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Coexpression cluster:C1106: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!4.41e-47!57;UBERON:0005068!4.41e-47!57;UBERON:0006241!4.41e-47!57;UBERON:0007135!4.41e-47!57;UBERON:0007023!5.12e-42!115;UBERON:0001017!5.31e-42!82;UBERON:0000955!7.02e-42!69;UBERON:0006238!7.02e-42!69;UBERON:0002780!8.51e-41!41;UBERON:0001890!8.51e-41!41;UBERON:0006240!8.51e-41!41;UBERON:0005743!2.40e-40!86;UBERON:0000073!1.37e-39!94;UBERON:0001016!1.37e-39!94;UBERON:0003080!2.13e-39!42;UBERON:0002346!9.83e-39!90;UBERON:0002616!1.14e-38!59;UBERON:0003075!1.15e-37!86;UBERON:0007284!1.15e-37!86;UBERON:0002020!2.27e-34!34;UBERON:0003528!2.27e-34!34;UBERON:0001893!5.87e-34!34;UBERON:0002791!5.60e-33!33;UBERON:0001869!9.91e-33!32;UBERON:0003056!1.82e-29!61;UBERON:0000956!1.20e-25!25;UBERON:0000203!1.20e-25!25;UBERON:0002619!2.55e-24!22;UBERON:0000153!3.68e-24!129;UBERON:0007811!3.68e-24!129;UBERON:0000924!6.25e-24!173;UBERON:0006601!6.25e-24!173;UBERON:0000033!3.30e-23!123;UBERON:0004121!7.74e-23!169;UBERON:0001950!2.93e-22!20;UBERON:0000025!1.09e-11!194;UBERON:0002420!2.98e-10!9;UBERON:0007245!2.98e-10!9;UBERON:0010009!2.98e-10!9;UBERON:0010011!2.98e-10!9;UBERON:0000454!2.98e-10!9;UBERON:0002308!4.40e-10!9;UBERON:0000125!4.40e-10!9;UBERON:0001871!1.86e-09!7;UBERON:0000064!3.09e-09!219;UBERON:0003076!4.46e-09!15;UBERON:0003057!4.46e-09!15;UBERON:0004111!5.64e-09!241;UBERON:0009663!3.52e-08!7;UBERON:0001894!3.83e-08!7;UBERON:0006222!3.83e-08!7;UBERON:0000200!1.17e-07!6;UBERON:0000483!1.26e-07!309;UBERON:0000477!1.68e-07!286;UBERON:0004732!2.06e-07!13;UBERON:0000119!2.62e-07!312
|ontology_enrichment_uberon=UBERON:0001049!4.41e-47!57;UBERON:0005068!4.41e-47!57;UBERON:0006241!4.41e-47!57;UBERON:0007135!4.41e-47!57;UBERON:0007023!5.12e-42!115;UBERON:0001017!5.31e-42!82;UBERON:0000955!7.02e-42!69;UBERON:0006238!7.02e-42!69;UBERON:0002780!8.51e-41!41;UBERON:0001890!8.51e-41!41;UBERON:0006240!8.51e-41!41;UBERON:0005743!2.40e-40!86;UBERON:0000073!1.37e-39!94;UBERON:0001016!1.37e-39!94;UBERON:0003080!2.13e-39!42;UBERON:0002346!9.83e-39!90;UBERON:0002616!1.14e-38!59;UBERON:0003075!1.15e-37!86;UBERON:0007284!1.15e-37!86;UBERON:0002020!2.27e-34!34;UBERON:0003528!2.27e-34!34;UBERON:0001893!5.87e-34!34;UBERON:0002791!5.60e-33!33;UBERON:0001869!9.91e-33!32;UBERON:0003056!1.82e-29!61;UBERON:0000956!1.20e-25!25;UBERON:0000203!1.20e-25!25;UBERON:0002619!2.55e-24!22;UBERON:0000153!3.68e-24!129;UBERON:0007811!3.68e-24!129;UBERON:0000924!6.25e-24!173;UBERON:0006601!6.25e-24!173;UBERON:0000033!3.30e-23!123;UBERON:0004121!7.74e-23!169;UBERON:0001950!2.93e-22!20;UBERON:0000025!1.09e-11!194;UBERON:0002420!2.98e-10!9;UBERON:0007245!2.98e-10!9;UBERON:0010009!2.98e-10!9;UBERON:0010011!2.98e-10!9;UBERON:0000454!2.98e-10!9;UBERON:0002308!4.40e-10!9;UBERON:0000125!4.40e-10!9;UBERON:0001871!1.86e-09!7;UBERON:0000064!3.09e-09!219;UBERON:0003076!4.46e-09!15;UBERON:0003057!4.46e-09!15;UBERON:0004111!5.64e-09!241;UBERON:0009663!3.52e-08!7;UBERON:0001894!3.83e-08!7;UBERON:0006222!3.83e-08!7;UBERON:0000200!1.17e-07!6;UBERON:0000483!1.26e-07!309;UBERON:0000477!1.68e-07!286;UBERON:0004732!2.06e-07!13;UBERON:0000119!2.62e-07!312
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}}
}}

