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Coexpression cluster:C1846: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!5.56e-44!56;UBERON:0005068!5.56e-44!56;UBERON:0006241!5.56e-44!56;UBERON:0007135!5.56e-44!56;UBERON:0000073!6.77e-40!53;UBERON:0002616!6.77e-40!53;UBERON:0007023!1.74e-34!114;UBERON:0001017!2.47e-34!81;UBERON:0000955!3.66e-32!68;UBERON:0006238!3.66e-32!68;UBERON:0002780!1.60e-31!41;UBERON:0001890!1.60e-31!41;UBERON:0003080!1.60e-31!41;UBERON:0006240!1.60e-31!41;UBERON:0001016!1.70e-30!89;UBERON:0003075!2.33e-29!82;UBERON:0007284!2.33e-29!82;UBERON:0002346!3.05e-27!86;UBERON:0003528!3.67e-26!34;UBERON:0002020!3.67e-26!34;UBERON:0001893!1.81e-25!34;UBERON:0002791!8.49e-24!32;UBERON:0001869!1.36e-23!32;UBERON:0010371!4.90e-22!104;UBERON:0002619!8.94e-21!22;UBERON:0011216!9.15e-21!223;UBERON:0003056!2.56e-20!61;UBERON:0010314!2.79e-19!132;UBERON:0001950!3.33e-18!20;UBERON:0000956!1.30e-17!25;UBERON:0000203!1.30e-17!25;UBERON:0003076!2.68e-13!15;UBERON:0003057!2.68e-13!15;UBERON:0004121!6.02e-13!171;UBERON:0000924!6.02e-13!171;UBERON:0006601!6.02e-13!171;UBERON:0000481!2.52e-12!342;UBERON:0000477!4.31e-12!373;UBERON:0000025!1.62e-10!192;UBERON:0000125!3.17e-10!9;UBERON:0002308!3.17e-10!9;UBERON:0004733!1.96e-09!12;UBERON:0002028!1.96e-09!12;UBERON:0007277!1.96e-09!12;UBERON:0000483!3.96e-09!306;UBERON:0002298!4.66e-09!6;UBERON:0000062!5.60e-09!503;UBERON:0000119!7.57e-09!309;UBERON:0004732!1.59e-08!13;UBERON:0000200!2.74e-08!6;UBERON:0004111!4.84e-08!240;UBERON:0002420!7.59e-08!9;UBERON:0007245!7.59e-08!9;UBERON:0010009!7.59e-08!9;UBERON:0010011!7.59e-08!9;UBERON:0000454!7.59e-08!9;UBERON:0009663!8.40e-08!7;UBERON:0001894!1.77e-07!7;UBERON:0006222!1.77e-07!7;UBERON:0001871!1.80e-07!6
|ontology_enrichment_uberon=UBERON:0001049!5.56e-44!56;UBERON:0005068!5.56e-44!56;UBERON:0006241!5.56e-44!56;UBERON:0007135!5.56e-44!56;UBERON:0000073!6.77e-40!53;UBERON:0002616!6.77e-40!53;UBERON:0007023!1.74e-34!114;UBERON:0001017!2.47e-34!81;UBERON:0000955!3.66e-32!68;UBERON:0006238!3.66e-32!68;UBERON:0002780!1.60e-31!41;UBERON:0001890!1.60e-31!41;UBERON:0003080!1.60e-31!41;UBERON:0006240!1.60e-31!41;UBERON:0001016!1.70e-30!89;UBERON:0003075!2.33e-29!82;UBERON:0007284!2.33e-29!82;UBERON:0002346!3.05e-27!86;UBERON:0003528!3.67e-26!34;UBERON:0002020!3.67e-26!34;UBERON:0001893!1.81e-25!34;UBERON:0002791!8.49e-24!32;UBERON:0001869!1.36e-23!32;UBERON:0010371!4.90e-22!104;UBERON:0002619!8.94e-21!22;UBERON:0011216!9.15e-21!223;UBERON:0003056!2.56e-20!61;UBERON:0010314!2.79e-19!132;UBERON:0001950!3.33e-18!20;UBERON:0000956!1.30e-17!25;UBERON:0000203!1.30e-17!25;UBERON:0003076!2.68e-13!15;UBERON:0003057!2.68e-13!15;UBERON:0004121!6.02e-13!171;UBERON:0000924!6.02e-13!171;UBERON:0006601!6.02e-13!171;UBERON:0000481!2.52e-12!342;UBERON:0000477!4.31e-12!373;UBERON:0000025!1.62e-10!192;UBERON:0000125!3.17e-10!9;UBERON:0002308!3.17e-10!9;UBERON:0004733!1.96e-09!12;UBERON:0002028!1.96e-09!12;UBERON:0007277!1.96e-09!12;UBERON:0000483!3.96e-09!306;UBERON:0002298!4.66e-09!6;UBERON:0000062!5.60e-09!503;UBERON:0000119!7.57e-09!309;UBERON:0004732!1.59e-08!13;UBERON:0000200!2.74e-08!6;UBERON:0004111!4.84e-08!240;UBERON:0002420!7.59e-08!9;UBERON:0007245!7.59e-08!9;UBERON:0010009!7.59e-08!9;UBERON:0010011!7.59e-08!9;UBERON:0000454!7.59e-08!9;UBERON:0009663!8.40e-08!7;UBERON:0001894!1.77e-07!7;UBERON:0006222!1.77e-07!7;UBERON:0001871!1.80e-07!6
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,1.57627,1.15291,0.653236,0.733342,0.324142,0.321368,0.703495,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,1.02276,0.784337,0.969147,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.432883,1.87167,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.476793,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,1.05625,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.536557,0.49825,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,1.35434,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,1.41294,0.953361,2.27985,0.126633,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.720819
}}
}}

