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Coexpression cluster:C2901: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!8.31e-31!94;UBERON:0001016!8.31e-31!94;UBERON:0001017!3.66e-30!82;UBERON:0005743!5.75e-30!86;UBERON:0001049!5.52e-29!57;UBERON:0005068!5.52e-29!57;UBERON:0006241!5.52e-29!57;UBERON:0007135!5.52e-29!57;UBERON:0000955!5.32e-27!69;UBERON:0006238!5.32e-27!69;UBERON:0007023!1.02e-26!115;UBERON:0002616!4.77e-25!59;UBERON:0002346!6.58e-24!90;UBERON:0003075!1.57e-23!86;UBERON:0007284!1.57e-23!86;UBERON:0003080!1.30e-22!42;UBERON:0002780!3.96e-22!41;UBERON:0001890!3.96e-22!41;UBERON:0006240!3.96e-22!41;UBERON:0001893!3.12e-20!34;UBERON:0002020!4.80e-20!34;UBERON:0003528!4.80e-20!34;UBERON:0002791!1.09e-19!33;UBERON:0001869!4.86e-19!32;UBERON:0000924!5.19e-18!173;UBERON:0006601!5.19e-18!173;UBERON:0003056!8.87e-18!61;UBERON:0004121!1.77e-17!169;UBERON:0000153!9.17e-16!129;UBERON:0007811!9.17e-16!129;UBERON:0000956!2.39e-15!25;UBERON:0000203!2.39e-15!25;UBERON:0000033!7.78e-15!123;UBERON:0002619!4.51e-14!22;UBERON:0001950!3.09e-13!20;UBERON:0003076!1.51e-07!15;UBERON:0003057!1.51e-07!15;UBERON:0000062!5.97e-07!511
|ontology_enrichment_uberon=UBERON:0000073!8.31e-31!94;UBERON:0001016!8.31e-31!94;UBERON:0001017!3.66e-30!82;UBERON:0005743!5.75e-30!86;UBERON:0001049!5.52e-29!57;UBERON:0005068!5.52e-29!57;UBERON:0006241!5.52e-29!57;UBERON:0007135!5.52e-29!57;UBERON:0000955!5.32e-27!69;UBERON:0006238!5.32e-27!69;UBERON:0007023!1.02e-26!115;UBERON:0002616!4.77e-25!59;UBERON:0002346!6.58e-24!90;UBERON:0003075!1.57e-23!86;UBERON:0007284!1.57e-23!86;UBERON:0003080!1.30e-22!42;UBERON:0002780!3.96e-22!41;UBERON:0001890!3.96e-22!41;UBERON:0006240!3.96e-22!41;UBERON:0001893!3.12e-20!34;UBERON:0002020!4.80e-20!34;UBERON:0003528!4.80e-20!34;UBERON:0002791!1.09e-19!33;UBERON:0001869!4.86e-19!32;UBERON:0000924!5.19e-18!173;UBERON:0006601!5.19e-18!173;UBERON:0003056!8.87e-18!61;UBERON:0004121!1.77e-17!169;UBERON:0000153!9.17e-16!129;UBERON:0007811!9.17e-16!129;UBERON:0000956!2.39e-15!25;UBERON:0000203!2.39e-15!25;UBERON:0000033!7.78e-15!123;UBERON:0002619!4.51e-14!22;UBERON:0001950!3.09e-13!20;UBERON:0003076!1.51e-07!15;UBERON:0003057!1.51e-07!15;UBERON:0000062!5.97e-07!511
|tf_chipseq_enrich=EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200110608836138!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101663664671474!MAX#4149;4:6.45255550900712:0.000576761319564549:0.0048667993418439!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000795528754584731!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129985863533511!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509184863052922!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.00068333925413298
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}}
}}

Revision as of 13:40, 5 September 2012


Full id: C2901_occipital_parietal_temporal_duodenum_non_brain_granulocyte



Phase1 CAGE Peaks

Hg19::chr7:69063408..69063445,+p1@AUTS2
Hg19::chr7:69063451..69063472,+p2@AUTS2
Hg19::chr7:69063473..69063494,+p5@AUTS2
Hg19::chr7:69063511..69063531,+p3@AUTS2


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 system8.31e-3194
nervous system8.31e-3194
central nervous system3.66e-3082
neural tube5.52e-2957
neural rod5.52e-2957
future spinal cord5.52e-2957
neural keel5.52e-2957
brain5.32e-2769
future brain5.32e-2769
adult organism1.02e-26115
regional part of brain4.77e-2559
neurectoderm6.58e-2490
neural plate1.57e-2386
presumptive neural plate1.57e-2386
anterior neural tube1.30e-2242
regional part of forebrain3.96e-2241
forebrain3.96e-2241
future forebrain3.96e-2241
telencephalon3.12e-2034
gray matter4.80e-2034
brain grey matter4.80e-2034
regional part of telencephalon1.09e-1933
cerebral hemisphere4.86e-1932
ectoderm5.19e-18173
presumptive ectoderm5.19e-18173
pre-chordal neural plate8.87e-1861
ectoderm-derived structure1.77e-17169
anterior region of body9.17e-16129
craniocervical region9.17e-16129
cerebral cortex2.39e-1525
pallium2.39e-1525
head7.78e-15123
regional part of cerebral cortex4.51e-1422
neocortex3.09e-1320
posterior neural tube1.51e-0715
chordal neural plate1.51e-0715
organ5.97e-07511


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
EBF1#187948.9064668465690.00015887907472010.00200110608836138
EGR1#195844.988179094810140.001615011500076050.0101663664671474
MAX#414946.452555509007120.0005767613195645490.0048667993418439
NRF1#4899412.21027944771094.49717228915276e-050.000795528754584731
RAD21#5885410.35503389545638.6948481184721e-050.00129985863533511
USF1#739146.361499277207960.0006105011399140830.00509184863052922
USF2#7392412.99219738506963.50833029870167e-050.00068333925413298



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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