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Coexpression cluster:C3838: Difference between revisions

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|full_id=C3838_skeletal_pineal_heart_tongue_throat_diaphragm_left
|full_id=C3838_skeletal_pineal_heart_tongue_throat_diaphragm_left
|id=C3838
|id=C3838
|ontology_enrichment_celltype=CL:0000147!6.15e-07!14
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:114!4.15e-10!2
|ontology_enrichment_uberon=UBERON:0007023!3.94e-60!115;UBERON:0001049!8.00e-40!57;UBERON:0005068!8.00e-40!57;UBERON:0006241!8.00e-40!57;UBERON:0007135!8.00e-40!57;UBERON:0005743!8.95e-36!86;UBERON:0003075!1.26e-35!86;UBERON:0007284!1.26e-35!86;UBERON:0002780!1.44e-35!41;UBERON:0001890!1.44e-35!41;UBERON:0006240!1.44e-35!41;UBERON:0003080!1.92e-34!42;UBERON:0002616!5.98e-34!59;UBERON:0001017!1.97e-33!82;UBERON:0002346!3.08e-33!90;UBERON:0000955!2.13e-32!69;UBERON:0006238!2.13e-32!69;UBERON:0000073!1.03e-30!94;UBERON:0001016!1.03e-30!94;UBERON:0003056!2.64e-27!61;UBERON:0001893!4.28e-27!34;UBERON:0002020!1.46e-26!34;UBERON:0003528!1.46e-26!34;UBERON:0002791!6.93e-26!33;UBERON:0001869!3.69e-25!32;UBERON:0000153!1.17e-24!129;UBERON:0007811!1.17e-24!129;UBERON:0000033!2.67e-22!123;UBERON:0001950!9.34e-21!20;UBERON:0002619!1.47e-20!22;UBERON:0004121!1.60e-19!169;UBERON:0000924!1.28e-18!173;UBERON:0006601!1.28e-18!173;UBERON:0000956!2.00e-17!25;UBERON:0000203!2.00e-17!25;UBERON:0000483!8.08e-12!309;UBERON:0000481!1.33e-11!347;UBERON:0000119!1.73e-11!312;UBERON:0002420!1.99e-11!9;UBERON:0007245!1.99e-11!9;UBERON:0010009!1.99e-11!9;UBERON:0010011!1.99e-11!9;UBERON:0000454!1.99e-11!9;UBERON:0002308!6.21e-11!9;UBERON:0000125!6.21e-11!9;UBERON:0001894!3.49e-10!7;UBERON:0006222!3.49e-10!7;UBERON:0000025!7.26e-10!194;UBERON:0004111!1.60e-09!241;UBERON:0000475!2.11e-09!365;UBERON:0009663!2.98e-09!7;UBERON:0000477!5.13e-09!286;UBERON:0000062!5.26e-09!511;UBERON:0000200!5.61e-09!6;UBERON:0001871!3.07e-08!7;UBERON:0000064!1.97e-07!219;UBERON:0002021!3.12e-07!5;UBERON:0003076!4.14e-07!15;UBERON:0003057!4.14e-07!15;UBERON:0000922!5.22e-07!612
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}}
}}

Revision as of 15:26, 19 October 2012


Full id: C3838_skeletal_pineal_heart_tongue_throat_diaphragm_left



Phase1 CAGE Peaks

Hg19::chr1:100643765..100643829,-p1@LRRC39
Hg19::chr2:97454321..97454332,+p6@CNNM4
Hg19::chr9:109681376..109681386,+p@chr9:109681376..109681386
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism3.67e-44114
regional part of nervous system1.42e-1853
regional part of brain1.42e-1853
neural tube2.16e-1756
neural rod2.16e-1756
future spinal cord2.16e-1756
neural keel2.16e-1756
structure with developmental contribution from neural crest7.86e-16132
neural plate8.24e-1682
presumptive neural plate8.24e-1682
brain3.08e-1568
future brain3.08e-1568
neurectoderm7.20e-1586
regional part of forebrain3.47e-1441
forebrain3.47e-1441
anterior neural tube3.47e-1441
future forebrain3.47e-1441
central nervous system7.84e-1481
nervous system4.67e-1289
ecto-epithelium1.56e-11104
pineal body1.68e-102
regional part of epithalamus1.68e-102
secretory circumventricular organ1.68e-102
circumventricular organ1.68e-102
epithalamus1.68e-102
pre-chordal neural plate2.49e-1061
muscle structure4.75e-102
muscle organ4.75e-102
telencephalon6.37e-1034
throat7.73e-102
primary circulatory organ1.22e-0927
ectoderm-derived structure1.65e-09171
ectoderm1.65e-09171
presumptive ectoderm1.65e-09171
neocortex8.33e-0920
cerebral hemisphere1.44e-0832
multi-tissue structure2.34e-08342
regional part of cerebral cortex5.82e-0822
tube3.06e-07192
valve3.74e-073
cardiac mesenchyme3.74e-073
cardial valve3.74e-073
tunica intima3.74e-073
heart layer3.74e-073
endocardium3.74e-073
endocardial cushion3.74e-073
presumptive endocardium3.74e-073
chordate pharynx4.54e-0710
pharyngeal region of foregut4.54e-0710
tongue4.74e-073
gustatory system4.74e-073
future tongue4.74e-073
cardiac chamber4.88e-073
cerebral cortex6.12e-0725
pallium6.12e-0725
anatomical conduit8.15e-07240
regional part of telencephalon8.38e-0732
Disease
Ontology termp-valuen
heart disease4.15e-102


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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