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Coexpression cluster:C1850: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!1.67e-47!114;UBERON:0000073!3.64e-37!53;UBERON:0002616!3.64e-37!53;UBERON:0001049!2.67e-36!56;UBERON:0005068!2.67e-36!56;UBERON:0006241!2.67e-36!56;UBERON:0007135!2.67e-36!56;UBERON:0001016!1.14e-33!89;UBERON:0002346!6.47e-33!86;UBERON:0000955!3.33e-32!68;UBERON:0006238!3.33e-32!68;UBERON:0003075!5.63e-32!82;UBERON:0007284!5.63e-32!82;UBERON:0001017!6.33e-32!81;UBERON:0002780!1.67e-28!41;UBERON:0001890!1.67e-28!41;UBERON:0003080!1.67e-28!41;UBERON:0006240!1.67e-28!41;UBERON:0010371!4.40e-26!104;UBERON:0004121!9.82e-25!171;UBERON:0000924!9.82e-25!171;UBERON:0006601!9.82e-25!171;UBERON:0003056!1.47e-22!61;UBERON:0011216!1.02e-21!223;UBERON:0010314!4.11e-21!132;UBERON:0003528!1.71e-20!34;UBERON:0002020!1.71e-20!34;UBERON:0001869!4.08e-20!32;UBERON:0001950!4.43e-20!20;UBERON:0001893!4.45e-20!34;UBERON:0002619!5.41e-20!22;UBERON:0002791!3.43e-18!32;UBERON:0000956!5.37e-17!25;UBERON:0000203!5.37e-17!25;UBERON:0000477!1.86e-14!373;UBERON:0000481!1.44e-11!342;UBERON:0001894!7.48e-11!7;UBERON:0006222!7.48e-11!7;UBERON:0000064!3.50e-10!218;UBERON:0004111!4.15e-10!240;UBERON:0004733!9.46e-10!12;UBERON:0002028!9.46e-10!12;UBERON:0007277!9.46e-10!12;UBERON:0000025!1.12e-09!192;UBERON:0002298!2.35e-09!6;UBERON:0000200!4.34e-09!6;UBERON:0003076!6.58e-09!15;UBERON:0003057!6.58e-09!15;UBERON:0004732!7.87e-09!13;UBERON:0000483!1.14e-08!306;UBERON:0002021!1.45e-08!5;UBERON:0000119!2.06e-08!309;UBERON:0000062!2.19e-08!503;UBERON:0003296!1.76e-07!4;UBERON:0010133!1.76e-07!4;UBERON:0000922!1.86e-07!592;UBERON:0002784!5.75e-07!4;UBERON:0000468!7.75e-07!656
|ontology_enrichment_uberon=UBERON:0007023!1.67e-47!114;UBERON:0000073!3.64e-37!53;UBERON:0002616!3.64e-37!53;UBERON:0001049!2.67e-36!56;UBERON:0005068!2.67e-36!56;UBERON:0006241!2.67e-36!56;UBERON:0007135!2.67e-36!56;UBERON:0001016!1.14e-33!89;UBERON:0002346!6.47e-33!86;UBERON:0000955!3.33e-32!68;UBERON:0006238!3.33e-32!68;UBERON:0003075!5.63e-32!82;UBERON:0007284!5.63e-32!82;UBERON:0001017!6.33e-32!81;UBERON:0002780!1.67e-28!41;UBERON:0001890!1.67e-28!41;UBERON:0003080!1.67e-28!41;UBERON:0006240!1.67e-28!41;UBERON:0010371!4.40e-26!104;UBERON:0004121!9.82e-25!171;UBERON:0000924!9.82e-25!171;UBERON:0006601!9.82e-25!171;UBERON:0003056!1.47e-22!61;UBERON:0011216!1.02e-21!223;UBERON:0010314!4.11e-21!132;UBERON:0003528!1.71e-20!34;UBERON:0002020!1.71e-20!34;UBERON:0001869!4.08e-20!32;UBERON:0001950!4.43e-20!20;UBERON:0001893!4.45e-20!34;UBERON:0002619!5.41e-20!22;UBERON:0002791!3.43e-18!32;UBERON:0000956!5.37e-17!25;UBERON:0000203!5.37e-17!25;UBERON:0000477!1.86e-14!373;UBERON:0000481!1.44e-11!342;UBERON:0001894!7.48e-11!7;UBERON:0006222!7.48e-11!7;UBERON:0000064!3.50e-10!218;UBERON:0004111!4.15e-10!240;UBERON:0004733!9.46e-10!12;UBERON:0002028!9.46e-10!12;UBERON:0007277!9.46e-10!12;UBERON:0000025!1.12e-09!192;UBERON:0002298!2.35e-09!6;UBERON:0000200!4.34e-09!6;UBERON:0003076!6.58e-09!15;UBERON:0003057!6.58e-09!15;UBERON:0004732!7.87e-09!13;UBERON:0000483!1.14e-08!306;UBERON:0002021!1.45e-08!5;UBERON:0000119!2.06e-08!309;UBERON:0000062!2.19e-08!503;UBERON:0003296!1.76e-07!4;UBERON:0010133!1.76e-07!4;UBERON:0000922!1.86e-07!592;UBERON:0002784!5.75e-07!4;UBERON:0000468!7.75e-07!656
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,0.703495,0.621241,0.778743,0.274093,0.721271,1.14971,0.478935,0.963929,0.395009,1.42981,0.969147,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,1.55072,0.458349,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,1.14615,0.0606304,0.533483,0.734485,0.609718,0.124583,2.02272,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,1.55219,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,0.189341,1.23387,0.269111,1.30959,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,2.59889,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,1.70662,1.35434,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,1.76469,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,2.41357,0.363423,2.27985,0.126633,1.15522,0.312599,5.61831,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,2.23409,0.906429,0.754576,0.923751,0.731946,0.0214572
}}
}}

