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Coexpression cluster:C1732: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.08e-48!82;UBERON:0005743!3.67e-48!86;UBERON:0001049!6.15e-48!57;UBERON:0005068!6.15e-48!57;UBERON:0006241!6.15e-48!57;UBERON:0007135!6.15e-48!57;UBERON:0000073!1.68e-44!94;UBERON:0001016!1.68e-44!94;UBERON:0002616!4.78e-41!59;UBERON:0000955!3.15e-40!69;UBERON:0006238!3.15e-40!69;UBERON:0002780!2.17e-38!41;UBERON:0001890!2.17e-38!41;UBERON:0006240!2.17e-38!41;UBERON:0002346!1.80e-37!90;UBERON:0003075!2.96e-37!86;UBERON:0007284!2.96e-37!86;UBERON:0003080!3.99e-37!42;UBERON:0002020!1.24e-33!34;UBERON:0003528!1.24e-33!34;UBERON:0001893!1.81e-33!34;UBERON:0002791!2.61e-32!33;UBERON:0001869!1.88e-31!32;UBERON:0003056!1.39e-26!61;UBERON:0002619!8.31e-26!22;UBERON:0000956!1.84e-23!25;UBERON:0000203!1.84e-23!25;UBERON:0001950!2.07e-23!20;UBERON:0007023!9.32e-23!115;UBERON:0000924!3.66e-21!173;UBERON:0006601!3.66e-21!173;UBERON:0000153!4.66e-21!129;UBERON:0007811!4.66e-21!129;UBERON:0004121!1.37e-20!169;UBERON:0000033!1.27e-19!123;UBERON:0000025!1.65e-12!194;UBERON:0002420!8.08e-12!9;UBERON:0007245!8.08e-12!9;UBERON:0010009!8.08e-12!9;UBERON:0010011!8.08e-12!9;UBERON:0000454!8.08e-12!9;UBERON:0002308!1.15e-11!9;UBERON:0000125!1.15e-11!9;UBERON:0003076!1.17e-11!15;UBERON:0003057!1.17e-11!15;UBERON:0000483!2.45e-10!309;UBERON:0000119!5.41e-10!312;UBERON:0000064!8.11e-10!219;UBERON:0004732!1.23e-09!13;UBERON:0009663!1.89e-09!7;UBERON:0004733!1.16e-08!12;UBERON:0002028!1.16e-08!12;UBERON:0007277!1.16e-08!12;UBERON:0000200!1.47e-08!6;UBERON:0001871!3.06e-08!7;UBERON:0000475!8.18e-08!365;UBERON:0001872!1.64e-07!5;UBERON:0000349!1.70e-07!5;UBERON:0002298!1.93e-07!8;UBERON:0002021!2.06e-07!5;UBERON:0004111!4.50e-07!241
|ontology_enrichment_uberon=UBERON:0001017!3.08e-48!82;UBERON:0005743!3.67e-48!86;UBERON:0001049!6.15e-48!57;UBERON:0005068!6.15e-48!57;UBERON:0006241!6.15e-48!57;UBERON:0007135!6.15e-48!57;UBERON:0000073!1.68e-44!94;UBERON:0001016!1.68e-44!94;UBERON:0002616!4.78e-41!59;UBERON:0000955!3.15e-40!69;UBERON:0006238!3.15e-40!69;UBERON:0002780!2.17e-38!41;UBERON:0001890!2.17e-38!41;UBERON:0006240!2.17e-38!41;UBERON:0002346!1.80e-37!90;UBERON:0003075!2.96e-37!86;UBERON:0007284!2.96e-37!86;UBERON:0003080!3.99e-37!42;UBERON:0002020!1.24e-33!34;UBERON:0003528!1.24e-33!34;UBERON:0001893!1.81e-33!34;UBERON:0002791!2.61e-32!33;UBERON:0001869!1.88e-31!32;UBERON:0003056!1.39e-26!61;UBERON:0002619!8.31e-26!22;UBERON:0000956!1.84e-23!25;UBERON:0000203!1.84e-23!25;UBERON:0001950!2.07e-23!20;UBERON:0007023!9.32e-23!115;UBERON:0000924!3.66e-21!173;UBERON:0006601!3.66e-21!173;UBERON:0000153!4.66e-21!129;UBERON:0007811!4.66e-21!129;UBERON:0004121!1.37e-20!169;UBERON:0000033!1.27e-19!123;UBERON:0000025!1.65e-12!194;UBERON:0002420!8.08e-12!9;UBERON:0007245!8.08e-12!9;UBERON:0010009!8.08e-12!9;UBERON:0010011!8.08e-12!9;UBERON:0000454!8.08e-12!9;UBERON:0002308!1.15e-11!9;UBERON:0000125!1.15e-11!9;UBERON:0003076!1.17e-11!15;UBERON:0003057!1.17e-11!15;UBERON:0000483!2.45e-10!309;UBERON:0000119!5.41e-10!312;UBERON:0000064!8.11e-10!219;UBERON:0004732!1.23e-09!13;UBERON:0009663!1.89e-09!7;UBERON:0004733!1.16e-08!12;UBERON:0002028!1.16e-08!12;UBERON:0007277!1.16e-08!12;UBERON:0000200!1.47e-08!6;UBERON:0001871!3.06e-08!7;UBERON:0000475!8.18e-08!365;UBERON:0001872!1.64e-07!5;UBERON:0000349!1.70e-07!5;UBERON:0002298!1.93e-07!8;UBERON:0002021!2.06e-07!5;UBERON:0004111!4.50e-07!241
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}}
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Revision as of 17:35, 8 August 2012


