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Coexpression cluster:C3121: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323660115991625!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.00022120416992845
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323660115991625!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.00022120416992845
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}}
}}

Revision as of 15:56, 26 November 2012


Full id: C3121_Osteoblast_cerebellum_temporal_postcentral_occipital_Myoblast_pons



Phase1 CAGE Peaks

Hg19::chr11:1770316..1770338,-p2@IFITM10
Hg19::chr11:1770353..1770372,-p4@IFITM10
Hg19::chr11:1770450..1770481,-p3@IFITM10


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
cell of skeletal muscle6.99e-079
Uber Anatomy
Ontology termp-valuen
neural tube6.81e-3356
neural rod6.81e-3356
future spinal cord6.81e-3356
neural keel6.81e-3356
regional part of nervous system4.48e-3153
regional part of brain4.48e-3153
neural plate3.51e-2782
presumptive neural plate3.51e-2782
adult organism4.00e-27114
brain4.29e-2768
future brain4.29e-2768
central nervous system7.14e-2681
neurectoderm8.01e-2586
ecto-epithelium3.02e-24104
nervous system3.50e-2289
regional part of forebrain2.74e-2141
forebrain2.74e-2141
anterior neural tube2.74e-2141
future forebrain2.74e-2141
telencephalon8.85e-2034
brain grey matter9.47e-2034
gray matter9.47e-2034
cerebral hemisphere1.34e-1832
pre-chordal neural plate1.65e-1861
structure with developmental contribution from neural crest1.80e-18132
regional part of telencephalon4.44e-1832
regional part of cerebral cortex1.32e-1722
ectoderm-derived structure2.16e-17171
ectoderm2.16e-17171
presumptive ectoderm2.16e-17171
neocortex2.99e-1620
cerebral cortex1.40e-1525
pallium1.40e-1525
posterior neural tube5.13e-1315
chordal neural plate5.13e-1315
segmental subdivision of nervous system4.15e-1213
segmental subdivision of hindbrain2.19e-1112
hindbrain2.19e-1112
presumptive hindbrain2.19e-1112
organ system subdivision4.21e-10223
multi-tissue structure6.92e-09342
regional part of metencephalon7.32e-099
metencephalon7.32e-099
future metencephalon7.32e-099
gyrus3.05e-076
brainstem7.88e-076


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
E2F1#186934.907389214879320.008460985347239390.0323660115991625
SUZ12#23512350.11578091106297.93834897779404e-060.00022120416992845



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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