Personal tools

Coexpression cluster:C1622

From FANTOM5_SSTAR

Revision as of 11:31, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1622_thymus_CD8_Natural_vein_blood_acute_Basophils



Phase1 CAGE Peaks

Hg19::chr11:128392309..128392350,-p3@ETS1
Hg19::chr1:26317321..26317401,-p2@PAFAH2
Hg19::chr3:18486936..18486954,-p@chr3:18486936..18486954
-
Hg19::chr7:142494795..142494838,+p1@TRBJ2-5
Hg19::chr7:99817566..99817579,+p1@PVRIG


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:00082472-acetyl-1-alkylglycerophosphocholine esterase complex0.0143037934536429
GO:0045648positive regulation of erythrocyte differentiation0.0143037934536429
GO:00038471-alkyl-2-acetylglycerophosphocholine esterase activity0.0143037934536429
GO:0045646regulation of erythrocyte differentiation0.0185910998909698
GO:0045639positive regulation of myeloid cell differentiation0.0185910998909698
GO:0030218erythrocyte differentiation0.0347091582755624
GO:0045637regulation of myeloid cell differentiation0.0347091582755624
GO:0045597positive regulation of cell differentiation0.0419666994026459



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
lymphocyte1.07e-4653
common lymphoid progenitor1.07e-4653
lymphoid lineage restricted progenitor cell1.47e-4552
nucleate cell2.13e-4455
nongranular leukocyte1.11e-31115
leukocyte2.29e-29136
T cell6.98e-2925
pro-T cell6.98e-2925
mature alpha-beta T cell4.21e-2618
alpha-beta T cell4.21e-2618
immature T cell4.21e-2618
mature T cell4.21e-2618
immature alpha-beta T cell4.21e-2618
hematopoietic stem cell5.50e-25168
angioblastic mesenchymal cell5.50e-25168
hematopoietic lineage restricted progenitor cell2.47e-24120
hematopoietic cell1.34e-22177
hematopoietic oligopotent progenitor cell1.13e-21161
hematopoietic multipotent progenitor cell1.13e-21161
CD8-positive, alpha-beta T cell2.91e-1711
B cell2.41e-1514
lymphocyte of B lineage1.23e-1424
pro-B cell1.23e-1424
CD4-positive, alpha-beta T cell2.90e-096
Uber Anatomy
Ontology termp-valuen
blood3.26e-1315
haemolymphatic fluid3.26e-1315
organism substance3.26e-1315
adult organism2.77e-11114
hemopoietic organ4.16e-087
immune organ4.16e-087
thymus2.49e-074
hemolymphoid system gland2.49e-074
thymic region2.49e-074
pharyngeal gland2.49e-074
thymus primordium2.49e-074
hematopoietic system7.62e-0798
blood island7.62e-0798


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.