Full id: C1732_parietal_maxillary_temporal_occipital_small_medial_putamen



Phase1 CAGE Peaks

Hg19::chr14:79489466..79489481,+p@chr14:79489466..79489481
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Hg19::chr14:79497000..79497004,+p@chr14:79497000..79497004
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Hg19::chr14:79511184..79511189,+p@chr14:79511184..79511189
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Hg19::chr14:79667198..79667202,+p@chr14:79667198..79667202
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Hg19::chr14:79731597..79731601,+p@chr14:79731597..79731601
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system3.08e-4882
neural tube6.15e-4857
neural rod6.15e-4857
future spinal cord6.15e-4857
neural keel6.15e-4857
regional part of nervous system1.68e-4494
nervous system1.68e-4494
regional part of brain4.78e-4159
brain3.15e-4069
future brain3.15e-4069
regional part of forebrain2.17e-3841
forebrain2.17e-3841
future forebrain2.17e-3841
neurectoderm1.80e-3790
neural plate2.96e-3786
presumptive neural plate2.96e-3786
anterior neural tube3.99e-3742
gray matter1.24e-3334
brain grey matter1.24e-3334
telencephalon1.81e-3334
regional part of telencephalon2.61e-3233
cerebral hemisphere1.88e-3132
pre-chordal neural plate1.39e-2661
regional part of cerebral cortex8.31e-2622
cerebral cortex1.84e-2325
pallium1.84e-2325
neocortex2.07e-2320
adult organism9.32e-23115
ectoderm3.66e-21173
presumptive ectoderm3.66e-21173
anterior region of body4.66e-21129
craniocervical region4.66e-21129
ectoderm-derived structure1.37e-20169
head1.27e-19123
tube1.65e-12194
basal ganglion8.08e-129
nuclear complex of neuraxis8.08e-129
aggregate regional part of brain8.08e-129
collection of basal ganglia8.08e-129
cerebral subcortex8.08e-129
nucleus of brain1.15e-119
neural nucleus1.15e-119
posterior neural tube1.17e-1115
chordal neural plate1.17e-1115
epithelium2.45e-10309
cell layer5.41e-10312
organ part8.11e-10219
segmental subdivision of nervous system1.23e-0913
telencephalic nucleus1.89e-097
segmental subdivision of hindbrain1.16e-0812
hindbrain1.16e-0812
presumptive hindbrain1.16e-0812
gyrus1.47e-086
temporal lobe3.06e-087
organism subdivision8.18e-08365
parietal lobe1.64e-075
limbic system1.70e-075
brainstem1.93e-078
occipital lobe2.06e-075
anatomical conduit4.50e-07241


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)

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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.