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|full_id=C4460_brain_occipital_diencephalon_temporal_postcentral_olfactory_amygdala
|full_id=C4460_brain_occipital_diencephalon_temporal_postcentral_olfactory_amygdala
|id=C4460
|id=C4460
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.42e-36!94;UBERON:0001016!1.42e-36!94;UBERON:0002346!5.10e-35!90;UBERON:0003075!5.38e-35!86;UBERON:0007284!5.38e-35!86;UBERON:0000924!9.85e-34!173;UBERON:0006601!9.85e-34!173;UBERON:0005743!1.41e-33!86;UBERON:0004121!2.74e-33!169;UBERON:0001017!2.21e-32!82;UBERON:0001049!3.47e-32!57;UBERON:0005068!3.47e-32!57;UBERON:0006241!3.47e-32!57;UBERON:0007135!3.47e-32!57;UBERON:0000955!1.03e-31!69;UBERON:0006238!1.03e-31!69;UBERON:0002616!2.52e-30!59;UBERON:0003056!5.96e-27!61;UBERON:0000033!1.64e-26!123;UBERON:0000119!3.40e-26!312;UBERON:0000483!1.34e-25!309;UBERON:0000153!5.84e-25!129;UBERON:0007811!5.84e-25!129;UBERON:0003080!4.48e-24!42;UBERON:0002780!1.36e-23!41;UBERON:0001890!1.36e-23!41;UBERON:0006240!1.36e-23!41;UBERON:0000064!8.36e-22!219;UBERON:0001893!9.94e-21!34;UBERON:0002020!1.15e-20!34;UBERON:0003528!1.15e-20!34;UBERON:0000475!1.39e-20!365;UBERON:0002791!4.58e-20!33;UBERON:0000025!4.96e-20!194;UBERON:0001869!1.75e-19!32;UBERON:0004111!1.33e-17!241;UBERON:0000477!1.47e-17!286;UBERON:0000481!2.68e-17!347;UBERON:0007023!4.13e-17!115;UBERON:0000956!3.83e-15!25;UBERON:0000203!3.83e-15!25;UBERON:0002619!8.29e-14!22;UBERON:0001950!1.31e-12!20;UBERON:0000468!6.60e-11!659;UBERON:0000922!1.04e-10!612;UBERON:0002050!1.62e-09!605;UBERON:0005423!1.62e-09!605;UBERON:0000467!2.26e-09!625;UBERON:0000480!2.27e-09!626;UBERON:0000923!2.48e-09!604;UBERON:0005291!2.48e-09!604;UBERON:0006598!2.48e-09!604;UBERON:0002532!2.48e-09!604;UBERON:0003076!3.59e-09!15;UBERON:0003057!3.59e-09!15;UBERON:0004732!4.93e-08!13;UBERON:0004733!1.87e-07!12;UBERON:0002028!1.87e-07!12;UBERON:0007277!1.87e-07!12;UBERON:0000062!2.69e-07!511;UBERON:0002308!5.28e-07!9;UBERON:0002420!5.28e-07!9;UBERON:0000125!5.28e-07!9;UBERON:0007245!5.28e-07!9;UBERON:0010009!5.28e-07!9;UBERON:0010011!5.28e-07!9;UBERON:0000454!5.28e-07!9
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Revision as of 14:48, 21 May 2012


Full id: C4460_brain_occipital_diencephalon_temporal_postcentral_olfactory_amygdala



Phase1 CAGE Peaks

Hg19::chr5:132113042..132113061,-p4@SEPT8
Hg19::chr5:132113063..132113082,-p3@SEPT8
Hg19::chr5:132113083..132113109,-p2@SEPT8


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 system1.42e-3694
nervous system1.42e-3694
neurectoderm5.10e-3590
neural plate5.38e-3586
presumptive neural plate5.38e-3586
ectoderm9.85e-34173
presumptive ectoderm9.85e-34173
ectoderm-derived structure2.74e-33169
central nervous system2.21e-3282
neural tube3.47e-3257
neural rod3.47e-3257
future spinal cord3.47e-3257
neural keel3.47e-3257
brain1.03e-3169
future brain1.03e-3169
regional part of brain2.52e-3059
pre-chordal neural plate5.96e-2761
head1.64e-26123
cell layer3.40e-26312
epithelium1.34e-25309
anterior region of body5.84e-25129
craniocervical region5.84e-25129
anterior neural tube4.48e-2442
regional part of forebrain1.36e-2341
forebrain1.36e-2341
future forebrain1.36e-2341
organ part8.36e-22219
telencephalon9.94e-2134
gray matter1.15e-2034
brain grey matter1.15e-2034
organism subdivision1.39e-20365
regional part of telencephalon4.58e-2033
tube4.96e-20194
cerebral hemisphere1.75e-1932
anatomical conduit1.33e-17241
anatomical cluster1.47e-17286
multi-tissue structure2.68e-17347
adult organism4.13e-17115
cerebral cortex3.83e-1525
pallium3.83e-1525
regional part of cerebral cortex8.29e-1422
neocortex1.31e-1220
multi-cellular organism6.60e-11659
embryo1.04e-10612
embryonic structure1.62e-09605
developing anatomical structure1.62e-09605
anatomical system2.26e-09625
anatomical group2.27e-09626
germ layer2.48e-09604
embryonic tissue2.48e-09604
presumptive structure2.48e-09604
epiblast (generic)2.48e-09604
posterior neural tube3.59e-0915
chordal neural plate3.59e-0915
segmental subdivision of nervous system4.93e-0813
segmental subdivision of hindbrain1.87e-0712
hindbrain1.87e-0712
presumptive hindbrain1.87e-0712
organ2.69e-07511
nucleus of brain5.28e-079
basal ganglion5.28e-079
neural nucleus5.28e-079
nuclear complex of neuraxis5.28e-079
aggregate regional part of brain5.28e-079
collection of basal ganglia5.28e-079
cerebral subcortex5.28e-079


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.