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Coexpression cluster:C257: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0031114!regulation of microtubule depolymerization!0.0132628609623142!4131;4133$GO:0007026!negative regulation of microtubule depolymerization!0.0132628609623142!4131;4133$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.0132628609623142!4131;4133$GO:0007019!microtubule depolymerization!0.0132628609623142!4131;4133$GO:0031110!regulation of microtubule polymerization or depolymerization!0.015800510186969!4131;4133$GO:0031109!microtubule polymerization or depolymerization!0.015800510186969!4131;4133$GO:0044464!cell part!0.015800510186969!5798;9628;83873;1607;2104;166336;22864;84871;8941;8997;29970;81849;1740;4131;11281;4133;9378;55531;9892;2566;2692;26045;460;79751;8499;5521$GO:0051261!protein depolymerization!0.0261605814414009!4131;4133$GO:0005515!protein binding!0.0261605814414009!5798;1740;4131;1607;9378;4133;2104;9892;2566;26045;460;8997;79751;29970;8499$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0261605814414009!4131;4133$GO:0007402!ganglion mother cell fate determination!0.0261605814414009!11281$GO:0016533!cyclin-dependent protein kinase 5 activator complex!0.0410943584387354!8941$GO:0048664!neuron fate determination!0.0410943584387354!11281$GO:0016534!cyclin-dependent protein kinase 5 activator activity!0.0410943584387354!8941
|gostat_on_coexpression_clusters=GO:0031114!regulation of microtubule depolymerization!0.0132628609623142!4131;4133$GO:0007026!negative regulation of microtubule depolymerization!0.0132628609623142!4131;4133$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.0132628609623142!4131;4133$GO:0007019!microtubule depolymerization!0.0132628609623142!4131;4133$GO:0031110!regulation of microtubule polymerization or depolymerization!0.015800510186969!4131;4133$GO:0031109!microtubule polymerization or depolymerization!0.015800510186969!4131;4133$GO:0044464!cell part!0.015800510186969!5798;9628;83873;1607;2104;166336;22864;84871;8941;8997;29970;81849;1740;4131;11281;4133;9378;55531;9892;2566;2692;26045;460;79751;8499;5521$GO:0051261!protein depolymerization!0.0261605814414009!4131;4133$GO:0005515!protein binding!0.0261605814414009!5798;1740;4131;1607;9378;4133;2104;9892;2566;26045;460;8997;79751;29970;8499$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0261605814414009!4131;4133$GO:0007402!ganglion mother cell fate determination!0.0261605814414009!11281$GO:0016533!cyclin-dependent protein kinase 5 activator complex!0.0410943584387354!8941$GO:0048664!neuron fate determination!0.0410943584387354!11281$GO:0016534!cyclin-dependent protein kinase 5 activator activity!0.0410943584387354!8941
|id=C257
|id=C257
|ontology_enrichment_celltype=CL:0000055!1.29e-11!180;CL:0002319!6.65e-09!25
|ontology_enrichment_celltype=
