Personal tools

Coexpression cluster:C3568

From FANTOM5_SSTAR

Revision as of 15:12, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3568_Mast_Eosinophils_CD4_immature_CD8_Neutrophils_Natural



Phase1 CAGE Peaks

Hg19::chr16:50776050..50776074,+p3@CYLD
Hg19::chr1:100818080..100818094,+p2@CDC14A
Hg19::chr9:2017714..2017737,+p@chr9:2017714..2017737
+


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:0007049cell cycle0.0463706779592514
GO:0016788hydrolase activity, acting on ester bonds0.0463706779592514
GO:0005856cytoskeleton0.0469426303635197
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.049963050018113
GO:0043687post-translational protein modification0.049963050018113
GO:0006464protein modification process0.049963050018113
GO:0043412biopolymer modification0.049963050018113
GO:0043232intracellular non-membrane-bound organelle0.049963050018113
GO:0043228non-membrane-bound organelle0.049963050018113
GO:0005813centrosome0.049963050018113
GO:0004221ubiquitin thiolesterase activity0.049963050018113
GO:0004843ubiquitin-specific protease activity0.049963050018113
GO:0019783small conjugating protein-specific protease activity0.049963050018113
GO:0005815microtubule organizing center0.049963050018113



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
leukocyte6.91e-31136
hematopoietic stem cell1.03e-28168
angioblastic mesenchymal cell1.03e-28168
hematopoietic cell3.46e-27177
hematopoietic oligopotent progenitor cell4.36e-26161
hematopoietic multipotent progenitor cell4.36e-26161
hematopoietic lineage restricted progenitor cell3.08e-23120
nongranular leukocyte5.74e-22115
myeloid leukocyte6.22e-1672
myeloid cell1.32e-14108
common myeloid progenitor1.32e-14108
granulocyte monocyte progenitor cell2.98e-1367
mature alpha-beta T cell1.22e-1218
alpha-beta T cell1.22e-1218
immature T cell1.22e-1218
mature T cell1.22e-1218
immature alpha-beta T cell1.22e-1218
myeloid lineage restricted progenitor cell1.77e-1166
lymphocyte2.54e-1153
common lymphoid progenitor2.54e-1153
lymphoid lineage restricted progenitor cell2.93e-1152
nucleate cell1.11e-1055
macrophage dendritic cell progenitor1.58e-1061
classical monocyte2.44e-1042
CD14-positive, CD16-negative classical monocyte2.44e-1042
monopoietic cell9.75e-1059
monocyte9.75e-1059
monoblast9.75e-1059
promonocyte9.75e-1059
T cell8.24e-0925
pro-T cell8.24e-0925
defensive cell2.29e-0848
phagocyte2.29e-0848
CD8-positive, alpha-beta T cell2.37e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.11e-1998
blood island1.11e-1998
hemolymphoid system1.19e-19108
adult organism8.02e-17114
immune system1.37e-1393
bone marrow4.98e-1176
bone element8.14e-1182
skeletal element1.00e-0890
blood2.41e-0815
haemolymphatic fluid2.41e-0815
organism substance2.41e-0815
skeletal system2.65e-07100
lateral plate mesoderm8.19e-07203


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ELF1#199734.258097958807540.01295179875054610.0461426883748348
SIN3A#2594235.408884726815140.006318961977991520.027619740102932
YY1#752834.911170749853860.008441455341808260.0328802131221092



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.