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Coexpression cluster:C4779: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!5.88e-22!94;UBERON:0001016!5.88e-22!94;UBERON:0002616!9.97e-22!59;UBERON:0001017!1.01e-20!82;UBERON:0005743!9.57e-20!86;UBERON:0001049!2.37e-19!57;UBERON:0005068!2.37e-19!57;UBERON:0006241!2.37e-19!57;UBERON:0007135!2.37e-19!57;UBERON:0000955!5.33e-19!69;UBERON:0006238!5.33e-19!69;UBERON:0007023!1.27e-18!115;UBERON:0003080!7.09e-18!42;UBERON:0002780!1.62e-17!41;UBERON:0001890!1.62e-17!41;UBERON:0006240!1.62e-17!41;UBERON:0000475!7.20e-17!365;UBERON:0000924!1.03e-16!173;UBERON:0006601!1.03e-16!173;UBERON:0004121!1.80e-16!169;UBERON:0001893!2.26e-16!34;UBERON:0001869!2.69e-16!32;UBERON:0002346!2.83e-16!90;UBERON:0003075!3.40e-16!86;UBERON:0007284!3.40e-16!86;UBERON:0002020!5.93e-16!34;UBERON:0003528!5.93e-16!34;UBERON:0002791!8.30e-16!33;UBERON:0000033!2.71e-14!123;UBERON:0002619!6.43e-14!22;UBERON:0000153!7.08e-14!129;UBERON:0007811!7.08e-14!129;UBERON:0003056!8.98e-14!61;UBERON:0001950!3.22e-13!20;UBERON:0000956!2.23e-12!25;UBERON:0000203!2.23e-12!25;UBERON:0002199!2.47e-12!45;UBERON:0002416!2.47e-12!45;UBERON:0002097!6.07e-11!40;UBERON:0000914!4.98e-10!83;UBERON:0002329!4.98e-10!83;UBERON:0003077!4.98e-10!83;UBERON:0003059!4.98e-10!83;UBERON:0007282!4.98e-10!83;UBERON:0009618!4.98e-10!83;UBERON:0007285!4.98e-10!83;UBERON:0003102!1.45e-09!95;UBERON:0000468!5.64e-09!659;UBERON:0000119!8.89e-09!312;UBERON:0000481!2.74e-08!347;UBERON:0000483!3.15e-08!309;UBERON:0004290!1.30e-07!70;UBERON:0000477!3.13e-07!286
|ontology_enrichment_uberon=UBERON:0000073!5.88e-22!94;UBERON:0001016!5.88e-22!94;UBERON:0002616!9.97e-22!59;UBERON:0001017!1.01e-20!82;UBERON:0005743!9.57e-20!86;UBERON:0001049!2.37e-19!57;UBERON:0005068!2.37e-19!57;UBERON:0006241!2.37e-19!57;UBERON:0007135!2.37e-19!57;UBERON:0000955!5.33e-19!69;UBERON:0006238!5.33e-19!69;UBERON:0007023!1.27e-18!115;UBERON:0003080!7.09e-18!42;UBERON:0002780!1.62e-17!41;UBERON:0001890!1.62e-17!41;UBERON:0006240!1.62e-17!41;UBERON:0000475!7.20e-17!365;UBERON:0000924!1.03e-16!173;UBERON:0006601!1.03e-16!173;UBERON:0004121!1.80e-16!169;UBERON:0001893!2.26e-16!34;UBERON:0001869!2.69e-16!32;UBERON:0002346!2.83e-16!90;UBERON:0003075!3.40e-16!86;UBERON:0007284!3.40e-16!86;UBERON:0002020!5.93e-16!34;UBERON:0003528!5.93e-16!34;UBERON:0002791!8.30e-16!33;UBERON:0000033!2.71e-14!123;UBERON:0002619!6.43e-14!22;UBERON:0000153!7.08e-14!129;UBERON:0007811!7.08e-14!129;UBERON:0003056!8.98e-14!61;UBERON:0001950!3.22e-13!20;UBERON:0000956!2.23e-12!25;UBERON:0000203!2.23e-12!25;UBERON:0002199!2.47e-12!45;UBERON:0002416!2.47e-12!45;UBERON:0002097!6.07e-11!40;UBERON:0000914!4.98e-10!83;UBERON:0002329!4.98e-10!83;UBERON:0003077!4.98e-10!83;UBERON:0003059!4.98e-10!83;UBERON:0007282!4.98e-10!83;UBERON:0009618!4.98e-10!83;UBERON:0007285!4.98e-10!83;UBERON:0003102!1.45e-09!95;UBERON:0000468!5.64e-09!659;UBERON:0000119!8.89e-09!312;UBERON:0000481!2.74e-08!347;UBERON:0000483!3.15e-08!309;UBERON:0004290!1.30e-07!70;UBERON:0000477!3.13e-07!286
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168599278642214!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187521327095786!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278505262499771
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}}
}}

Revision as of 13:54, 5 September 2012


Full id: C4779_cerebellum_occipital_Hair_Fibroblast_heart_caudate_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr8:93074803..93074845,-p1@RUNX1T1
Hg19::chr8:93074848..93074871,-p3@RUNX1T1
Hg19::chr8:93074872..93074884,-p10@RUNX1T1


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
fibroblast1.75e-2675
non-terminally differentiated cell2.96e-20180
skin fibroblast1.60e-1423
Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.88e-2294
nervous system5.88e-2294
regional part of brain9.97e-2259
central nervous system1.01e-2082
neural tube2.37e-1957
neural rod2.37e-1957
future spinal cord2.37e-1957
neural keel2.37e-1957
brain5.33e-1969
future brain5.33e-1969
adult organism1.27e-18115
anterior neural tube7.09e-1842
regional part of forebrain1.62e-1741
forebrain1.62e-1741
future forebrain1.62e-1741
organism subdivision7.20e-17365
ectoderm1.03e-16173
presumptive ectoderm1.03e-16173
ectoderm-derived structure1.80e-16169
telencephalon2.26e-1634
cerebral hemisphere2.69e-1632
neurectoderm2.83e-1690
neural plate3.40e-1686
presumptive neural plate3.40e-1686
gray matter5.93e-1634
brain grey matter5.93e-1634
regional part of telencephalon8.30e-1633
head2.71e-14123
regional part of cerebral cortex6.43e-1422
anterior region of body7.08e-14129
craniocervical region7.08e-14129
pre-chordal neural plate8.98e-1461
neocortex3.22e-1320
cerebral cortex2.23e-1225
pallium2.23e-1225
integument2.47e-1245
integumental system2.47e-1245
skin of body6.07e-1140
somite4.98e-1083
paraxial mesoderm4.98e-1083
presomitic mesoderm4.98e-1083
presumptive segmental plate4.98e-1083
trunk paraxial mesoderm4.98e-1083
presumptive paraxial mesoderm4.98e-1083
surface structure1.45e-0995
multi-cellular organism5.64e-09659
cell layer8.89e-09312
multi-tissue structure2.74e-08347
epithelium3.15e-08309
dermomyotome1.30e-0770
anatomical cluster3.13e-07286


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EP300#203336.77394172622320.003216880500103790.0168599278642214
MAX#414936.452555509007120.003721913834265510.0187521327095786
SIN3A#2594235.408884726815140.006318961977991520.0278505262499771



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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