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Coexpression cluster:C2016: Difference between revisions

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|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0319007109210127
|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0319007109210127
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}}
}}

Revision as of 15:14, 26 November 2012


Full id: C2016_Fibroblast_corpus_Nucleus_Anulus_globus_tridermal_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr9:113800341..113800373,-p4@LPAR1
Hg19::chr9:113800377..113800400,-p6@LPAR1
Hg19::chr9:113800467..113800520,-p2@LPAR1
Hg19::chr9:113800705..113800781,-p1@LPAR1
Hg19::chr9:113800994..113801032,-p3@LPAR1


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
multi-tissue structure1.12e-22342
multi-cellular organism2.87e-21656
anatomical system6.51e-18624
structure with developmental contribution from neural crest1.24e-17132
anatomical group1.41e-17625
dense mesenchyme tissue1.24e-1573
paraxial mesoderm3.62e-1572
presumptive paraxial mesoderm3.62e-1572
embryonic structure5.22e-15564
multilaminar epithelium5.34e-1583
somite6.62e-1571
presomitic mesoderm6.62e-1571
presumptive segmental plate6.62e-1571
dermomyotome6.62e-1571
trunk paraxial mesoderm6.62e-1571
germ layer6.69e-15560
germ layer / neural crest6.69e-15560
embryonic tissue6.69e-15560
presumptive structure6.69e-15560
germ layer / neural crest derived structure6.69e-15560
epiblast (generic)6.69e-15560
cell layer1.37e-14309
surface structure2.73e-1499
epithelium5.46e-14306
tissue1.17e-13773
developing anatomical structure1.31e-13581
adult organism1.56e-13114
embryo2.15e-13592
muscle tissue7.85e-1364
musculature7.85e-1364
musculature of body7.85e-1364
epithelial vesicle1.22e-1278
neural tube1.36e-1256
neural rod1.36e-1256
future spinal cord1.36e-1256
neural keel1.36e-1256
skeletal muscle tissue1.56e-1262
striated muscle tissue1.56e-1262
myotome1.56e-1262
brain1.65e-1268
future brain1.65e-1268
mesenchyme2.06e-12160
entire embryonic mesenchyme2.06e-12160
organ2.11e-12503
anatomical cluster2.13e-12373
ectoderm-derived structure2.49e-12171
ectoderm2.49e-12171
presumptive ectoderm2.49e-12171
trunk mesenchyme3.28e-11122
nervous system3.40e-1189
regional part of nervous system3.90e-1153
regional part of brain3.90e-1153
organ system subdivision5.50e-11223
organism subdivision6.16e-11264
neural plate7.21e-1182
presumptive neural plate7.21e-1182
central nervous system7.45e-1181
neurectoderm2.19e-1086
ecto-epithelium2.55e-09104
regional part of forebrain3.45e-0941
forebrain3.45e-0941
anterior neural tube3.45e-0941
future forebrain3.45e-0941
telencephalon4.85e-0934
brain grey matter6.54e-0934
gray matter6.54e-0934
anatomical conduit7.43e-09240
regional part of telencephalon4.37e-0832
cerebral hemisphere5.34e-0832
subdivision of skeletal system9.96e-0816
trunk3.01e-07199
integument4.29e-0746
integumental system4.29e-0746
organ part4.52e-07218
organ component layer7.72e-0766
musculoskeletal system7.77e-07167
regional part of cerebral cortex9.28e-0722


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
RAD21#588536.21302033727380.007751055068811640.0319007109210127



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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