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Coexpression cluster:C2825: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.78672274784957e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444079077739603!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024490764305245!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114765301871352
|tf_chipseq_enrich=GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.78672274784957e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444079077739603!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024490764305245!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114765301871352
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}}
}}

Revision as of 15:44, 26 November 2012


Full id: C2825_cervical_gall_bile_rectal_epitheloid_large_umbilical



Phase1 CAGE Peaks

Hg19::chr5:58571724..58571727,-p8@uc003jsd.1
Hg19::chr5:58571770..58571781,-p7@uc003jsd.1
Hg19::chr5:58571807..58571821,-p24@PDE4D
Hg19::chr5:58571829..58571862,-p9@PDE4D


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


GO IDGO nameFDR corrected p-value
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.00638761332862357
GO:0005626insoluble fraction0.00912516189803367
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0107220652301896
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0107220652301896
GO:0005813centrosome0.0191628399858707
GO:0008081phosphoric diester hydrolase activity0.0191628399858707
GO:0005815microtubule organizing center0.0191628399858707
GO:0005625soluble fraction0.0266910985517485



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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism2.76e-26114
larynx1.85e-179
upper respiratory tract5.56e-1419
organ part8.34e-13218
organ system subdivision1.58e-12223
respiratory primordium2.68e-1238
endoderm of foregut2.68e-1238
respiratory tract4.78e-1154
subdivision of digestive tract1.14e-10118
digestive system2.71e-10145
digestive tract2.71e-10145
primitive gut2.71e-10145
segment of respiratory tract1.67e-0947
anatomical cluster2.18e-09373
organ4.20e-09503
endoderm-derived structure5.71e-09160
endoderm5.71e-09160
presumptive endoderm5.71e-09160
organ segment6.48e-0998
multi-tissue structure7.51e-09342
neocortex1.17e-0820
telencephalon8.24e-0834
regional part of cerebral cortex1.14e-0722
cerebral hemisphere2.08e-0732
foregut2.32e-0787
respiratory system3.48e-0774
large intestine5.01e-0711
neural tube5.93e-0756
neural rod5.93e-0756
future spinal cord5.93e-0756
neural keel5.93e-0756
regional part of forebrain6.22e-0741
forebrain6.22e-0741
anterior neural tube6.22e-0741
future forebrain6.22e-0741
Disease
Ontology termp-valuen
carcinoma7.78e-07106


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
GATA3#2625427.2365163572061.81561517799785e-066.78672274784957e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000444079077739603
TBP#690843.706770687096390.005296377814784350.024490764305245
TFAP2C#7022410.80922860986027.32289634782688e-050.00114765301871352



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.