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Coexpression cluster:C1657: Difference between revisions

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|ontology_enrichment_disease=DOID:169!8.43e-08!6;DOID:171!2.30e-07!10
|ontology_enrichment_disease=DOID:169!8.43e-08!6;DOID:171!2.30e-07!10
|ontology_enrichment_uberon=UBERON:0000073!1.05e-62!94;UBERON:0001016!1.05e-62!94;UBERON:0001017!3.90e-61!82;UBERON:0005743!2.72e-59!86;UBERON:0001049!1.67e-54!57;UBERON:0005068!1.67e-54!57;UBERON:0006241!1.67e-54!57;UBERON:0007135!1.67e-54!57;UBERON:0000955!2.15e-47!69;UBERON:0006238!2.15e-47!69;UBERON:0002780!4.99e-46!41;UBERON:0001890!4.99e-46!41;UBERON:0006240!4.99e-46!41;UBERON:0002616!1.86e-45!59;UBERON:0003080!1.38e-44!42;UBERON:0002346!8.74e-41!90;UBERON:0003075!2.52e-40!86;UBERON:0007284!2.52e-40!86;UBERON:0002020!6.36e-38!34;UBERON:0003528!6.36e-38!34;UBERON:0001893!7.86e-38!34;UBERON:0002791!1.32e-36!33;UBERON:0001869!6.47e-36!32;UBERON:0000924!2.16e-33!173;UBERON:0006601!2.16e-33!173;UBERON:0007023!3.93e-33!115;UBERON:0003056!9.58e-33!61;UBERON:0004121!1.42e-32!169;UBERON:0002619!3.09e-28!22;UBERON:0000956!5.22e-28!25;UBERON:0000203!5.22e-28!25;UBERON:0001950!9.56e-26!20;UBERON:0000153!8.23e-24!129;UBERON:0007811!8.23e-24!129;UBERON:0000033!2.31e-22!123;UBERON:0000025!1.17e-12!194;UBERON:0002420!1.48e-11!9;UBERON:0007245!1.48e-11!9;UBERON:0010009!1.48e-11!9;UBERON:0010011!1.48e-11!9;UBERON:0000454!1.48e-11!9;UBERON:0002308!3.04e-11!9;UBERON:0000125!3.04e-11!9;UBERON:0003076!4.87e-11!15;UBERON:0003057!4.87e-11!15;UBERON:0000483!1.22e-09!309;UBERON:0001894!1.83e-09!7;UBERON:0006222!1.83e-09!7;UBERON:0000119!2.49e-09!312;UBERON:0000200!2.74e-09!6;UBERON:0001871!3.65e-09!7;UBERON:0009663!5.10e-09!7;UBERON:0004733!3.01e-08!12;UBERON:0002028!3.01e-08!12;UBERON:0007277!3.01e-08!12;UBERON:0002021!4.44e-08!5;UBERON:0001872!5.10e-08!5;UBERON:0004111!7.89e-08!241;UBERON:0000349!7.91e-08!5;UBERON:0004732!1.98e-07!13;UBERON:0002298!2.25e-07!8;UBERON:0000922!3.76e-07!612;UBERON:0000064!8.15e-07!219;UBERON:0000475!8.39e-07!365;UBERON:0000013!9.06e-07!5;UBERON:0002410!9.06e-07!5
|ontology_enrichment_uberon=UBERON:0000073!1.05e-62!94;UBERON:0001016!1.05e-62!94;UBERON:0001017!3.90e-61!82;UBERON:0005743!2.72e-59!86;UBERON:0001049!1.67e-54!57;UBERON:0005068!1.67e-54!57;UBERON:0006241!1.67e-54!57;UBERON:0007135!1.67e-54!57;UBERON:0000955!2.15e-47!69;UBERON:0006238!2.15e-47!69;UBERON:0002780!4.99e-46!41;UBERON:0001890!4.99e-46!41;UBERON:0006240!4.99e-46!41;UBERON:0002616!1.86e-45!59;UBERON:0003080!1.38e-44!42;UBERON:0002346!8.74e-41!90;UBERON:0003075!2.52e-40!86;UBERON:0007284!2.52e-40!86;UBERON:0002020!6.36e-38!34;UBERON:0003528!6.36e-38!34;UBERON:0001893!7.86e-38!34;UBERON:0002791!1.32e-36!33;UBERON:0001869!6.47e-36!32;UBERON:0000924!2.16e-33!173;UBERON:0006601!2.16e-33!173;UBERON:0007023!3.93e-33!115;UBERON:0003056!9.58e-33!61;UBERON:0004121!1.42e-32!169;UBERON:0002619!3.09e-28!22;UBERON:0000956!5.22e-28!25;UBERON:0000203!5.22e-28!25;UBERON:0001950!9.56e-26!20;UBERON:0000153!8.23e-24!129;UBERON:0007811!8.23e-24!129;UBERON:0000033!2.31e-22!123;UBERON:0000025!1.17e-12!194;UBERON:0002420!1.48e-11!9;UBERON:0007245!1.48e-11!9;UBERON:0010009!1.48e-11!9;UBERON:0010011!1.48e-11!9;UBERON:0000454!1.48e-11!9;UBERON:0002308!3.04e-11!9;UBERON:0000125!3.04e-11!9;UBERON:0003076!4.87e-11!15;UBERON:0003057!4.87e-11!15;UBERON:0000483!1.22e-09!309;UBERON:0001894!1.83e-09!7;UBERON:0006222!1.83e-09!7;UBERON:0000119!2.49e-09!312;UBERON:0000200!2.74e-09!6;UBERON:0001871!3.65e-09!7;UBERON:0009663!5.10e-09!7;UBERON:0004733!3.01e-08!12;UBERON:0002028!3.01e-08!12;UBERON:0007277!3.01e-08!12;UBERON:0002021!4.44e-08!5;UBERON:0001872!5.10e-08!5;UBERON:0004111!7.89e-08!241;UBERON:0000349!7.91e-08!5;UBERON:0004732!1.98e-07!13;UBERON:0002298!2.25e-07!8;UBERON:0000922!3.76e-07!612;UBERON:0000064!8.15e-07!219;UBERON:0000475!8.39e-07!365;UBERON:0000013!9.06e-07!5;UBERON:0002410!9.06e-07!5
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}}
}}

