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Coexpression cluster:C2629: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!4.83e-52!56;UBERON:0005068!4.83e-52!56;UBERON:0006241!4.83e-52!56;UBERON:0007135!4.83e-52!56;UBERON:0000073!2.28e-49!53;UBERON:0002616!2.28e-49!53;UBERON:0002780!5.55e-44!41;UBERON:0001890!5.55e-44!41;UBERON:0003080!5.55e-44!41;UBERON:0006240!5.55e-44!41;UBERON:0001893!1.43e-42!34;UBERON:0003528!1.94e-42!34;UBERON:0002020!1.94e-42!34;UBERON:0001017!3.59e-41!81;UBERON:0000955!8.61e-41!68;UBERON:0006238!8.61e-41!68;UBERON:0007023!1.60e-40!114;UBERON:0001016!3.36e-38!89;UBERON:0002791!3.95e-38!32;UBERON:0001869!5.61e-38!32;UBERON:0003075!1.85e-36!82;UBERON:0007284!1.85e-36!82;UBERON:0002346!2.92e-34!86;UBERON:0003056!2.43e-31!61;UBERON:0002619!1.05e-27!22;UBERON:0001950!3.66e-27!20;UBERON:0010371!1.81e-26!104;UBERON:0000956!5.86e-24!25;UBERON:0000203!5.86e-24!25;UBERON:0000125!6.62e-22!9;UBERON:0002308!6.62e-22!9;UBERON:0010314!3.61e-21!132;UBERON:0004111!7.55e-21!240;UBERON:0000025!6.77e-20!192;UBERON:0000477!6.80e-18!373;UBERON:0009663!2.53e-17!7;UBERON:0002420!5.51e-17!9;UBERON:0007245!5.51e-17!9;UBERON:0010009!5.51e-17!9;UBERON:0010011!5.51e-17!9;UBERON:0000454!5.51e-17!9;UBERON:0004121!1.47e-16!171;UBERON:0000924!1.47e-16!171;UBERON:0006601!1.47e-16!171;UBERON:0011216!1.47e-16!223;UBERON:0000200!1.19e-14!6;UBERON:0002298!7.06e-11!6;UBERON:0000369!3.16e-10!4;UBERON:0002435!3.16e-10!4;UBERON:0000204!3.16e-10!4;UBERON:0010082!3.16e-10!4;UBERON:0000483!1.29e-09!306;UBERON:0003076!1.32e-09!15;UBERON:0003057!1.32e-09!15;UBERON:0000119!2.12e-09!309;UBERON:0004732!5.08e-09!13;UBERON:0002021!8.04e-09!5;UBERON:0000988!8.79e-09!3;UBERON:0001871!2.07e-08!6;UBERON:0001870!2.36e-08!3;UBERON:0001473!3.53e-08!8;UBERON:0004536!3.53e-08!8;UBERON:0006558!3.53e-08!8;UBERON:0005383!5.74e-08!3;UBERON:0005382!5.74e-08!3;UBERON:0004638!8.60e-08!18;UBERON:0001986!8.60e-08!18;UBERON:0004852!8.60e-08!18;UBERON:0000064!9.21e-08!218;UBERON:0004733!2.97e-07!12;UBERON:0002028!2.97e-07!12;UBERON:0007277!2.97e-07!12
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,1.31925,0.559384,1.05593,0.471262,0.356737,1.18986,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.849366,1.72987,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,1.23481,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,2.21427,0.594299,1.14697,1.40954,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:37, 26 November 2012


Full id: C2629_Endothelial_adult_corpus_thalamus_optic_pons_substantia



Phase1 CAGE Peaks

Hg19::chr21:27284138..27284164,-p@chr21:27284138..27284164
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Hg19::chr21:27284346..27284358,-p@chr21:27284346..27284358
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Hg19::chr21:27284472..27284500,-p@chr21:27284472..27284500
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Hg19::chr21:27284505..27284518,-p@chr21:27284505..27284518
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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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.83e-5256
neural rod4.83e-5256
future spinal cord4.83e-5256
neural keel4.83e-5256
regional part of nervous system2.28e-4953
regional part of brain2.28e-4953
regional part of forebrain5.55e-4441
forebrain5.55e-4441
anterior neural tube5.55e-4441
future forebrain5.55e-4441
telencephalon1.43e-4234
brain grey matter1.94e-4234
gray matter1.94e-4234
central nervous system3.59e-4181
brain8.61e-4168
future brain8.61e-4168
adult organism1.60e-40114
nervous system3.36e-3889
regional part of telencephalon3.95e-3832
cerebral hemisphere5.61e-3832
neural plate1.85e-3682
presumptive neural plate1.85e-3682
neurectoderm2.92e-3486
pre-chordal neural plate2.43e-3161
regional part of cerebral cortex1.05e-2722
neocortex3.66e-2720
ecto-epithelium1.81e-26104
cerebral cortex5.86e-2425
pallium5.86e-2425
neural nucleus6.62e-229
nucleus of brain6.62e-229
structure with developmental contribution from neural crest3.61e-21132
anatomical conduit7.55e-21240
tube6.77e-20192
anatomical cluster6.80e-18373
telencephalic nucleus2.53e-177
basal ganglion5.51e-179
nuclear complex of neuraxis5.51e-179
aggregate regional part of brain5.51e-179
collection of basal ganglia5.51e-179
cerebral subcortex5.51e-179
ectoderm-derived structure1.47e-16171
ectoderm1.47e-16171
presumptive ectoderm1.47e-16171
organ system subdivision1.47e-16223
gyrus1.19e-146
brainstem7.06e-116
corpus striatum3.16e-104
striatum3.16e-104
ventral part of telencephalon3.16e-104
future corpus striatum3.16e-104
epithelium1.29e-09306
posterior neural tube1.32e-0915
chordal neural plate1.32e-0915
cell layer2.12e-09309
segmental subdivision of nervous system5.08e-0913
occipital lobe8.04e-095
pons8.79e-093
temporal lobe2.07e-086
frontal cortex2.36e-083
lymphatic vessel3.53e-088
lymph vasculature3.53e-088
lymphatic part of lymphoid system3.53e-088
caudate-putamen5.74e-083
dorsal striatum5.74e-083
blood vessel endothelium8.60e-0818
endothelium8.60e-0818
cardiovascular system endothelium8.60e-0818
organ part9.21e-08218
segmental subdivision of hindbrain2.97e-0712
hindbrain2.97e-0712
presumptive hindbrain2.97e-0712


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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