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Coexpression cluster:C4294: Difference between revisions

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|full_id=C4294_Smooth_lung_bladder_colon_medulla_pituitary_retina
|full_id=C4294_Smooth_lung_bladder_colon_medulla_pituitary_retina
|id=C4294
|id=C4294
|ontology_enrichment_celltype=CL:0002504!1.59e-07!3;CL:1000279!1.59e-07!3;CL:1000280!1.59e-07!3
|ontology_enrichment_celltype=CL:0002504!2.70e-11!3;CL:1000279!2.70e-11!3;CL:1000280!2.70e-11!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.41e-59!115;UBERON:0001049!9.58e-40!57;UBERON:0005068!9.58e-40!57;UBERON:0006241!9.58e-40!57;UBERON:0007135!9.58e-40!57;UBERON:0002780!8.97e-36!41;UBERON:0001890!8.97e-36!41;UBERON:0006240!8.97e-36!41;UBERON:0002616!1.04e-35!59;UBERON:0003080!1.04e-34!42;UBERON:0003075!1.08e-31!86;UBERON:0007284!1.08e-31!86;UBERON:0001893!4.14e-30!34;UBERON:0000955!4.90e-30!69;UBERON:0006238!4.90e-30!69;UBERON:0001869!9.14e-30!32;UBERON:0002346!1.08e-29!90;UBERON:0001017!1.61e-29!82;UBERON:0005743!2.24e-29!86;UBERON:0002791!1.03e-28!33;UBERON:0002020!9.96e-28!34;UBERON:0003528!9.96e-28!34;UBERON:0000073!2.04e-25!94;UBERON:0001016!2.04e-25!94;UBERON:0002619!2.02e-23!22;UBERON:0001950!3.79e-23!20;UBERON:0003056!6.29e-23!61;UBERON:0000956!4.39e-20!25;UBERON:0000203!4.39e-20!25;UBERON:0000153!1.12e-17!129;UBERON:0007811!1.12e-17!129;UBERON:0000033!4.33e-16!123;UBERON:0004121!1.60e-13!169;UBERON:0000924!6.48e-13!173;UBERON:0006601!6.48e-13!173;UBERON:0000025!4.13e-12!194;UBERON:0000064!4.77e-12!219;UBERON:0000059!8.64e-12!11;UBERON:0001155!2.28e-11!9;UBERON:0000062!4.88e-11!511;UBERON:0000481!1.52e-10!347;UBERON:0001871!2.62e-10!7;UBERON:0004111!2.78e-10!241;UBERON:0000483!3.10e-09!309;UBERON:0002021!4.29e-09!5;UBERON:0002308!4.34e-09!9;UBERON:0000125!4.34e-09!9;UBERON:0000119!5.37e-09!312;UBERON:0002420!5.66e-09!9;UBERON:0007245!5.66e-09!9;UBERON:0010009!5.66e-09!9;UBERON:0010011!5.66e-09!9;UBERON:0000454!5.66e-09!9;UBERON:0000477!7.44e-09!286;UBERON:0009663!8.21e-09!7;UBERON:0003296!2.70e-08!4;UBERON:0010133!2.70e-08!4;UBERON:0000369!1.66e-07!4;UBERON:0002435!1.66e-07!4;UBERON:0000204!1.66e-07!4;UBERON:0010082!1.66e-07!4;UBERON:0000200!2.05e-07!6;UBERON:0000475!2.69e-07!365;UBERON:0001894!5.21e-07!7;UBERON:0006222!5.21e-07!7;UBERON:0003076!7.21e-07!15;UBERON:0003057!7.21e-07!15;UBERON:0001896!9.60e-07!3;UBERON:0005290!9.60e-07!3;UBERON:0010096!9.60e-07!3
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}}
}}

Revision as of 15:50, 19 October 2012


Full id: C4294_Smooth_lung_bladder_colon_medulla_pituitary_retina



Phase1 CAGE Peaks

Hg19::chr3:150966697..150966714,-p8@P2RY14
Hg19::chr3:150966718..150966738,-p9@P2RY14
Hg19::chr3:150966773..150966784,-p7@P2RY14


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
enteric smooth muscle cell2.70e-113
smooth muscle cell of large intestine2.70e-113
smooth muscle cell of colon2.70e-113
Uber Anatomy
Ontology termp-valuen
adult organism5.03e-47114
regional part of nervous system6.75e-2953
regional part of brain6.75e-2953
neural tube4.99e-2756
neural rod4.99e-2756
future spinal cord4.99e-2756
neural keel4.99e-2756
brain1.10e-2268
future brain1.10e-2268
regional part of forebrain2.22e-2141
forebrain2.22e-2141
anterior neural tube2.22e-2141
future forebrain2.22e-2141
neural plate5.42e-2082
presumptive neural plate5.42e-2082
central nervous system1.11e-1981
neurectoderm9.39e-1986
telencephalon5.17e-1834
organ system subdivision2.33e-17223
nervous system4.39e-1789
cerebral hemisphere7.82e-1732
ecto-epithelium8.79e-16104
brain grey matter1.15e-1534
gray matter1.15e-1534
structure with developmental contribution from neural crest2.15e-15132
large intestine8.48e-1511
pre-chordal neural plate1.07e-1461
regional part of telencephalon1.50e-1432
colon1.27e-139
regional part of cerebral cortex1.50e-1322
brainstem6.86e-136
neocortex2.56e-1220
multi-tissue structure3.90e-12342
cerebral cortex1.01e-1125
pallium1.01e-1125
intestine3.70e-1117
anatomical cluster1.03e-10373
organ part2.03e-10218
medulla oblongata2.82e-103
myelencephalon2.82e-103
future myelencephalon2.82e-103
ectoderm-derived structure5.59e-10171
ectoderm5.59e-10171
presumptive ectoderm5.59e-10171
segmental subdivision of hindbrain8.55e-0912
hindbrain8.55e-0912
presumptive hindbrain8.55e-0912
tube2.23e-08192
gyrus2.64e-086
segmental subdivision of nervous system4.58e-0813
anatomical conduit7.80e-08240
epithelium8.84e-08306
organ1.07e-07503
cell layer1.29e-07309
gastrointestinal system2.91e-0725
throat3.47e-072
posterior neural tube6.72e-0715
chordal neural plate6.72e-0715


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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