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Coexpression cluster:C4017: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4017_Mesenchymal_Dendritic_salivary_submaxillary_brain_retina_CD14
|full_id=C4017_Mesenchymal_Dendritic_salivary_submaxillary_brain_retina_CD14
|id=C4017
|id=C4017

Revision as of 17:03, 12 September 2012


Full id: C4017_Mesenchymal_Dendritic_salivary_submaxillary_brain_retina_CD14



Phase1 CAGE Peaks

Hg19::chr20:23614470..23614517,+p@chr20:23614470..23614517
+
Hg19::chr20:23618279..23618323,+p@chr20:23618279..23618323
+
Hg19::chr20:23618584..23618603,-p1@CST3


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-cellular organism2.79e-32659
anatomical system2.45e-31625
anatomical group5.37e-31626
adult organism2.71e-29115
germ layer8.31e-28604
embryonic tissue8.31e-28604
presumptive structure8.31e-28604
epiblast (generic)8.31e-28604
embryonic structure1.26e-27605
developing anatomical structure1.26e-27605
embryo2.13e-26612
organ1.14e-23511
lateral plate mesoderm5.59e-18216
mesoderm4.58e-16448
mesoderm-derived structure4.58e-16448
presumptive mesoderm4.58e-16448
musculoskeletal system5.20e-16167
immune system4.64e-15115
anatomical conduit8.50e-15241
tube1.19e-14194
anatomical cluster1.13e-13286
bone marrow1.35e-1380
neural tube6.29e-1357
neural rod6.29e-1357
future spinal cord6.29e-1357
neural keel6.29e-1357
hemolymphoid system1.73e-12112
regional part of brain3.59e-1259
epithelium5.84e-12309
cell layer8.36e-12312
hematopoietic system9.66e-12102
blood island9.66e-12102
bone element1.97e-1186
organism subdivision2.36e-11365
skeletal element2.52e-11101
skeletal system2.52e-11101
neural plate2.73e-1186
presumptive neural plate2.73e-1186
tissue4.89e-11787
multi-tissue structure7.60e-10347
brain8.11e-1069
future brain8.11e-1069
anterior neural tube1.98e-0942
telencephalon2.06e-0934
head2.20e-09123
neurectoderm2.55e-0990
gray matter2.58e-0934
brain grey matter2.58e-0934
regional part of forebrain4.89e-0941
forebrain4.89e-0941
future forebrain4.89e-0941
regional part of telencephalon6.34e-0933
anterior region of body7.67e-09129
craniocervical region7.67e-09129
cerebral hemisphere9.94e-0932
central nervous system1.36e-0882
pre-chordal neural plate5.37e-0861
epithelial tube1.81e-07118
regional part of cerebral cortex2.23e-0722
organ part8.35e-07219


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
NR3C1#290829.982015554115360.01278474365547170.0460502101270498



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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