Personal tools

Coexpression cluster:C1117

From FANTOM5_SSTAR

Revision as of 14:07, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1117_CD19_Eosinophils_Dendritic_Neutrophils_Basophils_CD14_CD34



Phase1 CAGE Peaks

Hg19::chr10:43932296..43932360,+p1@ZNF487P
Hg19::chr22:50629895..50629908,-p@chr22:50629895..50629908
-
Hg19::chr22:50630977..50630984,-p@chr22:50630977..50630984
-
Hg19::chr22:50639164..50639182,-p@chr22:50639164..50639182
-
Hg19::chr2:64880894..64880977,-p2@SERTAD2
Hg19::chr3:135914798..135914850,+p@chr3:135914798..135914850
+
Hg19::chr5:40681669..40681698,+p4@PTGER4


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:0004957prostaglandin E receptor activity0.0254229767174927
GO:0030278regulation of ossification0.0254229767174927
GO:0004955prostaglandin receptor activity0.0254229767174927
GO:0046850regulation of bone remodeling0.0254229767174927
GO:0004953icosanoid receptor activity0.0254229767174927
GO:0004954prostanoid receptor activity0.0254229767174927
GO:0030308negative regulation of cell growth0.0344450048876544
GO:0045792negative regulation of cell size0.0344450048876544
GO:0048856anatomical structure development0.0344450048876544
GO:0045926negative regulation of growth0.0344450048876544
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0354795642737389
GO:0019933cAMP-mediated signaling0.0354795642737389
GO:0031214biomineral formation0.0354795642737389
GO:0001503ossification0.0354795642737389
GO:0046849bone remodeling0.0361203882202558
GO:0048771tissue remodeling0.0370325943749413
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0382378355329935
GO:0019935cyclic-nucleotide-mediated signaling0.0382378355329935
GO:0001558regulation of cell growth0.0465793516965004
GO:0032502developmental process0.0465793516965004
GO:0003713transcription coactivator activity0.0471036744921992
GO:0016049cell growth0.0471036744921992
GO:0040008regulation of growth0.0471036744921992
GO:0008361regulation of cell size0.0471036744921992
GO:0001501skeletal development0.0471036744921992
GO:0045893positive regulation of transcription, DNA-dependent0.0483159197004316



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>


Cell Type
Ontology termp-valuen
leukocyte1.37e-52140
hematopoietic stem cell2.20e-50172
angioblastic mesenchymal cell2.20e-50172
hematopoietic cell1.48e-47182
hematopoietic oligopotent progenitor cell5.64e-46165
hematopoietic multipotent progenitor cell5.64e-46165
hematopoietic lineage restricted progenitor cell9.13e-41124
nongranular leukocyte5.75e-40119
myeloid leukocyte1.20e-2876
myeloid cell1.75e-27112
common myeloid progenitor1.75e-27112
granulocyte monocyte progenitor cell3.10e-2571
CD14-positive, CD16-negative classical monocyte3.59e-2242
macrophage dendritic cell progenitor4.97e-2265
myeloid lineage restricted progenitor cell7.99e-2270
monopoietic cell6.15e-2163
monocyte6.15e-2163
monoblast6.15e-2163
promonocyte6.15e-2163
classical monocyte1.04e-1845
lymphoid lineage restricted progenitor cell6.19e-1752
lymphocyte1.74e-1653
common lymphoid progenitor1.74e-1653
mesenchymal cell2.96e-13358
connective tissue cell3.74e-13365
motile cell3.04e-10390
mature alpha-beta T cell5.40e-0918
alpha-beta T cell5.40e-0918
immature T cell5.40e-0918
mature T cell5.40e-0918
immature alpha-beta T cell5.40e-0918
T cell9.54e-0925
pro-T cell9.54e-0925
B cell1.37e-0814
lymphocyte of B lineage7.67e-0824
pro-B cell7.67e-0824
intermediate monocyte3.29e-079
CD14-positive, CD16-positive monocyte3.29e-079
granulocyte8.79e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.73e-31102
blood island1.73e-31102
hemolymphoid system5.70e-31112
bone marrow3.14e-2380
bone element4.84e-2286
immune system1.51e-17115
skeletal element2.60e-17101
skeletal system2.60e-17101
connective tissue2.00e-12375
adult organism1.30e-08115
blood5.71e-0815
haemolymphatic fluid5.71e-0815
organism substance5.71e-0815


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.