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Coexpression cluster:C1463: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!1.05e-96!53;UBERON:0002616!1.05e-96!53;UBERON:0001049!1.54e-96!56;UBERON:0005068!1.54e-96!56;UBERON:0006241!1.54e-96!56;UBERON:0007135!1.54e-96!56;UBERON:0000955!9.80e-87!68;UBERON:0006238!9.80e-87!68;UBERON:0001017!5.76e-84!81;UBERON:0002780!1.58e-81!41;UBERON:0001890!1.58e-81!41;UBERON:0003080!1.58e-81!41;UBERON:0006240!1.58e-81!41;UBERON:0003528!1.26e-79!34;UBERON:0002020!1.26e-79!34;UBERON:0001893!1.69e-79!34;UBERON:0001016!8.78e-79!89;UBERON:0001869!2.04e-72!32;UBERON:0002791!3.99e-72!32;UBERON:0002619!1.02e-65!22;UBERON:0003075!8.84e-64!82;UBERON:0007284!8.84e-64!82;UBERON:0002346!1.78e-60!86;UBERON:0001950!1.23e-57!20;UBERON:0000956!1.37e-57!25;UBERON:0000203!1.37e-57!25;UBERON:0003056!5.37e-53!61;UBERON:0010371!1.37e-51!104;UBERON:0007023!1.82e-46!114;UBERON:0004121!1.22e-39!171;UBERON:0000924!1.22e-39!171;UBERON:0006601!1.22e-39!171;UBERON:0010314!4.13e-39!132;UBERON:0011216!3.61e-30!223;UBERON:0000125!6.66e-23!9;UBERON:0002308!6.66e-23!9;UBERON:0000025!8.58e-23!192;UBERON:0001872!2.35e-22!5;UBERON:0000200!1.83e-18!6;UBERON:0004111!7.67e-18!240;UBERON:0002420!2.46e-17!9;UBERON:0007245!2.46e-17!9;UBERON:0010009!2.46e-17!9;UBERON:0010011!2.46e-17!9;UBERON:0000454!2.46e-17!9;UBERON:0002298!6.30e-17!6;UBERON:0003076!1.87e-16!15;UBERON:0003057!1.87e-16!15;UBERON:0004733!4.87e-16!12;UBERON:0002028!4.87e-16!12;UBERON:0007277!4.87e-16!12;UBERON:0001871!7.42e-16!6;UBERON:0009663!1.18e-15!7;UBERON:0000477!1.28e-15!373;UBERON:0004732!9.78e-15!13;UBERON:0000349!1.17e-14!5;UBERON:0002021!1.30e-14!5;UBERON:0000064!3.88e-13!218;UBERON:0000988!4.25e-13!3;UBERON:0000483!3.37e-12!306;UBERON:0000119!5.32e-12!309;UBERON:0002680!1.68e-11!9;UBERON:0001895!1.68e-11!9;UBERON:0010092!1.68e-11!9;UBERON:0000369!6.73e-11!4;UBERON:0002435!6.73e-11!4;UBERON:0000204!6.73e-11!4;UBERON:0010082!6.73e-11!4;UBERON:0000481!4.31e-10!342;UBERON:0002771!4.75e-10!2;UBERON:0001954!6.20e-10!2;UBERON:0003022!6.20e-10!2;UBERON:0002421!6.20e-10!2;UBERON:0002600!6.20e-10!2;UBERON:0002148!1.93e-09!2;UBERON:0006331!1.93e-09!2;UBERON:0009662!1.93e-09!2;UBERON:0000923!4.95e-08!560;UBERON:0010316!4.95e-08!560;UBERON:0005291!4.95e-08!560;UBERON:0006598!4.95e-08!560;UBERON:0010317!4.95e-08!560;UBERON:0002532!4.95e-08!560;UBERON:0002050!6.57e-08!564;UBERON:0000062!8.90e-08!503;UBERON:0005423!2.10e-07!581;UBERON:0005383!3.85e-07!3;UBERON:0005382!3.85e-07!3;UBERON:0000922!4.30e-07!592;UBERON:0001870!5.49e-07!3
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.267027,0.075749,0.553339,0.707204,0.635275,0.650887,1.01544,0.415981,0.889639,0.336106,0.236034,0.127969,1.11315,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.134746,0.35388,0.585658,0.878269,0.248856,0.936389,0.513952,0.0979105,0.390088,0.636689,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,1.07049,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,1.87735,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,1.5087,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,1.27188,0.306342,0.136746,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.986797,1.21528,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.0115686
}}
}}

