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Coexpression cluster:C2012: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!5.14e-78!114;UBERON:0001049!1.71e-29!56;UBERON:0005068!1.71e-29!56;UBERON:0006241!1.71e-29!56;UBERON:0007135!1.71e-29!56;UBERON:0000073!1.20e-26!53;UBERON:0002616!1.20e-26!53;UBERON:0003075!4.35e-23!82;UBERON:0007284!4.35e-23!82;UBERON:0002780!5.80e-23!41;UBERON:0001890!5.80e-23!41;UBERON:0003080!5.80e-23!41;UBERON:0006240!5.80e-23!41;UBERON:0002346!2.79e-21!86;UBERON:0001017!2.83e-21!81;UBERON:0000955!8.04e-21!68;UBERON:0006238!8.04e-21!68;UBERON:0001016!8.35e-19!89;UBERON:0003528!7.53e-18!34;UBERON:0002020!7.53e-18!34;UBERON:0001893!1.06e-17!34;UBERON:0010314!1.27e-17!132;UBERON:0010371!1.49e-16!104;UBERON:0011216!2.34e-16!223;UBERON:0002791!2.94e-16!32;UBERON:0001869!3.81e-16!32;UBERON:0003056!1.96e-15!61;UBERON:0004121!4.69e-13!171;UBERON:0000924!4.69e-13!171;UBERON:0006601!4.69e-13!171;UBERON:0002619!5.46e-13!22;UBERON:0000477!1.65e-11!373;UBERON:0000481!2.29e-11!342;UBERON:0001950!2.32e-11!20;UBERON:0000956!7.25e-11!25;UBERON:0000203!7.25e-11!25;UBERON:0004111!7.76e-10!240;UBERON:0000062!8.78e-10!503;UBERON:0002420!2.72e-09!9;UBERON:0007245!2.72e-09!9;UBERON:0010009!2.72e-09!9;UBERON:0010011!2.72e-09!9;UBERON:0000454!2.72e-09!9;UBERON:0000125!3.88e-09!9;UBERON:0002308!3.88e-09!9;UBERON:0000064!3.89e-09!218;UBERON:0004457!1.56e-08!12;UBERON:0000042!1.56e-08!12;UBERON:0000025!7.13e-08!192;UBERON:0003076!1.04e-07!15;UBERON:0003057!1.04e-07!15;UBERON:0000468!1.70e-07!656;UBERON:0009663!1.82e-07!7;UBERON:0003688!2.34e-07!6;UBERON:0002358!2.34e-07!6;UBERON:0003684!2.34e-07!6;UBERON:0001178!2.34e-07!6;UBERON:0002298!3.46e-07!6;UBERON:0001894!6.45e-07!7;UBERON:0006222!6.45e-07!7
|ontology_enrichment_uberon=UBERON:0007023!5.14e-78!114;UBERON:0001049!1.71e-29!56;UBERON:0005068!1.71e-29!56;UBERON:0006241!1.71e-29!56;UBERON:0007135!1.71e-29!56;UBERON:0000073!1.20e-26!53;UBERON:0002616!1.20e-26!53;UBERON:0003075!4.35e-23!82;UBERON:0007284!4.35e-23!82;UBERON:0002780!5.80e-23!41;UBERON:0001890!5.80e-23!41;UBERON:0003080!5.80e-23!41;UBERON:0006240!5.80e-23!41;UBERON:0002346!2.79e-21!86;UBERON:0001017!2.83e-21!81;UBERON:0000955!8.04e-21!68;UBERON:0006238!8.04e-21!68;UBERON:0001016!8.35e-19!89;UBERON:0003528!7.53e-18!34;UBERON:0002020!7.53e-18!34;UBERON:0001893!1.06e-17!34;UBERON:0010314!1.27e-17!132;UBERON:0010371!1.49e-16!104;UBERON:0011216!2.34e-16!223;UBERON:0002791!2.94e-16!32;UBERON:0001869!3.81e-16!32;UBERON:0003056!1.96e-15!61;UBERON:0004121!4.69e-13!171;UBERON:0000924!4.69e-13!171;UBERON:0006601!4.69e-13!171;UBERON:0002619!5.46e-13!22;UBERON:0000477!1.65e-11!373;UBERON:0000481!2.29e-11!342;UBERON:0001950!2.32e-11!20;UBERON:0000956!7.25e-11!25;UBERON:0000203!7.25e-11!25;UBERON:0004111!7.76e-10!240;UBERON:0000062!8.78e-10!503;UBERON:0002420!2.72e-09!9;UBERON:0007245!2.72e-09!9;UBERON:0010009!2.72e-09!9;UBERON:0010011!2.72e-09!9;UBERON:0000454!2.72e-09!9;UBERON:0000125!3.88e-09!9;UBERON:0002308!3.88e-09!9;UBERON:0000064!3.89e-09!218;UBERON:0004457!1.56e-08!12;UBERON:0000042!1.56e-08!12;UBERON:0000025!7.13e-08!192;UBERON:0003076!1.04e-07!15;UBERON:0003057!1.04e-07!15;UBERON:0000468!1.70e-07!656;UBERON:0009663!1.82e-07!7;UBERON:0003688!2.34e-07!6;UBERON:0002358!2.34e-07!6;UBERON:0003684!2.34e-07!6;UBERON:0001178!2.34e-07!6;UBERON:0002298!3.46e-07!6;UBERON:0001894!6.45e-07!7;UBERON:0006222!6.45e-07!7
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}}
}}