Revision as of 15:08, 26 November 2012


Full id: C1846_pancreas_anaplastic_duodenum_temporal_spinal_gall_locus



Phase1 CAGE Peaks

Hg19::chr1:208216610..208216649,-p@chr1:208216610..208216649
-
Hg19::chr4:72052474..72052490,+p@chr4:72052474..72052490
+
Hg19::chr4:72052624..72052640,+p7@SLC4A4
Hg19::chr4:72133815..72133816,+p@chr4:72133815..72133816
+
Hg19::chr4:72338539..72338551,+p@chr4:72338539..72338551
+


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
neural tube5.56e-4456
neural rod5.56e-4456
future spinal cord5.56e-4456
neural keel5.56e-4456
regional part of nervous system6.77e-4053
regional part of brain6.77e-4053
adult organism1.74e-34114
central nervous system2.47e-3481
brain3.66e-3268
future brain3.66e-3268
regional part of forebrain1.60e-3141
forebrain1.60e-3141
anterior neural tube1.60e-3141
future forebrain1.60e-3141
nervous system1.70e-3089
neural plate2.33e-2982
presumptive neural plate2.33e-2982
neurectoderm3.05e-2786
brain grey matter3.67e-2634
gray matter3.67e-2634
telencephalon1.81e-2534
regional part of telencephalon8.49e-2432
cerebral hemisphere1.36e-2332
ecto-epithelium4.90e-22104
regional part of cerebral cortex8.94e-2122
organ system subdivision9.15e-21223
pre-chordal neural plate2.56e-2061
structure with developmental contribution from neural crest2.79e-19132
neocortex3.33e-1820
cerebral cortex1.30e-1725
pallium1.30e-1725
posterior neural tube2.68e-1315
chordal neural plate2.68e-1315
ectoderm-derived structure6.02e-13171
ectoderm6.02e-13171
presumptive ectoderm6.02e-13171
multi-tissue structure2.52e-12342
anatomical cluster4.31e-12373
tube1.62e-10192
neural nucleus3.17e-109
nucleus of brain3.17e-109
segmental subdivision of hindbrain1.96e-0912
hindbrain1.96e-0912
presumptive hindbrain1.96e-0912
epithelium3.96e-09306
brainstem4.66e-096
organ5.60e-09503
cell layer7.57e-09309
segmental subdivision of nervous system1.59e-0813
gyrus2.74e-086
anatomical conduit4.84e-08240
basal ganglion7.59e-089
nuclear complex of neuraxis7.59e-089
aggregate regional part of brain7.59e-089
collection of basal ganglia7.59e-089
cerebral subcortex7.59e-089
telencephalic nucleus8.40e-087
diencephalon1.77e-077
future diencephalon1.77e-077
temporal lobe1.80e-076


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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