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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C1526_cervical_chorionic_alveolar_Synoviocyte_oral_CD14_normal
|full_id=C1526_cervical_chorionic_alveolar_Synoviocyte_oral_CD14_normal
|gostat_on_coexpression_clusters=GO:0030217!T cell differentiation!0.0328211468267985!1958$GO:0007611!learning and/or memory!0.0328211468267985!1958$GO:0030098!lymphocyte differentiation!0.0328211468267985!1958$GO:0002521!leukocyte differentiation!0.0328211468267985!1958$GO:0042110!T cell activation!0.0328211468267985!1958$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0328211468267985!1958$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0328211468267985!1958$GO:0046649!lymphocyte activation!0.0328211468267985!1958$GO:0030097!hemopoiesis!0.0328211468267985!1958$GO:0048534!hemopoietic or lymphoid organ development!0.0328211468267985!1958$GO:0045321!leukocyte activation!0.0328211468267985!1958$GO:0002520!immune system development!0.0328211468267985!1958$GO:0045892!negative regulation of transcription, DNA-dependent!0.0328211468267985!1958$GO:0001775!cell activation!0.0328211468267985!1958$GO:0045893!positive regulation of transcription, DNA-dependent!0.0328211468267985!1958$GO:0045941!positive regulation of transcription!0.0335360212612067!1958$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0335360212612067!1958$GO:0016481!negative regulation of transcription!0.0335360212612067!1958$GO:0007610!behavior!0.0335360212612067!1958$GO:0016563!transcription activator activity!0.0335360212612067!1958$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0335360212612067!1958$GO:0031325!positive regulation of cellular metabolic process!0.0359671199811609!1958$GO:0031324!negative regulation of cellular metabolic process!0.0359671199811609!1958$GO:0009893!positive regulation of metabolic process!0.0359671199811609!1958$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.03702143846969!1958$GO:0009892!negative regulation of metabolic process!0.03702143846969!1958
|id=C1526
|id=C1526
}}
}}

Revision as of 17:35, 18 May 2012


Full id: C1526_cervical_chorionic_alveolar_Synoviocyte_oral_CD14_normal



Phase1 CAGE Peaks

Hg19::chr5:137801546..137801573,-p@chr5:137801546..137801573
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Hg19::chr5:137802485..137802611,-p@chr5:137802485..137802611
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Hg19::chr5:137802624..137802791,-p@chr5:137802624..137802791
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Hg19::chr5:137803060..137803134,-p@chr5:137803060..137803134
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Hg19::chr5:137803278..137803323,-p1@CU687283
Hg19::chr5:137804484..137804498,+p2@EGR1


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:0030217T cell differentiation0.0328211468267985
GO:0007611learning and/or memory0.0328211468267985
GO:0030098lymphocyte differentiation0.0328211468267985
GO:0002521leukocyte differentiation0.0328211468267985
GO:0042110T cell activation0.0328211468267985
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0328211468267985
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0328211468267985
GO:0046649lymphocyte activation0.0328211468267985
GO:0030097hemopoiesis0.0328211468267985
GO:0048534hemopoietic or lymphoid organ development0.0328211468267985
GO:0045321leukocyte activation0.0328211468267985
GO:0002520immune system development0.0328211468267985
GO:0045892negative regulation of transcription, DNA-dependent0.0328211468267985
GO:0001775cell activation0.0328211468267985
GO:0045893positive regulation of transcription, DNA-dependent0.0328211468267985
GO:0045941positive regulation of transcription0.0335360212612067
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0335360212612067
GO:0016481negative regulation of transcription0.0335360212612067
GO:0007610behavior0.0335360212612067
GO:0016563transcription activator activity0.0335360212612067
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0335360212612067
GO:0031325positive regulation of cellular metabolic process0.0359671199811609
GO:0031324negative regulation of cellular metabolic process0.0359671199811609
GO:0009893positive regulation of metabolic process0.0359671199811609
GO:0006357regulation of transcription from RNA polymerase II promoter0.03702143846969
GO:0009892negative regulation of metabolic process0.03702143846969



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.