Revision as of 15:14, 26 November 2012


Full id: C2012_mature_lung_adipose_medulla_breast_vagina_penis



Phase1 CAGE Peaks

Hg19::chr8:38585834..38585867,+p6@TACC1
Hg19::chr8:38585882..38585897,+p12@TACC1
Hg19::chr8:38585926..38585943,+p16@TACC1
Hg19::chr8:38585964..38585975,+p19@TACC1
Hg19::chr8:38586002..38586022,+p8@TACC1


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><br>

Cell Type
Ontology termp-valuen
fat cell8.81e-1015
Uber Anatomy
Ontology termp-valuen
adult organism5.14e-78114
neural tube1.71e-2956
neural rod1.71e-2956
future spinal cord1.71e-2956
neural keel1.71e-2956
regional part of nervous system1.20e-2653
regional part of brain1.20e-2653
neural plate4.35e-2382
presumptive neural plate4.35e-2382
regional part of forebrain5.80e-2341
forebrain5.80e-2341
anterior neural tube5.80e-2341
future forebrain5.80e-2341
neurectoderm2.79e-2186
central nervous system2.83e-2181
brain8.04e-2168
future brain8.04e-2168
nervous system8.35e-1989
brain grey matter7.53e-1834
gray matter7.53e-1834
telencephalon1.06e-1734
structure with developmental contribution from neural crest1.27e-17132
ecto-epithelium1.49e-16104
organ system subdivision2.34e-16223
regional part of telencephalon2.94e-1632
cerebral hemisphere3.81e-1632
pre-chordal neural plate1.96e-1561
ectoderm-derived structure4.69e-13171
ectoderm4.69e-13171
presumptive ectoderm4.69e-13171
regional part of cerebral cortex5.46e-1322
anatomical cluster1.65e-11373
multi-tissue structure2.29e-11342
neocortex2.32e-1120
cerebral cortex7.25e-1125
pallium7.25e-1125
anatomical conduit7.76e-10240
organ8.78e-10503
basal ganglion2.72e-099
nuclear complex of neuraxis2.72e-099
aggregate regional part of brain2.72e-099
collection of basal ganglia2.72e-099
cerebral subcortex2.72e-099
neural nucleus3.88e-099
nucleus of brain3.88e-099
organ part3.89e-09218
cavity lining1.56e-0812
serous membrane1.56e-0812
tube7.13e-08192
posterior neural tube1.04e-0715
chordal neural plate1.04e-0715
multi-cellular organism1.70e-07656
telencephalic nucleus1.82e-077
omentum2.34e-076
peritoneum2.34e-076
abdominal cavity2.34e-076
visceral peritoneum2.34e-076
brainstem3.46e-076
diencephalon6.45e-077
future diencephalon6.45e-077


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.

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