Personal tools

Coexpression cluster:C1446

From FANTOM5_SSTAR

Revision as of 13:32, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1446_CD14_Mast_CD14CD16_Basophils_Melanocyte_Neutrophils_immature



Phase1 CAGE Peaks

Hg19::chr18:74826350..74826370,-p@chr18:74826350..74826370
-
Hg19::chr18:74843480..74843491,+p@chr18:74843480..74843491
+
Hg19::chr18:74844048..74844062,-p16@MBP
Hg19::chr18:74844167..74844184,+p@chr18:74844167..74844184
+
Hg19::chr2:43764398..43764438,-p@chr2:43764398..43764438
-
Hg19::chr2:43767323..43767344,-p@chr2:43767323..43767344
-


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


No GOStat results

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
myeloid leukocyte2.07e-3876
myeloid cell1.47e-37112
common myeloid progenitor1.47e-37112
granulocyte monocyte progenitor cell2.95e-3671
hematopoietic stem cell7.19e-36172
angioblastic mesenchymal cell7.19e-36172
myeloid lineage restricted progenitor cell1.46e-3470
hematopoietic cell2.17e-34182
macrophage dendritic cell progenitor2.86e-3465
hematopoietic oligopotent progenitor cell3.89e-33165
hematopoietic multipotent progenitor cell3.89e-33165
monopoietic cell4.25e-3363
monocyte4.25e-3363
monoblast4.25e-3363
promonocyte4.25e-3363
leukocyte4.42e-33140
CD14-positive, CD16-negative classical monocyte2.53e-3042
hematopoietic lineage restricted progenitor cell9.30e-29124
classical monocyte1.37e-2845
nongranular leukocyte6.33e-27119
motile cell4.45e-10390
mesenchymal cell1.07e-09358
connective tissue cell1.28e-08365
intermediate monocyte6.40e-089
CD14-positive, CD16-positive monocyte6.40e-089
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.35e-35102
blood island5.35e-35102
hemolymphoid system4.16e-32112
bone marrow1.13e-2980
bone element1.87e-2686
immune system1.43e-24115
skeletal element1.67e-18101
skeletal system1.67e-18101
lateral plate mesoderm4.60e-11216
connective tissue7.43e-08375
musculoskeletal system1.71e-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


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

TF#promotersEnrichmentp-valueq-value
POLR2A#543062.147453176558070.01019570676818780.038032338708578



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.