Personal tools

Coexpression cluster:C1500

From FANTOM5_SSTAR

Revision as of 14:56, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1500_Melanocyte_Monocytederived_CD14_melanoma_retina_Macrophage_Mast



Phase1 CAGE Peaks

Hg19::chr2:170335297..170335305,+p2@BBS5
Hg19::chr3:126675836..126675847,+p5@CHCHD6
Hg19::chr3:126675939..126675962,+p3@CHCHD6
Hg19::chr3:126675964..126675975,+p6@CHCHD6
Hg19::chr3:126675978..126675988,+p4@CHCHD6
Hg19::chr3:126676020..126676029,+p9@CHCHD6


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:0005929cilium0.0120687625103026
GO:0007601visual perception0.021880764551199
GO:0050953sensory perception of light stimulus0.021880764551199
GO:0042995cell projection0.0230336747910043



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
melanocyte6.30e-4410
melanoblast6.30e-4410
macrophage2.16e-376
pigment cell3.24e-3114
adult endothelial progenitor cell1.07e-283
light melanocyte6.84e-283
neurecto-epithelial cell1.15e-2120
histamine secreting cell1.41e-165
biogenic amine secreting cell1.41e-165
granulocytopoietic cell1.41e-165
mast cell1.41e-165
mast cell progenitor1.41e-165
basophil mast progenitor cell1.41e-165
columnar/cuboidal epithelial cell7.14e-1627
myeloid lineage restricted progenitor cell1.25e-1466
granulocyte monocyte progenitor cell2.17e-1467
myeloid leukocyte2.75e-1372
stuff accumulating cell4.42e-1387
ecto-epithelial cell1.85e-1234
dark melanocyte1.73e-101
migratory neural crest cell1.07e-0941
endocrine cell1.84e-099
monopoietic cell9.37e-0959
monocyte9.37e-0959
monoblast9.37e-0959
promonocyte9.37e-0959
macrophage dendritic cell progenitor1.94e-0861
myeloid cell2.51e-08108
common myeloid progenitor2.51e-08108
hematopoietic lineage restricted progenitor cell2.49e-07120
Uber Anatomy
Ontology termp-valuen
bone marrow1.66e-1276
bone element1.77e-1182
skeletal element2.56e-1090
immune system6.22e-1093
hematopoietic system2.41e-0998
blood island2.41e-0998
skeletal system4.00e-09100
hemolymphoid system2.51e-08108
Disease
Ontology termp-valuen
melanoma1.97e-192


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
NFKB1#479054.57338618682820.00102196259371130.00724741979524778



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.