Personal tools

Coexpression cluster:C1796

From FANTOM5_SSTAR

Revision as of 12:13, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1796_Keratinocyte_Small_Mallassezderived_cervical_Mammary_oral_malignant



Phase1 CAGE Peaks

Hg19::chr18:20494023..20494034,+p@chr18:20494023..20494034
+
Hg19::chr18:20494048..20494055,+p@chr18:20494048..20494055
+
Hg19::chr18:20494064..20494069,+p@chr18:20494064..20494069
+
Hg19::chr18:20494078..20494108,+p@chr18:20494078..20494108
+
Hg19::chr18:20494114..20494129,+p@chr18:20494114..20494129
+


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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.42e-24169
endoderm1.42e-24169
presumptive endoderm1.42e-24169
digestive system2.52e-18155
digestive tract2.52e-18155
primitive gut2.52e-18155
respiratory system2.36e-1672
subdivision of digestive tract4.72e-14129
endodermal part of digestive tract4.72e-14129
mixed endoderm/mesoderm-derived structure4.39e-13130
orifice3.38e-1235
anatomical space8.41e-12104
oral opening3.76e-1121
endo-epithelium9.82e-1182
immaterial anatomical entity3.07e-10126
respiratory tract1.02e-0953
mouth1.92e-0928
stomodeum1.92e-0928
foregut7.16e-0998
neck2.40e-0810
epithelial bud2.46e-0837
gland of gut8.11e-0810
thoracic cavity element1.18e-0734
thoracic cavity1.18e-0734
organ1.52e-07511
thoracic segment organ2.74e-0735
gland4.01e-0759
tracheobronchial tree6.41e-0714
lower respiratory tract6.41e-0714
urinary system structure6.43e-0744
embryo7.12e-07612
urothelium7.34e-075
Disease
Ontology termp-valuen
squamous cell carcinoma1.52e-1414
carcinoma1.64e-08106


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
BCL11A#53335528.36945510360715.43377642717329e-083.43938288653061e-06
EP300#203356.77394172622327.00901578206049e-050.0011081056604036
ESR1#2099530.76860329615453.62044058097993e-082.40837703080868e-06
FOXA1#3169511.08141974938555.98116883436141e-060.000178936491518726
GATA3#2625527.2365163572066.66232132211975e-084.0619158001218e-06
HDAC2#3066513.41562023662632.29961139448262e-068.17736174424143e-05
JUND#372756.994663941871035.97069468343598e-050.000984019854889332
NANOG#79923529.24477848101274.66760911383881e-083.04294899026349e-06
NR3C1#2908514.9730233311731.32777388277837e-065.24475705535136e-05
SP1#666755.69838137814090.000166391843712550.00204276451927766
TCF7L2#6934510.77017656313736.89693748574565e-060.000199752982272266



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.