Personal tools

Coexpression cluster:C1446

From FANTOM5_SSTAR

Revision as of 14:54, 26 November 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 leukocyte1.02e-10272
granulocyte monocyte progenitor cell1.44e-9167
defensive cell7.29e-8948
phagocyte7.29e-8948
macrophage dendritic cell progenitor7.27e-8861
classical monocyte1.50e-8642
CD14-positive, CD16-negative classical monocyte1.50e-8642
myeloid lineage restricted progenitor cell2.74e-8666
monopoietic cell3.70e-8459
monocyte3.70e-8459
monoblast3.70e-8459
promonocyte3.70e-8459
myeloid cell2.48e-74108
common myeloid progenitor2.48e-74108
leukocyte6.20e-72136
hematopoietic stem cell1.35e-59168
angioblastic mesenchymal cell1.35e-59168
stuff accumulating cell3.57e-5887
hematopoietic cell1.55e-55177
hematopoietic lineage restricted progenitor cell4.56e-55120
hematopoietic oligopotent progenitor cell1.51e-53161
hematopoietic multipotent progenitor cell1.51e-53161
nongranular leukocyte2.40e-52115
motile cell1.79e-20386
intermediate monocyte3.50e-209
CD14-positive, CD16-positive monocyte3.50e-209
mesenchymal cell3.45e-19354
connective tissue cell2.00e-18361
granulocyte1.70e-138
multi fate stem cell1.68e-12427
somatic stem cell4.69e-12433
stem cell1.75e-11441
blood cell1.88e-0911
non-classical monocyte6.25e-083
CD14-low, CD16-positive monocyte6.25e-083
basophil9.54e-083
neutrophil1.69e-073
somatic cell3.06e-07588
single nucleate cell4.05e-073
mononuclear cell4.05e-073
light melanocyte5.66e-073
melanocyte9.66e-0710
melanoblast9.66e-0710
Uber Anatomy
Ontology termp-valuen
bone marrow7.45e-7976
hematopoietic system2.27e-7798
blood island2.27e-7798
bone element6.50e-7282
hemolymphoid system1.48e-68108
skeletal element4.34e-6490
immune system6.68e-6493
skeletal system4.65e-56100
lateral plate mesoderm4.22e-28203
musculoskeletal system4.39e-27167
connective tissue2.18e-17371
mesoderm2.60e-13315
mesoderm-derived structure2.60e-13315
presumptive mesoderm2.60e-13315


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.