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Coexpression cluster:C2892: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!2.14e-54!114;UBERON:0001049!2.07e-39!56;UBERON:0005068!2.07e-39!56;UBERON:0006241!2.07e-39!56;UBERON:0007135!2.07e-39!56;UBERON:0001017!2.17e-37!81;UBERON:0000073!3.71e-37!53;UBERON:0002616!3.71e-37!53;UBERON:0002780!2.43e-35!41;UBERON:0001890!2.43e-35!41;UBERON:0003080!2.43e-35!41;UBERON:0006240!2.43e-35!41;UBERON:0001016!5.20e-34!89;UBERON:0001893!7.19e-31!34;UBERON:0003528!2.14e-30!34;UBERON:0002020!2.14e-30!34;UBERON:0001869!1.01e-29!32;UBERON:0003075!1.49e-29!82;UBERON:0007284!1.49e-29!82;UBERON:0002791!2.82e-29!32;UBERON:0002346!4.70e-29!86;UBERON:0000955!1.17e-28!68;UBERON:0006238!1.17e-28!68;UBERON:0003056!1.78e-24!61;UBERON:0000956!2.46e-23!25;UBERON:0000203!2.46e-23!25;UBERON:0011216!1.15e-22!223;UBERON:0002619!4.40e-22!22;UBERON:0010371!1.04e-21!104;UBERON:0001950!3.85e-20!20;UBERON:0004121!1.85e-19!171;UBERON:0000924!1.85e-19!171;UBERON:0006601!1.85e-19!171;UBERON:0010314!5.28e-17!132;UBERON:0000477!8.22e-12!373;UBERON:0000481!7.66e-11!342;UBERON:0002420!2.87e-09!9;UBERON:0007245!2.87e-09!9;UBERON:0010009!2.87e-09!9;UBERON:0010011!2.87e-09!9;UBERON:0000454!2.87e-09!9;UBERON:0000064!7.20e-09!218;UBERON:0000025!1.04e-08!192;UBERON:0004111!1.36e-08!240;UBERON:0000125!1.83e-08!9;UBERON:0002308!1.83e-08!9;UBERON:0000062!3.75e-08!503;UBERON:0000922!9.55e-08!592;UBERON:0001871!1.28e-07!6;UBERON:0009663!2.17e-07!7;UBERON:0003135!3.42e-07!11;UBERON:0000200!4.93e-07!6;UBERON:0002553!8.85e-07!61
|ontology_enrichment_uberon=UBERON:0007023!2.14e-54!114;UBERON:0001049!2.07e-39!56;UBERON:0005068!2.07e-39!56;UBERON:0006241!2.07e-39!56;UBERON:0007135!2.07e-39!56;UBERON:0001017!2.17e-37!81;UBERON:0000073!3.71e-37!53;UBERON:0002616!3.71e-37!53;UBERON:0002780!2.43e-35!41;UBERON:0001890!2.43e-35!41;UBERON:0003080!2.43e-35!41;UBERON:0006240!2.43e-35!41;UBERON:0001016!5.20e-34!89;UBERON:0001893!7.19e-31!34;UBERON:0003528!2.14e-30!34;UBERON:0002020!2.14e-30!34;UBERON:0001869!1.01e-29!32;UBERON:0003075!1.49e-29!82;UBERON:0007284!1.49e-29!82;UBERON:0002791!2.82e-29!32;UBERON:0002346!4.70e-29!86;UBERON:0000955!1.17e-28!68;UBERON:0006238!1.17e-28!68;UBERON:0003056!1.78e-24!61;UBERON:0000956!2.46e-23!25;UBERON:0000203!2.46e-23!25;UBERON:0011216!1.15e-22!223;UBERON:0002619!4.40e-22!22;UBERON:0010371!1.04e-21!104;UBERON:0001950!3.85e-20!20;UBERON:0004121!1.85e-19!171;UBERON:0000924!1.85e-19!171;UBERON:0006601!1.85e-19!171;UBERON:0010314!5.28e-17!132;UBERON:0000477!8.22e-12!373;UBERON:0000481!7.66e-11!342;UBERON:0002420!2.87e-09!9;UBERON:0007245!2.87e-09!9;UBERON:0010009!2.87e-09!9;UBERON:0010011!2.87e-09!9;UBERON:0000454!2.87e-09!9;UBERON:0000064!7.20e-09!218;UBERON:0000025!1.04e-08!192;UBERON:0004111!1.36e-08!240;UBERON:0000125!1.83e-08!9;UBERON:0002308!1.83e-08!9;UBERON:0000062!3.75e-08!503;UBERON:0000922!9.55e-08!592;UBERON:0001871!1.28e-07!6;UBERON:0009663!2.17e-07!7;UBERON:0003135!3.42e-07!11;UBERON:0000200!4.93e-07!6;UBERON:0002553!8.85e-07!61
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}}
}}

Revision as of 15:47, 26 November 2012


Full id: C2892_caudate_hippocampus_putamen_amygdala_testis_granulosa_skeletal



Phase1 CAGE Peaks

Hg19::chr7:29845929..29845940,+p4@WIPF3
Hg19::chr7:29846099..29846181,+p1@WIPF3
Hg19::chr7:29874392..29874406,+p9@WIPF3
Hg19::chr7:29954723..29954724,+p@chr7:29954723..29954724
+


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
adult organism2.14e-54114
neural tube2.07e-3956
neural rod2.07e-3956
future spinal cord2.07e-3956
neural keel2.07e-3956
central nervous system2.17e-3781
regional part of nervous system3.71e-3753
regional part of brain3.71e-3753
regional part of forebrain2.43e-3541
forebrain2.43e-3541
anterior neural tube2.43e-3541
future forebrain2.43e-3541
nervous system5.20e-3489
telencephalon7.19e-3134
brain grey matter2.14e-3034
gray matter2.14e-3034
cerebral hemisphere1.01e-2932
neural plate1.49e-2982
presumptive neural plate1.49e-2982
regional part of telencephalon2.82e-2932
neurectoderm4.70e-2986
brain1.17e-2868
future brain1.17e-2868
pre-chordal neural plate1.78e-2461
cerebral cortex2.46e-2325
pallium2.46e-2325
organ system subdivision1.15e-22223
regional part of cerebral cortex4.40e-2222
ecto-epithelium1.04e-21104
neocortex3.85e-2020
ectoderm-derived structure1.85e-19171
ectoderm1.85e-19171
presumptive ectoderm1.85e-19171
structure with developmental contribution from neural crest5.28e-17132
anatomical cluster8.22e-12373
multi-tissue structure7.66e-11342
basal ganglion2.87e-099
nuclear complex of neuraxis2.87e-099
aggregate regional part of brain2.87e-099
collection of basal ganglia2.87e-099
cerebral subcortex2.87e-099
organ part7.20e-09218
tube1.04e-08192
anatomical conduit1.36e-08240
neural nucleus1.83e-089
nucleus of brain1.83e-089
organ3.75e-08503
embryo9.55e-08592
temporal lobe1.28e-076
telencephalic nucleus2.17e-077
male reproductive organ3.42e-0711
gyrus4.93e-076
anatomical cavity8.85e-0761


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.

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