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Coexpression cluster:C4269: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.80e-45!115;UBERON:0001049!8.13e-32!57;UBERON:0005068!8.13e-32!57;UBERON:0006241!8.13e-32!57;UBERON:0007135!8.13e-32!57;UBERON:0001017!1.15e-30!82;UBERON:0002616!1.03e-29!59;UBERON:0005743!1.04e-28!86;UBERON:0000955!1.32e-28!69;UBERON:0006238!1.32e-28!69;UBERON:0000073!5.63e-27!94;UBERON:0001016!5.63e-27!94;UBERON:0003080!6.41e-25!42;UBERON:0002780!1.92e-24!41;UBERON:0001890!1.92e-24!41;UBERON:0006240!1.92e-24!41;UBERON:0002346!1.03e-21!90;UBERON:0003075!3.08e-21!86;UBERON:0007284!3.08e-21!86;UBERON:0001893!7.47e-20!34;UBERON:0002020!1.01e-19!34;UBERON:0003528!1.01e-19!34;UBERON:0002791!2.36e-19!33;UBERON:0001869!9.04e-19!32;UBERON:0000153!1.03e-16!129;UBERON:0007811!1.03e-16!129;UBERON:0003056!1.80e-15!61;UBERON:0000033!2.41e-15!123;UBERON:0000956!1.16e-14!25;UBERON:0000203!1.16e-14!25;UBERON:0002619!7.92e-14!22;UBERON:0001950!8.25e-13!20;UBERON:0000924!8.95e-13!173;UBERON:0006601!8.95e-13!173;UBERON:0004121!2.98e-12!169;UBERON:0000477!1.63e-08!286;UBERON:0003076!4.86e-08!15;UBERON:0003057!4.86e-08!15;UBERON:0000025!3.10e-07!194;UBERON:0004111!6.04e-07!241;UBERON:0002420!9.71e-07!9;UBERON:0007245!9.71e-07!9;UBERON:0010009!9.71e-07!9;UBERON:0010011!9.71e-07!9;UBERON:0000454!9.71e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.80e-45!115;UBERON:0001049!8.13e-32!57;UBERON:0005068!8.13e-32!57;UBERON:0006241!8.13e-32!57;UBERON:0007135!8.13e-32!57;UBERON:0001017!1.15e-30!82;UBERON:0002616!1.03e-29!59;UBERON:0005743!1.04e-28!86;UBERON:0000955!1.32e-28!69;UBERON:0006238!1.32e-28!69;UBERON:0000073!5.63e-27!94;UBERON:0001016!5.63e-27!94;UBERON:0003080!6.41e-25!42;UBERON:0002780!1.92e-24!41;UBERON:0001890!1.92e-24!41;UBERON:0006240!1.92e-24!41;UBERON:0002346!1.03e-21!90;UBERON:0003075!3.08e-21!86;UBERON:0007284!3.08e-21!86;UBERON:0001893!7.47e-20!34;UBERON:0002020!1.01e-19!34;UBERON:0003528!1.01e-19!34;UBERON:0002791!2.36e-19!33;UBERON:0001869!9.04e-19!32;UBERON:0000153!1.03e-16!129;UBERON:0007811!1.03e-16!129;UBERON:0003056!1.80e-15!61;UBERON:0000033!2.41e-15!123;UBERON:0000956!1.16e-14!25;UBERON:0000203!1.16e-14!25;UBERON:0002619!7.92e-14!22;UBERON:0001950!8.25e-13!20;UBERON:0000924!8.95e-13!173;UBERON:0006601!8.95e-13!173;UBERON:0004121!2.98e-12!169;UBERON:0000477!1.63e-08!286;UBERON:0003076!4.86e-08!15;UBERON:0003057!4.86e-08!15;UBERON:0000025!3.10e-07!194;UBERON:0004111!6.04e-07!241;UBERON:0002420!9.71e-07!9;UBERON:0007245!9.71e-07!9;UBERON:0010009!9.71e-07!9;UBERON:0010011!9.71e-07!9;UBERON:0000454!9.71e-07!9
|tf_chipseq_enrich=FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582665954735712!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107456175007658!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015716655048321!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666145354902322!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197525072852855!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330317405186629!ZZZ3#26009;3:239.413212435233:7.25894005043406e-08:4.37964436699759e-06
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}}
}}

Revision as of 12:31, 5 September 2012


Full id: C4269_anaplastic_parietal_salivary_small_seminal_pineal_ductus



Phase1 CAGE Peaks

Hg19::chr3:114819047..114819069,-p16@ZBTB20
Hg19::chr3:114819073..114819100,-p10@ZBTB20
Hg19::chr3:114819101..114819121,-p7@ZBTB20


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 organism1.80e-45115
neural tube8.13e-3257
neural rod8.13e-3257
future spinal cord8.13e-3257
neural keel8.13e-3257
central nervous system1.15e-3082
regional part of brain1.03e-2959
brain1.32e-2869
future brain1.32e-2869
regional part of nervous system5.63e-2794
nervous system5.63e-2794
anterior neural tube6.41e-2542
regional part of forebrain1.92e-2441
forebrain1.92e-2441
future forebrain1.92e-2441
neurectoderm1.03e-2190
neural plate3.08e-2186
presumptive neural plate3.08e-2186
telencephalon7.47e-2034
gray matter1.01e-1934
brain grey matter1.01e-1934
regional part of telencephalon2.36e-1933
cerebral hemisphere9.04e-1932
anterior region of body1.03e-16129
craniocervical region1.03e-16129
pre-chordal neural plate1.80e-1561
head2.41e-15123
cerebral cortex1.16e-1425
pallium1.16e-1425
regional part of cerebral cortex7.92e-1422
neocortex8.25e-1320
ectoderm8.95e-13173
presumptive ectoderm8.95e-13173
ectoderm-derived structure2.98e-12169
anatomical cluster1.63e-08286
posterior neural tube4.86e-0815
chordal neural plate4.86e-0815
tube3.10e-07194
anatomical conduit6.04e-07241
basal ganglion9.71e-079
nuclear complex of neuraxis9.71e-079
aggregate regional part of brain9.71e-079
collection of basal ganglia9.71e-079
cerebral subcortex9.71e-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

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

TF#promotersEnrichmentp-valueq-value
FOXA1#3169311.08141974938550.000734755275698670.00582665954735712
FOXA2#3170324.63046375266526.68983856509345e-050.00107456175007658
JUND#372736.994663941871030.002921845042734990.015716655048321
RAD21#5885310.35503389545630.0009004912073565420.00666145354902322
TRIM28#10155318.59052504526250.0001555969297255280.00197525072852855
YY1#752834.911170749853860.008441455341808260.0330317405186629
ZZZ3#260093239.4132124352337.25894005043406e-084.37964436699759e-06



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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