|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:0001049!9.43e-131!56;UBERON:0005068!9.43e-131!56;UBERON:0006241!9.43e-131!56;UBERON:0007135!9.43e-131!56;UBERON:0000073!3.49e-122!53;UBERON:0002616!3.49e-122!53;UBERON:0001017!5.46e-114!81;UBERON:0000955!6.41e-105!68;UBERON:0006238!6.41e-105!68;UBERON:0002780!7.22e-104!41;UBERON:0001890!7.22e-104!41;UBERON:0003080!7.22e-104!41;UBERON:0006240!7.22e-104!41;UBERON:0001016!1.35e-101!89;UBERON:0003075!2.45e-93!82;UBERON:0007284!2.45e-93!82;UBERON:0002346!1.76e-88!86;UBERON:0001893!6.17e-83!34;UBERON:0003528!7.77e-83!34;UBERON:0002020!7.77e-83!34;UBERON:0001869!1.09e-77!32;UBERON:0002791!4.80e-77!32;UBERON:0003056!1.77e-74!61;UBERON:0010371!3.35e-71!104;UBERON:0002619!1.69e-65!22;UBERON:0007023!3.93e-62!114;UBERON:0010314!7.47e-61!132;UBERON:0001950!1.17e-59!20;UBERON:0000956!3.25e-57!25;UBERON:0000203!3.25e-57!25;UBERON:0004121!1.17e-51!171;UBERON:0000924!1.17e-51!171;UBERON:0006601!1.17e-51!171;UBERON:0011216!1.00e-36!223;UBERON:0000025!1.51e-31!192;UBERON:0002420!4.06e-27!9;UBERON:0007245!4.06e-27!9;UBERON:0010009!4.06e-27!9;UBERON:0010011!4.06e-27!9;UBERON:0000454!4.06e-27!9;UBERON:0000125!1.13e-26!9;UBERON:0002308!1.13e-26!9;UBERON:0003076!1.18e-26!15;UBERON:0003057!1.18e-26!15;UBERON:0004111!7.79e-23!240;UBERON:0001894!1.05e-21!7;UBERON:0006222!1.05e-21!7;UBERON:0009663!4.39e-21!7;UBERON:0000200!1.03e-20!6;UBERON:0000477!1.11e-19!373;UBERON:0004733!3.90e-19!12;UBERON:0002028!3.90e-19!12;UBERON:0007277!3.90e-19!12;UBERON:0002298!4.73e-18!6;UBERON:0004732!1.56e-17!13;UBERON:0000483!3.73e-17!306;UBERON:0000119!7.21e-17!309;UBERON:0001871!7.42e-17!6;UBERON:0001872!8.02e-17!5;UBERON:0000349!1.39e-16!5;UBERON:0002021!1.58e-16!5;UBERON:0000064!1.56e-14!218;UBERON:0002784!1.21e-13!4;UBERON:0003296!1.78e-13!4;UBERON:0010133!1.78e-13!4;UBERON:0000369!2.46e-13!4;UBERON:0002435!2.46e-13!4;UBERON:0000204!2.46e-13!4;UBERON:0010082!2.46e-13!4;UBERON:0000481!3.27e-13!342;UBERON:0002680!6.04e-12!9;UBERON:0001895!6.04e-12!9;UBERON:0010092!6.04e-12!9;UBERON:0001870!2.28e-11!3;UBERON:0000988!3.20e-10!3;UBERON:0005383!3.30e-10!3;UBERON:0005382!3.30e-10!3;UBERON:0000062!9.06e-10!503;UBERON:0002240!1.33e-09!3;UBERON:0005174!1.33e-09!3;UBERON:0001137!1.33e-09!3;UBERON:0001896!1.51e-09!3;UBERON:0005290!1.51e-09!3;UBERON:0010096!1.51e-09!3;UBERON:0000922!1.14e-08!592;UBERON:0000923!1.27e-08!560;UBERON:0010316!1.27e-08!560;UBERON:0005291!1.27e-08!560;UBERON:0006598!1.27e-08!560;UBERON:0010317!1.27e-08!560;UBERON:0002532!1.27e-08!560;UBERON:0002050!1.83e-08!564;UBERON:0001905!3.06e-08!2;UBERON:0002757!3.06e-08!2;UBERON:0010134!3.06e-08!2;UBERON:0005408!3.06e-08!2;UBERON:0001899!3.06e-08!2;UBERON:0002702!4.16e-08!2;UBERON:0002771!5.45e-08!2;UBERON:0005423!8.08e-08!581;UBERON:0001876!9.58e-08!2;UBERON:0001954!2.16e-07!2;UBERON:0003022!2.16e-07!2;UBERON:0002421!2.16e-07!2;UBERON:0002600!2.16e-07!2;UBERON:0002148!2.78e-07!2;UBERON:0006331!2.78e-07!2;UBERON:0009662!2.78e-07!2;UBERON:0001873!3.16e-07!2;UBERON:0010122!3.16e-07!2;UBERON:0001897!4.19e-07!2;UBERON:0010225!4.19e-07!2;UBERON:0001875!5.37e-07!2;UBERON:0006514!5.37e-07!2;UBERON:0002360!5.54e-07!2;UBERON:0000094!5.54e-07!2;UBERON:0010743!5.54e-07!2;UBERON:0000007!6.08e-07!2;UBERON:0000467!6.31e-07!624;UBERON:0000480!6.82e-07!625
|tf_chipseq_enrich=CTBP2#1488;4:4.91898041877083:0.00889265822188434:0.0337343479000174!RAD21#5885;11:2.23343868333372:0.00845143374874908:0.0328004195200894
