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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C4399_Neutrophils_CD14_Whole_Eosinophils_CD19_migratory_spleen
|full_id=C4399_Neutrophils_CD14_Whole_Eosinophils_CD19_migratory_spleen
|gostat_on_coexpression_clusters=GO:0004409!homoaconitate hydratase activity!0.00322604381779525!6891$GO:0046967!cytosol to ER transport!0.00322604381779525!6891$GO:0042825!TAP complex!0.00322604381779525!6891$GO:0015433!peptide antigen-transporting ATPase activity!0.00322604381779525!6891$GO:0015440!peptide-transporting ATPase activity!0.00322604381779525!6891$GO:0046980!tapasin binding!0.00322604381779525!6891$GO:0046977!TAP binding!0.00322604381779525!6891$GO:0042824!MHC class I peptide loading complex!0.00322604381779525!6891$GO:0046979!TAP2 binding!0.00322604381779525!6891$GO:0046978!TAP1 binding!0.00322604381779525!6891$GO:0042301!phosphate binding!0.00403243606120116!6891$GO:0015198!oligopeptide transporter activity!0.00403243606120116!6891$GO:0015197!peptide transporter activity!0.00496285212327168!6891$GO:0042288!MHC class I protein binding!0.00518433170739016!6891$GO:0002483!antigen processing and presentation of endogenous peptide antigen!0.00763905561147222!6891$GO:0019885!antigen processing and presentation of endogenous peptide antigen via MHC class I!0.00763905561147222!6891$GO:0006857!oligopeptide transport!0.00763905561147222!6891$GO:0042605!peptide antigen binding!0.00763905561147222!6891$GO:0019883!antigen processing and presentation of endogenous antigen!0.00763905561147222!6891$GO:0042287!MHC protein binding!0.00927228213987372!6891$GO:0015833!peptide transport!0.0149703443648315!6891$GO:0005788!endoplasmic reticulum lumen!0.0234414163837479!6891$GO:0016836!hydro-lyase activity!0.0313176878355985!6891$GO:0016835!carbon-oxygen lyase activity!0.0313176878355985!6891$GO:0002474!antigen processing and presentation of peptide antigen via MHC class I!0.0313176878355985!6891$GO:0048002!antigen processing and presentation of peptide antigen!0.0313176878355985!6891$GO:0046982!protein heterodimerization activity!0.0313176878355985!6891$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0365148045338801!3660$GO:0042803!protein homodimerization activity!0.0438413389976883!6891$GO:0003823!antigen binding!0.0474629779509783!6891
|id=C4399
|id=C4399
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C4399_Neutrophils_CD14_Whole_Eosinophils_CD19_migratory_spleen



Phase1 CAGE Peaks

Hg19::chr4:185395633..185395651,-p2@IRF2
Hg19::chr6:32806472..32806481,-p7@TAP2
Hg19::chr6:32806483..32806503,-p3@TAP2


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:0004409homoaconitate hydratase activity0.00322604381779525
GO:0046967cytosol to ER transport0.00322604381779525
GO:0042825TAP complex0.00322604381779525
GO:0015433peptide antigen-transporting ATPase activity0.00322604381779525
GO:0015440peptide-transporting ATPase activity0.00322604381779525
GO:0046980tapasin binding0.00322604381779525
GO:0046977TAP binding0.00322604381779525
GO:0042824MHC class I peptide loading complex0.00322604381779525
GO:0046979TAP2 binding0.00322604381779525
GO:0046978TAP1 binding0.00322604381779525
GO:0042301phosphate binding0.00403243606120116
GO:0015198oligopeptide transporter activity0.00403243606120116
GO:0015197peptide transporter activity0.00496285212327168
GO:0042288MHC class I protein binding0.00518433170739016
GO:0002483antigen processing and presentation of endogenous peptide antigen0.00763905561147222
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.00763905561147222
GO:0006857oligopeptide transport0.00763905561147222
GO:0042605peptide antigen binding0.00763905561147222
GO:0019883antigen processing and presentation of endogenous antigen0.00763905561147222
GO:0042287MHC protein binding0.00927228213987372
GO:0015833peptide transport0.0149703443648315
GO:0005788endoplasmic reticulum lumen0.0234414163837479
GO:0016836hydro-lyase activity0.0313176878355985
GO:0016835carbon-oxygen lyase activity0.0313176878355985
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0313176878355985
GO:0048002antigen processing and presentation of peptide antigen0.0313176878355985
GO:0046982protein heterodimerization activity0.0313176878355985
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0365148045338801
GO:0042803protein homodimerization activity0.0438413389976883
GO:0003823antigen binding0.0474629779509783



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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


No analysis results for this cluster

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.