Personal tools

Coexpression cluster:C2609

From FANTOM5_SSTAR

Revision as of 08:37, 18 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2609_Dendritic_anaplastic_Neutrophils_hairy_migratory_adult_acute



Phase1 CAGE Peaks

Hg19::chr20:23029233..23029266,-p2@THBD
Hg19::chr9:139926533..139926546,-p1@FUT7
Hg19::chr9:139926550..139926561,-p2@FUT7
Hg19::chr9:139926567..139926578,-p4@FUT7


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:0032496response to lipopolysaccharide0.00793183603597481
GO:0046920alpha(1,3)-fucosyltransferase activity0.00793183603597481
GO:0010165response to X-ray0.00793183603597481
GO:0019317fucose catabolic process0.00793183603597481
GO:0042355L-fucose catabolic process0.00793183603597481
GO:0002237response to molecule of bacterial origin0.00793183603597481
GO:0042354L-fucose metabolic process0.00793183603597481
GO:0051591response to cAMP0.00793183603597481
GO:0010212response to ionizing radiation0.00833218849866979
GO:0006004fucose metabolic process0.00865240253491506
GO:0008417fucosyltransferase activity0.00943856771636449
GO:0010033response to organic substance0.0297820990700115
GO:0007565female pregnancy0.033923185148474
GO:0007596blood coagulation0.033923185148474
GO:0009314response to radiation0.033923185148474
GO:0050817coagulation0.033923185148474
GO:0007599hemostasis0.033923185148474
GO:0009617response to bacterium0.033923185148474
GO:0050878regulation of body fluid levels0.0377176375041188
GO:0042060wound healing0.0377176375041188
GO:0019320hexose catabolic process0.0380163926467462
GO:0046365monosaccharide catabolic process0.0380163926467462
GO:0046164alcohol catabolic process0.0380163926467462
GO:0009628response to abiotic stimulus0.0380163926467462
GO:0006486protein amino acid glycosylation0.0380163926467462
GO:0043413biopolymer glycosylation0.0380163926467462
GO:0009101glycoprotein biosynthetic process0.0380163926467462
GO:0044275cellular carbohydrate catabolic process0.0380163926467462
GO:0016052carbohydrate catabolic process0.0380904031704503
GO:0051707response to other organism0.0385932546624681
GO:0009100glycoprotein metabolic process0.0385932546624681
GO:0009790embryonic development0.0422235260882838
GO:0019318hexose metabolic process0.0461195912984867
GO:0005996monosaccharide metabolic process0.0461195912984867
GO:0016758transferase activity, transferring hexosyl groups0.0461195912984867
GO:0009607response to biotic stimulus0.0461195912984867
GO:0022414reproductive process0.047346240696365



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.