|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, 19 October 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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube9.43e-13156
neural rod9.43e-13156
future spinal cord9.43e-13156
neural keel9.43e-13156
regional part of nervous system3.49e-12253
regional part of brain3.49e-12253
central nervous system5.46e-11481
brain6.41e-10568
future brain6.41e-10568
regional part of forebrain7.22e-10441
forebrain7.22e-10441
anterior neural tube7.22e-10441
future forebrain7.22e-10441
nervous system1.35e-10189
neural plate2.45e-9382
presumptive neural plate2.45e-9382
neurectoderm1.76e-8886
telencephalon6.17e-8334
brain grey matter7.77e-8334
gray matter7.77e-8334
cerebral hemisphere1.09e-7732
regional part of telencephalon4.80e-7732
pre-chordal neural plate1.77e-7461
ecto-epithelium3.35e-71104
regional part of cerebral cortex1.69e-6522
adult organism3.93e-62114
structure with developmental contribution from neural crest7.47e-61132
neocortex1.17e-5920
cerebral cortex3.25e-5725
pallium3.25e-5725
ectoderm-derived structure1.17e-51171
ectoderm1.17e-51171
presumptive ectoderm1.17e-51171
organ system subdivision1.00e-36223
tube1.51e-31192
basal ganglion4.06e-279
nuclear complex of neuraxis4.06e-279
aggregate regional part of brain4.06e-279
collection of basal ganglia4.06e-279
cerebral subcortex4.06e-279
neural nucleus1.13e-269
nucleus of brain1.13e-269
posterior neural tube1.18e-2615
chordal neural plate1.18e-2615
anatomical conduit7.79e-23240
diencephalon1.05e-217
future diencephalon1.05e-217
telencephalic nucleus4.39e-217
gyrus1.03e-206
anatomical cluster1.11e-19373
segmental subdivision of hindbrain3.90e-1912
hindbrain3.90e-1912
presumptive hindbrain3.90e-1912
brainstem4.73e-186
segmental subdivision of nervous system1.56e-1713
epithelium3.73e-17306
cell layer7.21e-17309
temporal lobe7.42e-176
parietal lobe8.02e-175
limbic system1.39e-165
occipital lobe1.58e-165
organ part1.56e-14218
regional part of diencephalon1.21e-134
gland of diencephalon1.78e-134
neuroendocrine gland1.78e-134
corpus striatum2.46e-134
striatum2.46e-134
ventral part of telencephalon2.46e-134
future corpus striatum2.46e-134
multi-tissue structure3.27e-13342
regional part of metencephalon6.04e-129
metencephalon6.04e-129
future metencephalon6.04e-129
frontal cortex2.28e-113
pons3.20e-103
caudate-putamen3.30e-103
dorsal striatum3.30e-103
organ9.06e-10503
spinal cord1.33e-093
dorsal region element1.33e-093
dorsum1.33e-093
medulla oblongata1.51e-093
myelencephalon1.51e-093
future myelencephalon1.51e-093
embryo1.14e-08592
germ layer1.27e-08560
germ layer / neural crest1.27e-08560
embryonic tissue1.27e-08560
presumptive structure1.27e-08560
germ layer / neural crest derived structure1.27e-08560
epiblast (generic)1.27e-08560
embryonic structure1.83e-08564
pineal body3.06e-082
regional part of epithalamus3.06e-082
secretory circumventricular organ3.06e-082
circumventricular organ3.06e-082
epithalamus3.06e-082
middle frontal gyrus4.16e-082
middle temporal gyrus5.45e-082
developing anatomical structure8.08e-08581


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