Revision as of 17:31, 8 August 2012


Full id: C1657_pineal_cerebellum_temporal_occipital_duodenum_middle_brain



Phase1 CAGE Peaks

Hg19::chr12:119419286..119419293,+p4@SRRM4
Hg19::chr12:119419294..119419308,+p2@SRRM4
Hg19::chr15:89147826..89147846,+p@chr15:89147826..89147846
+
Hg19::chr20:61808928..61808938,+p@chr20:61808928..61808938
+
Hg19::chr3:52001995..52002004,-p@chr3:52001995..52002004
-


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>disease_data<br>


Cell Type
Ontology termp-valuen
neuronal stem cell1.47e-098
neural cell5.37e-0825
neurectodermal cell5.71e-0859
neuron1.33e-076
neuroblast1.33e-076
electrically signaling cell1.33e-076
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.05e-6294
nervous system1.05e-6294
central nervous system3.90e-6182
neural tube1.67e-5457
neural rod1.67e-5457
future spinal cord1.67e-5457
neural keel1.67e-5457
brain2.15e-4769
future brain2.15e-4769
regional part of forebrain4.99e-4641
forebrain4.99e-4641
future forebrain4.99e-4641
regional part of brain1.86e-4559
anterior neural tube1.38e-4442
neurectoderm8.74e-4190
neural plate2.52e-4086
presumptive neural plate2.52e-4086
gray matter6.36e-3834
brain grey matter6.36e-3834
telencephalon7.86e-3834
regional part of telencephalon1.32e-3633
cerebral hemisphere6.47e-3632
ectoderm2.16e-33173
presumptive ectoderm2.16e-33173
adult organism3.93e-33115
pre-chordal neural plate9.58e-3361
ectoderm-derived structure1.42e-32169
regional part of cerebral cortex3.09e-2822
cerebral cortex5.22e-2825
pallium5.22e-2825
neocortex9.56e-2620
anterior region of body8.23e-24129
craniocervical region8.23e-24129
head2.31e-22123
tube1.17e-12194
basal ganglion1.48e-119
nuclear complex of neuraxis1.48e-119
aggregate regional part of brain1.48e-119
collection of basal ganglia1.48e-119
cerebral subcortex1.48e-119
nucleus of brain3.04e-119
neural nucleus3.04e-119
posterior neural tube4.87e-1115
chordal neural plate4.87e-1115
epithelium1.22e-09309
diencephalon1.83e-097
future diencephalon1.83e-097
cell layer2.49e-09312
gyrus2.74e-096
temporal lobe3.65e-097
telencephalic nucleus5.10e-097
segmental subdivision of hindbrain3.01e-0812
hindbrain3.01e-0812
presumptive hindbrain3.01e-0812
occipital lobe4.44e-085
parietal lobe5.10e-085
anatomical conduit7.89e-08241
limbic system7.91e-085
segmental subdivision of nervous system1.98e-0713
brainstem2.25e-078
embryo3.76e-07612
organ part8.15e-07219
organism subdivision8.39e-07365
sympathetic nervous system9.06e-075
autonomic nervous system9.06e-075
Disease
Ontology termp-valuen
neuroendocrine tumor8.43e-086
neuroectodermal tumor2.30e-0710


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.