Revision as of 14:54, 26 November 2012


Full id: C1463_occipital_caudate_parietal_amygdala_hippocampus_temporal_brain



Phase1 CAGE Peaks

Hg19::chr1:147719335..147719348,-p@chr1:147719335..147719348
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Hg19::chr1:183221308..183221326,-p@chr1:183221308..183221326
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Hg19::chr6:12793089..12793093,+p@chr6:12793089..12793093
+
Hg19::chr6:12916788..12916791,+p@chr6:12916788..12916791
+
Hg19::chr8:4377261..4377265,-p@chr8:4377261..4377265
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Hg19::chr8:4657117..4657119,-p@chr8:4657117..4657119
-


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
regional part of nervous system1.05e-9653
regional part of brain1.05e-9653
neural tube1.54e-9656
neural rod1.54e-9656
future spinal cord1.54e-9656
neural keel1.54e-9656
brain9.80e-8768
future brain9.80e-8768
central nervous system5.76e-8481
regional part of forebrain1.58e-8141
forebrain1.58e-8141
anterior neural tube1.58e-8141
future forebrain1.58e-8141
brain grey matter1.26e-7934
gray matter1.26e-7934
telencephalon1.69e-7934
nervous system8.78e-7989
cerebral hemisphere2.04e-7232
regional part of telencephalon3.99e-7232
regional part of cerebral cortex1.02e-6522
neural plate8.84e-6482
presumptive neural plate8.84e-6482
neurectoderm1.78e-6086
neocortex1.23e-5720
cerebral cortex1.37e-5725
pallium1.37e-5725
pre-chordal neural plate5.37e-5361
ecto-epithelium1.37e-51104
adult organism1.82e-46114
ectoderm-derived structure1.22e-39171
ectoderm1.22e-39171
presumptive ectoderm1.22e-39171
structure with developmental contribution from neural crest4.13e-39132
organ system subdivision3.61e-30223
neural nucleus6.66e-239
nucleus of brain6.66e-239
tube8.58e-23192
parietal lobe2.35e-225
gyrus1.83e-186
anatomical conduit7.67e-18240
basal ganglion2.46e-179
nuclear complex of neuraxis2.46e-179
aggregate regional part of brain2.46e-179
collection of basal ganglia2.46e-179
cerebral subcortex2.46e-179
brainstem6.30e-176
posterior neural tube1.87e-1615
chordal neural plate1.87e-1615
segmental subdivision of hindbrain4.87e-1612
hindbrain4.87e-1612
presumptive hindbrain4.87e-1612
temporal lobe7.42e-166
telencephalic nucleus1.18e-157
anatomical cluster1.28e-15373
segmental subdivision of nervous system9.78e-1513
limbic system1.17e-145
occipital lobe1.30e-145
organ part3.88e-13218
pons4.25e-133
epithelium3.37e-12306
cell layer5.32e-12309
regional part of metencephalon1.68e-119
metencephalon1.68e-119
future metencephalon1.68e-119
corpus striatum6.73e-114
striatum6.73e-114
ventral part of telencephalon6.73e-114
future corpus striatum6.73e-114
multi-tissue structure4.31e-10342
middle temporal gyrus4.75e-102
Ammon's horn6.20e-102
lobe parts of cerebral cortex6.20e-102
hippocampal formation6.20e-102
limbic lobe6.20e-102
locus ceruleus1.93e-092
brainstem nucleus1.93e-092
hindbrain nucleus1.93e-092
germ layer4.95e-08560
germ layer / neural crest4.95e-08560
embryonic tissue4.95e-08560
presumptive structure4.95e-08560
germ layer / neural crest derived structure4.95e-08560
epiblast (generic)4.95e-08560
embryonic structure6.57e-08564
organ8.90e-08503
developing anatomical structure2.10e-07581
caudate-putamen3.85e-073
dorsal striatum3.85e-073
embryo4.30e-07592
frontal cortex5.49e-073


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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