309
cell layer1.10e-13312
multi-tissue structure1.83e-13347
anatomical conduit2.06e-12241
multi-cellular organism9.98e-11659
anatomical cluster1.03e-09286
posterior neural tube5.44e-0815
chordal neural plate5.44e-0815
embryo1.27e-07612
anatomical group4.20e-07626
anatomical system4.23e-07625
segmental subdivision of nervous system7.07e-0713
basal ganglion7.16e-079
nuclear complex of neuraxis7.16e-079
aggregate regional part of brain7.16e-079
collection of basal ganglia7.16e-079
cerebral subcortex7.16e-079
nucleus of brain8.32e-079
neural nucleus8.32e-079


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#148844.918980418770830.008892658221884340.0337343479000174
RAD21#5885112.233438683333720.008451433748749080.0328004195200894



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


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