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Coexpression cluster:C1684: Difference between revisions

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|tf_chipseq_enrich=REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301384546151783!TAL1#6886;4:23.8948933419522:6.10828383356726e-06:0.000181543271284556
|tf_chipseq_enrich=REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301384546151783!TAL1#6886;4:23.8948933419522:6.10828383356726e-06:0.000181543271284556
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}}
}}

Revision as of 15:02, 26 November 2012


Full id: C1684_serous_gall_rectal_colon_chorionic_adult_non



Phase1 CAGE Peaks

Hg19::chr12:71148228..71148248,-p6@PTPRR
Hg19::chr12:71148329..71148334,-p15@PTPRR
Hg19::chr12:71148357..71148369,-p7@PTPRR
Hg19::chr12:71148381..71148405,-p3@PTPRR
Hg19::chr12:71148413..71148422,-p11@PTPRR


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>disease_data<br>

Cell Type
Ontology termp-valuen
chorionic membrane mesenchymal stem cell2.73e-103
seromucus secreting cell3.82e-072
Uber Anatomy
Ontology termp-valuen
regional part of cerebral cortex7.67e-2022
regional part of forebrain7.42e-1941
forebrain7.42e-1941
anterior neural tube7.42e-1941
future forebrain7.42e-1941
neocortex8.75e-1920
adult organism4.39e-18114
neural tube1.28e-1756
neural rod1.28e-1756
future spinal cord1.28e-1756
neural keel1.28e-1756
cerebral cortex3.64e-1725
pallium3.64e-1725
cerebral hemisphere3.93e-1732
regional part of nervous system5.12e-1753
regional part of brain5.12e-1753
telencephalon6.27e-1634
regional part of telencephalon6.16e-1532
brain grey matter7.04e-1434
gray matter7.04e-1434
brain2.66e-1368
future brain2.66e-1368
central nervous system1.46e-1181
pre-chordal neural plate3.04e-1161
organ system subdivision3.08e-11223
gyrus4.61e-116
neural plate2.21e-1082
presumptive neural plate2.21e-1082
acellular anatomical structure2.73e-103
egg chorion2.73e-103
nervous system6.86e-1089
neurectoderm1.15e-0986
hindgut2.04e-0819
ecto-epithelium4.71e-08104
gastrointestinal system1.02e-0725
intestine1.49e-0717
gland of diencephalon2.01e-074
neuroendocrine gland2.01e-074
chorion2.08e-077
pineal body2.66e-072
regional part of epithalamus2.66e-072
secretory circumventricular organ2.66e-072
circumventricular organ2.66e-072
epithalamus2.66e-072
organ part4.96e-07218
large intestine7.78e-0711
urinary bladder8.96e-072
lower urinary tract8.96e-072
Disease
Ontology termp-valuen
carcinoma3.22e-08106
squamous cell carcinoma9.90e-0714


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
REST#597859.650028716128021.19441074361324e-050.000301384546151783
TAL1#6886423.89489334195226.10828383356726e-060.000181543271284556



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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