Revision as of 15:09, 26 November 2012


Full id: C1850_small_pineal_pons_placenta_eye_heart_merkel



Phase1 CAGE Peaks

Hg19::chr1:216680229..216680242,-p@chr1:216680229..216680242
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Hg19::chr1:216680257..216680268,-p@chr1:216680257..216680268
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Hg19::chr1:216896752..216896778,-p1@ESRRG
Hg19::chr1:216896780..216896800,-p2@ESRRG
Hg19::chr1:216896801..216896812,-p5@ESRRG


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 organism1.67e-47114
regional part of nervous system3.64e-3753
regional part of brain3.64e-3753
neural tube2.67e-3656
neural rod2.67e-3656
future spinal cord2.67e-3656
neural keel2.67e-3656
nervous system1.14e-3389
neurectoderm6.47e-3386
brain3.33e-3268
future brain3.33e-3268
neural plate5.63e-3282
presumptive neural plate5.63e-3282
central nervous system6.33e-3281
regional part of forebrain1.67e-2841
forebrain1.67e-2841
anterior neural tube1.67e-2841
future forebrain1.67e-2841
ecto-epithelium4.40e-26104
ectoderm-derived structure9.82e-25171
ectoderm9.82e-25171
presumptive ectoderm9.82e-25171
pre-chordal neural plate1.47e-2261
organ system subdivision1.02e-21223
structure with developmental contribution from neural crest4.11e-21132
brain grey matter1.71e-2034
gray matter1.71e-2034
cerebral hemisphere4.08e-2032
neocortex4.43e-2020
telencephalon4.45e-2034
regional part of cerebral cortex5.41e-2022
regional part of telencephalon3.43e-1832
cerebral cortex5.37e-1725
pallium5.37e-1725
anatomical cluster1.86e-14373
multi-tissue structure1.44e-11342
diencephalon7.48e-117
future diencephalon7.48e-117
organ part3.50e-10218
anatomical conduit4.15e-10240
segmental subdivision of hindbrain9.46e-1012
hindbrain9.46e-1012
presumptive hindbrain9.46e-1012
tube1.12e-09192
brainstem2.35e-096
gyrus4.34e-096
posterior neural tube6.58e-0915
chordal neural plate6.58e-0915
segmental subdivision of nervous system7.87e-0913
epithelium1.14e-08306
occipital lobe1.45e-085
cell layer2.06e-08309
organ2.19e-08503
gland of diencephalon1.76e-074
neuroendocrine gland1.76e-074
embryo1.86e-07592
regional part of diencephalon5.75e-074
multi-cellular organism7.75e-07656


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

No analysis results for this cluster

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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