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{{Coexpression_clusters
 
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|gostat_on_coexpression_clusters=GO:0003702!RNA polymerase II transcription factor activity!0.0105280880666253!2494;3171$GO:0001678!cell glucose homeostasis!0.0105280880666253!3171$GO:0042592!homeostatic process!0.0105280880666253!2494;3171$GO:0009267!cellular response to starvation!0.0105280880666253!3171$GO:0031669!cellular response to nutrient levels!0.0105280880666253!3171$GO:0004065!arylsulfatase activity!0.0105280880666253!415$GO:0042594!response to starvation!0.0105280880666253!3171$GO:0031668!cellular response to extracellular stimulus!0.0105280880666253!3171$GO:0042593!glucose homeostasis!0.0105280880666253!3171$GO:0033554!cellular response to stress!0.0105280880666253!3171$GO:0033500!carbohydrate homeostasis!0.0105280880666253!3171$GO:0043565!sequence-specific DNA binding!0.0130242900715327!2494;3171$GO:0051716!cellular response to stimulus!0.0130242900715327!3171$GO:0065008!regulation of biological quality!0.0130242900715327!2494;3171$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0130242900715327!2494$GO:0008484!sulfuric ester hydrolase activity!0.0144693029843891!415$GO:0003704!specific RNA polymerase II transcription factor activity!0.016593720844225!3171$GO:0031667!response to nutrient levels!0.0238504556699512!3171$GO:0003700!transcription factor activity!0.0238504556699512!2494;3171$GO:0009991!response to extracellular stimulus!0.0238504556699512!3171$GO:0048856!anatomical structure development!0.0383789720749396!2494;415$GO:0003707!steroid hormone receptor activity!0.0383789720749396!2494$GO:0007275!multicellular organismal development!0.0459567706342884!2494;415$GO:0004879!ligand-dependent nuclear receptor activity!0.0459567706342884!2494
 
|id=C1825
 
|id=C1825
 
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Revision as of 08:36, 18 May 2012


Full id: C1825_pancreas_Hepatocyte_liver_colon_gastric_hepatoma_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr19:46367576..46367592,+p1@FOXA3
Hg19::chr1:199996702..199996732,+p5@NR5A2
Hg19::chr1:199996733..199996781,+p1@NR5A2
Hg19::chr6:107235378..107235418,-p1@ENST00000430094
Hg19::chrX:2882296..2882356,-p1@ARSE


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:0003702RNA polymerase II transcription factor activity0.0105280880666253
GO:0001678cell glucose homeostasis0.0105280880666253
GO:0042592homeostatic process0.0105280880666253
GO:0009267cellular response to starvation0.0105280880666253
GO:0031669cellular response to nutrient levels0.0105280880666253
GO:0004065arylsulfatase activity0.0105280880666253
GO:0042594response to starvation0.0105280880666253
GO:0031668cellular response to extracellular stimulus0.0105280880666253
GO:0042593glucose homeostasis0.0105280880666253
GO:0033554cellular response to stress0.0105280880666253
GO:0033500carbohydrate homeostasis0.0105280880666253
GO:0043565sequence-specific DNA binding0.0130242900715327
GO:0051716cellular response to stimulus0.0130242900715327
GO:0065008regulation of biological quality0.0130242900715327
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0130242900715327
GO:0008484sulfuric ester hydrolase activity0.0144693029843891
GO:0003704specific RNA polymerase II transcription factor activity0.016593720844225
GO:0031667response to nutrient levels0.0238504556699512
GO:0003700transcription factor activity0.0238504556699512
GO:0009991response to extracellular stimulus0.0238504556699512
GO:0048856anatomical structure development0.0383789720749396
GO:0003707steroid hormone receptor activity0.0383789720749396
GO:0007275multicellular organismal development0.0459567706342884
GO:0004879ligand-dependent nuclear receptor activity0.0459567706342884



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.