Personal tools

Coexpression cluster:C1188

From FANTOM5_SSTAR

Revision as of 14:44, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1188_Urothelial_Gingival_Keratinocyte_Mallassezderived_Bronchial_Tracheal_Prostate



Phase1 CAGE Peaks

Hg19::chr13:75017232..75017235,+p@chr13:75017232..75017235
+
Hg19::chr14:21510511..21510528,+p1@RNASE7
Hg19::chr14:67878804..67878812,-p3@PLEK2
Hg19::chr14:67878829..67878909,-p1@PLEK2
Hg19::chr19:3136220..3136277,+p1@GNA15
Hg19::chr2:74649337..74649349,+p2@WDR54
Hg19::chr3:12800723..12800747,-p2@TMEM40


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:0007207muscarinic acetylcholine receptor, phospholipase C activating pathway0.0392052976735397



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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.78e-18160
endoderm1.78e-18160
presumptive endoderm1.78e-18160
respiratory system9.63e-1474
orifice1.70e-1236
digestive system4.98e-12145
digestive tract4.98e-12145
primitive gut4.98e-12145
endo-epithelium1.30e-1082
oral opening1.81e-1022
respiratory tract2.75e-0954
epithelial bud5.37e-0937
urothelium5.38e-095
surface structure6.04e-0999
anatomical space1.07e-0895
subdivision of digestive tract2.70e-08118
mouth2.99e-0829
stomodeum2.99e-0829
epithelial fold5.83e-0847
neck6.19e-0810
foregut7.69e-0887
extraembryonic membrane9.19e-0814
membranous layer9.19e-0814
pharyngeal arch system1.16e-0718
anterior region of body1.26e-0762
craniocervical region1.26e-0762
urinary system structure1.44e-0747
transitional epithelium2.35e-076
mucosa2.58e-0720
renal system2.68e-0748
respiratory system epithelium2.90e-0728
immaterial anatomical entity4.20e-07117
thoracic cavity element4.42e-0734
thoracic cavity4.42e-0734
organism subdivision6.73e-07264
thoracic segment organ9.21e-0735
Disease
Ontology termp-valuen
squamous cell carcinoma1.54e-1514


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
TFAP2A#702037.079414731304980.006452554472180970.0280300447766454



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.