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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3736_Keratinocyte_Mammary_salivary_Mallassezderived_Bronchial_keratoacanthoma_Gingival
|full_id=C3736_Keratinocyte_Mammary_salivary_Mallassezderived_Bronchial_keratoacanthoma_Gingival
|id=C3736
|id=C3736

Revision as of 16:42, 12 September 2012


Full id: C3736_Keratinocyte_Mammary_salivary_Mallassezderived_Bronchial_keratoacanthoma_Gingival



Phase1 CAGE Peaks

Hg19::chr18:61144049..61144064,+p2@SERPINB5
Hg19::chr18:61144160..61144214,+p1@SERPINB5
Hg19::chr18:61171128..61171130,+p@chr18:61171128..61171130
+


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
respiratory system3.68e-2872
endoderm-derived structure6.86e-27169
endoderm6.86e-27169
presumptive endoderm6.86e-27169
respiratory tract1.12e-2153
digestive system4.17e-20155
digestive tract4.17e-20155
primitive gut4.17e-20155
mixed endoderm/mesoderm-derived structure1.26e-18130
segment of respiratory tract1.51e-1846
subdivision of digestive tract1.27e-17129
endodermal part of digestive tract1.27e-17129
respiratory primordium3.81e-1738
endoderm of foregut3.81e-1738
foregut2.51e-1498
thoracic segment organ1.37e-1135
epithelial bud1.56e-1137
orifice1.61e-1135
thoracic cavity element3.23e-1134
thoracic cavity3.23e-1134
anatomical space5.92e-11104
oral opening1.96e-0921
respiratory system epithelium2.08e-0928
endo-epithelium4.47e-0982
upper respiratory tract6.77e-0919
immaterial anatomical entity1.01e-08126
larynx1.20e-089
respiratory tract epithelium1.52e-0819
lung epithelium1.52e-0819
lung1.84e-0822
respiratory tube1.84e-0822
respiration organ1.84e-0822
pair of lungs1.84e-0822
lung primordium1.84e-0822
lung bud1.84e-0822
epithelial fold3.39e-0851
reproductive structure5.25e-0859
reproductive system5.25e-0859
internal genitalia5.96e-0825
organ1.33e-07511
mouth1.67e-0728
stomodeum1.67e-0728
thoracic segment of trunk2.70e-0752
embryonic uterus4.85e-0722
mesenchyme5.24e-07238
entire embryonic mesenchyme5.24e-07238
internal female genitalia6.38e-0722
organ segment6.82e-0797
reproductive organ6.99e-0748
female organism7.34e-0741
extraembryonic membrane8.93e-0714
membranous layer8.93e-0714
Disease
Ontology termp-valuen
carcinoma1.52e-25106
cell type cancer4.61e-17143
squamous cell carcinoma2.19e-1214
adenocarcinoma2.77e-0825
cancer5.87e-08235
disease of cellular proliferation1.23e-07239


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
SMC3#9126210.02995522995520.0126656379767470.0457442530225639



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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