Personal tools

Coexpression cluster:C3704

From FANTOM5_SSTAR

Revision as of 19:23, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3704_Eosinophils_Basophils_Mast_CD14_mature_immature_Neutrophils



Phase1 CAGE Peaks

Hg19::chr17:8339189..8339285,+p1@NDEL1
Hg19::chr19:39897478..39897493,+p1@ZFP36
Hg19::chr8:103667935..103667960,-p1@KLF10


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:0000289poly(A) tail shortening0.00339482700640546
GO:0017091AU-rich element binding0.00339482700640546
GO:0050779RNA destabilization0.00339482700640546
GO:0048731system development0.00339482700640546
GO:0048856anatomical structure development0.00529648511130244
GO:0007275multicellular organismal development0.00650898764464172
GO:0000288mRNA catabolic process, deadenylation-dependent decay0.00650898764464172
GO:0043487regulation of RNA stability0.00931831515612074
GO:0043488regulation of mRNA stability0.00931831515612074
GO:0031348negative regulation of defense response0.00931831515612074
GO:0050728negative regulation of inflammatory response0.00931831515612074
GO:0032502developmental process0.0102721473776894
GO:0031124mRNA 3'-end processing0.0122633274630083
GO:0032501multicellular organismal process0.0126504045457779
GO:0045638negative regulation of myeloid cell differentiation0.0126504045457779
GO:0031123RNA 3'-end processing0.0126504045457779
GO:0051252regulation of RNA metabolic process0.0126504045457779
GO:0003727single-stranded RNA binding0.0126504045457779
GO:0031347regulation of defense response0.0142296101213018
GO:0050727regulation of inflammatory response0.0142296101213018
GO:0006402mRNA catabolic process0.0157184797707154
GO:0045637regulation of myeloid cell differentiation0.016401392162261
GO:0003729mRNA binding0.016401392162261
GO:0048583regulation of response to stimulus0.016401392162261
GO:0048523negative regulation of cellular process0.016401392162261
GO:0048513organ development0.016401392162261
GO:0048519negative regulation of biological process0.0169359510998705
GO:0006401RNA catabolic process0.0186902118941852
GO:0007179transforming growth factor beta receptor signaling pathway0.0196126044726536
GO:0045596negative regulation of cell differentiation0.0246356198112062
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.026074786722757
GO:0030099myeloid cell differentiation0.026074786722757
GO:0051093negative regulation of developmental process0.026074786722757
GO:0005819spindle0.026074786722757
GO:0048869cellular developmental process0.0294175409287247
GO:0030154cell differentiation0.0294175409287247
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0385264091806844
GO:0005813centrosome0.0385264091806844
GO:0045595regulation of cell differentiation0.0416849547241876
GO:0005815microtubule organizing center0.0416849547241876
GO:0030097hemopoiesis0.0445230348524182
GO:0048534hemopoietic or lymphoid organ development0.0466859166721047
GO:0002520immune system development0.0479597324192457



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><br>

Uber Anatomy
Ontology termp-valuen
hematopoietic system3.34e-21102
blood island3.34e-21102
hemolymphoid system2.29e-19112
bone marrow4.50e-1880
bone element4.80e-1686
skeletal element1.15e-14101
skeletal system1.15e-14101
immune system3.46e-14115
adult organism2.82e-12115
musculoskeletal system2.67e-07167


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3704&oldid=1992199"