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Coexpression cluster:C4557: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.16e-22!115;UBERON:0001049!1.06e-20!57;UBERON:0005068!1.06e-20!57;UBERON:0006241!1.06e-20!57;UBERON:0007135!1.06e-20!57;UBERON:0003080!6.63e-19!42;UBERON:0002780!1.61e-18!41;UBERON:0001890!1.61e-18!41;UBERON:0006240!1.61e-18!41;UBERON:0002346!1.33e-17!90;UBERON:0001017!3.11e-17!82;UBERON:0000955!7.08e-17!69;UBERON:0006238!7.08e-17!69;UBERON:0002020!7.68e-17!34;UBERON:0003528!7.68e-17!34;UBERON:0001893!1.50e-16!34;UBERON:0002616!1.89e-16!59;UBERON:0005743!3.86e-16!86;UBERON:0002791!4.07e-16!33;UBERON:0003075!7.73e-16!86;UBERON:0007284!7.73e-16!86;UBERON:0000073!1.00e-15!94;UBERON:0001016!1.00e-15!94;UBERON:0001869!1.88e-15!32;UBERON:0000956!1.24e-11!25;UBERON:0000203!1.24e-11!25;UBERON:0002619!2.33e-11!22;UBERON:0003056!4.83e-11!61;UBERON:0001950!3.59e-10!20;UBERON:0000924!4.00e-08!173;UBERON:0006601!4.00e-08!173;UBERON:0000033!3.45e-07!123;UBERON:0004121!4.35e-07!169;UBERON:0000153!5.06e-07!129;UBERON:0007811!5.06e-07!129;UBERON:0002308!7.93e-07!9;UBERON:0000125!7.93e-07!9;UBERON:0002420!9.96e-07!9;UBERON:0007245!9.96e-07!9;UBERON:0010009!9.96e-07!9;UBERON:0010011!9.96e-07!9;UBERON:0000454!9.96e-07!9
|ontology_enrichment_uberon=UBERON:0007023!7.76e-23!114;UBERON:0001049!6.18e-20!56;UBERON:0005068!6.18e-20!56;UBERON:0006241!6.18e-20!56;UBERON:0007135!6.18e-20!56;UBERON:0002780!1.78e-18!41;UBERON:0001890!1.78e-18!41;UBERON:0003080!1.78e-18!41;UBERON:0006240!1.78e-18!41;UBERON:0000073!3.70e-18!53;UBERON:0002616!3.70e-18!53;UBERON:0001017!7.91e-17!81;UBERON:0003528!8.62e-17!34;UBERON:0002020!8.62e-17!34;UBERON:0002346!1.24e-16!86;UBERON:0001016!1.35e-16!89;UBERON:0001893!1.41e-16!34;UBERON:0000955!1.57e-16!68;UBERON:0006238!1.57e-16!68;UBERON:0002791!1.17e-15!32;UBERON:0001869!1.83e-15!32;UBERON:0003075!6.42e-15!82;UBERON:0007284!6.42e-15!82;UBERON:0010314!1.49e-12!132;UBERON:0000956!1.46e-11!25;UBERON:0000203!1.46e-11!25;UBERON:0002619!4.58e-11!22;UBERON:0003056!7.07e-11!61;UBERON:0011216!1.13e-10!223;UBERON:0010371!6.78e-10!104;UBERON:0001950!7.17e-10!20;UBERON:0004121!5.67e-08!171;UBERON:0000924!5.67e-08!171;UBERON:0006601!5.67e-08!171;UBERON:0000477!5.58e-07!373;UBERON:0002420!6.98e-07!9;UBERON:0007245!6.98e-07!9;UBERON:0010009!6.98e-07!9;UBERON:0010011!6.98e-07!9;UBERON:0000454!6.98e-07!9;UBERON:0000125!7.46e-07!9;UBERON:0002308!7.46e-07!9
|tf_chipseq_enrich=TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197837688624353
|tf_chipseq_enrich=TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197837688624353
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}}
}}

Revision as of 16:02, 19 October 2012


Full id: C4557_eye_olfactory_spinal_thalamus_testicular_putamen_Cardiac



Phase1 CAGE Peaks

Hg19::chr6:131277237..131277257,-p7@EPB41L2
Hg19::chr6:131277274..131277298,-p8@EPB41L2
Hg19::chr6:131277349..131277414,-p3@EPB41L2


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 organism7.76e-23114
neural tube6.18e-2056
neural rod6.18e-2056
future spinal cord6.18e-2056
neural keel6.18e-2056
regional part of forebrain1.78e-1841
forebrain1.78e-1841
anterior neural tube1.78e-1841
future forebrain1.78e-1841
regional part of nervous system3.70e-1853
regional part of brain3.70e-1853
central nervous system7.91e-1781
brain grey matter8.62e-1734
gray matter8.62e-1734
neurectoderm1.24e-1686
nervous system1.35e-1689
telencephalon1.41e-1634
brain1.57e-1668
future brain1.57e-1668
regional part of telencephalon1.17e-1532
cerebral hemisphere1.83e-1532
neural plate6.42e-1582
presumptive neural plate6.42e-1582
structure with developmental contribution from neural crest1.49e-12132
cerebral cortex1.46e-1125
pallium1.46e-1125
regional part of cerebral cortex4.58e-1122
pre-chordal neural plate7.07e-1161
organ system subdivision1.13e-10223
ecto-epithelium6.78e-10104
neocortex7.17e-1020
ectoderm-derived structure5.67e-08171
ectoderm5.67e-08171
presumptive ectoderm5.67e-08171
anatomical cluster5.58e-07373
basal ganglion6.98e-079
nuclear complex of neuraxis6.98e-079
aggregate regional part of brain6.98e-079
collection of basal ganglia6.98e-079
cerebral subcortex6.98e-079
neural nucleus7.46e-079
nucleus of brain7.46e-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
TRIM28#10155318.59052504526250.0001555969297255280.00197837688624353



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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