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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C4496_oral_chronic_small_Hep2_cervical_choriocarcinoma_synovial
|full_id=C4496_oral_chronic_small_Hep2_cervical_choriocarcinoma_synovial
|gostat_on_coexpression_clusters=GO:0017056!structural constituent of nuclear pore!0.00989049805722359!9631$GO:0065002!intracellular protein transport across a membrane!0.014257730965608!9631$GO:0051028!mRNA transport!0.014257730965608!9631$GO:0005643!nuclear pore!0.014257730965608!9631$GO:0050658!RNA transport!0.014257730965608!9631$GO:0051236!establishment of RNA localization!0.014257730965608!9631$GO:0050657!nucleic acid transport!0.014257730965608!9631$GO:0006403!RNA localization!0.014257730965608!9631$GO:0046930!pore complex!0.014257730965608!9631$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.014257730965608!9631$GO:0044453!nuclear membrane part!0.014257730965608!9631$GO:0031965!nuclear membrane!0.0157440581319069!9631$GO:0006913!nucleocytoplasmic transport!0.0157440581319069!9631$GO:0051169!nuclear transport!0.0157440581319069!9631$GO:0005635!nuclear envelope!0.0182738726009655!9631$GO:0006886!intracellular protein transport!0.0467149417167079!9631$GO:0031967!organelle envelope!0.0489815141881549!9631$GO:0031975!envelope!0.0489815141881549!9631
|id=C4496
|id=C4496
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C4496_oral_chronic_small_Hep2_cervical_choriocarcinoma_synovial



Phase1 CAGE Peaks

Hg19::chr5:34915771..34915791,+p3@BRIX1
Hg19::chr5:34915805..34915847,+p1@BRIX1
Hg19::chr5:37371163..37371231,-p1@NUP155


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:0017056structural constituent of nuclear pore0.00989049805722359
GO:0065002intracellular protein transport across a membrane0.014257730965608
GO:0051028mRNA transport0.014257730965608
GO:0005643nuclear pore0.014257730965608
GO:0050658RNA transport0.014257730965608
GO:0051236establishment of RNA localization0.014257730965608
GO:0050657nucleic acid transport0.014257730965608
GO:0006403RNA localization0.014257730965608
GO:0046930pore complex0.014257730965608
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.014257730965608
GO:0044453nuclear membrane part0.014257730965608
GO:0031965nuclear membrane0.0157440581319069
GO:0006913nucleocytoplasmic transport0.0157440581319069
GO:0051169nuclear transport0.0157440581319069
GO:0005635nuclear envelope0.0182738726009655
GO:0006886intracellular protein transport0.0467149417167079
GO:0031967organelle envelope0.0489815141881549
GO:0031975envelope0.0489815141881549



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.