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Coexpression cluster:C2243: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.0095376984328009
|tf_chipseq_enrich=CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.0095376984328009
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}}
}}

Revision as of 15:23, 26 November 2012


Full id: C2243_extraskeletal_pineal_Neutrophils_cerebellum_small_large_Prostate



Phase1 CAGE Peaks

Hg19::chr12:81206226..81206230,-p@chr12:81206226..81206230
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Hg19::chr12:81273421..81273425,-p@chr12:81273421..81273425
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Hg19::chr12:81331460..81331505,-p1@LIN7A
Hg19::chr12:81331512..81331533,-p3@LIN7A


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>


Uber Anatomy
Ontology termp-valuen
adult organism4.18e-22114
central nervous system1.27e-2081
nervous system3.16e-2089
regional part of nervous system1.39e-1853
regional part of brain1.39e-1853
neural tube1.50e-1856
neural rod1.50e-1856
future spinal cord1.50e-1856
neural keel1.50e-1856
neurectoderm8.83e-1886
brain3.03e-1768
future brain3.03e-1768
neural plate6.02e-1682
presumptive neural plate6.02e-1682
regional part of forebrain1.01e-1541
forebrain1.01e-1541
anterior neural tube1.01e-1541
future forebrain1.01e-1541
hematopoietic system1.08e-1498
blood island1.08e-1498
multi-cellular organism2.86e-14656
hemolymphoid system3.21e-13108
brain grey matter5.23e-1334
gray matter5.23e-1334
cerebral hemisphere9.72e-1332
telencephalon1.05e-1234
regional part of telencephalon1.58e-1232
skeletal system1.59e-12100
pre-chordal neural plate1.71e-1261
bone marrow4.03e-1276
ectoderm-derived structure6.57e-12171
ectoderm6.57e-12171
presumptive ectoderm6.57e-12171
cerebral cortex1.70e-1125
pallium1.70e-1125
bone element1.74e-1182
skeletal element1.75e-1190
germ layer4.19e-11560
germ layer / neural crest4.19e-11560
embryonic tissue4.19e-11560
presumptive structure4.19e-11560
germ layer / neural crest derived structure4.19e-11560
epiblast (generic)4.19e-11560
embryonic structure9.44e-11564
embryo1.45e-10592
regional part of cerebral cortex1.71e-1022
anatomical system4.03e-10624
anatomical group6.66e-10625
developing anatomical structure7.41e-10581
structure with developmental contribution from neural crest9.91e-10132
neocortex1.81e-0920
ecto-epithelium2.29e-09104
organ system subdivision2.46e-09223
immune system4.16e-0993
tissue9.00e-09773
musculoskeletal system2.05e-07167
organ3.80e-07503


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
CTBP2#1488231.35850016966410.001492676882047230.0095376984328009



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.