Revision as of 16:53, 8 August 2012


Full id: C1106_pineal_occipital_middle_parietal_olfactory_amygdala_caudate



Phase1 CAGE Peaks

Hg19::chr10:115802982..115802997,+p@chr10:115802982..115802997
+
Hg19::chr4:21056328..21056331,-p@chr4:21056328..21056331
-
Hg19::chr4:21418996..21419012,-p@chr4:21418996..21419012
-
Hg19::chr4:21419073..21419100,-p@chr4:21419073..21419100
-
Hg19::chr4:21594781..21594810,-p@chr4:21594781..21594810
-
Hg19::chr4:21867081..21867096,-p1@AK057907
Hg19::chr8:105265029..105265058,+p@chr8:105265029..105265058
+


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 tube4.41e-4757
neural rod4.41e-4757
future spinal cord4.41e-4757
neural keel4.41e-4757
adult organism5.12e-42115
central nervous system5.31e-4282
brain7.02e-4269
future brain7.02e-4269
regional part of forebrain8.51e-4141
forebrain8.51e-4141
future forebrain8.51e-4141
regional part of nervous system1.37e-3994
nervous system1.37e-3994
anterior neural tube2.13e-3942
neurectoderm9.83e-3990
regional part of brain1.14e-3859
neural plate1.15e-3786
presumptive neural plate1.15e-3786
gray matter2.27e-3434
brain grey matter2.27e-3434
telencephalon5.87e-3434
regional part of telencephalon5.60e-3333
cerebral hemisphere9.91e-3332
pre-chordal neural plate1.82e-2961
cerebral cortex1.20e-2525
pallium1.20e-2525
regional part of cerebral cortex2.55e-2422
anterior region of body3.68e-24129
craniocervical region3.68e-24129
ectoderm6.25e-24173
presumptive ectoderm6.25e-24173
head3.30e-23123
ectoderm-derived structure7.74e-23169
neocortex2.93e-2220
tube1.09e-11194
basal ganglion2.98e-109
nuclear complex of neuraxis2.98e-109
aggregate regional part of brain2.98e-109
collection of basal ganglia2.98e-109
cerebral subcortex2.98e-109
nucleus of brain4.40e-109
neural nucleus4.40e-109
temporal lobe1.86e-097
organ part3.09e-09219
posterior neural tube4.46e-0915
chordal neural plate4.46e-0915
anatomical conduit5.64e-09241
telencephalic nucleus3.52e-087
diencephalon3.83e-087
future diencephalon3.83e-087
gyrus1.17e-076
epithelium1.26e-07309
anatomical cluster1.68e-07286
segmental subdivision of nervous system2.06e-0713
cell layer2.62e-07312


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.