Personal tools

Coexpression cluster:C602

From FANTOM5_SSTAR

Revision as of 16:28, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C602_Macrophage_Monocytederived_CD14_Mast_Dendritic_lung_adipose



Phase1 CAGE Peaks

Hg19::chr18:43409037..43409056,+p2@SIGLEC15
Hg19::chr1:46008415..46008441,-p@chr1:46008415..46008441
-
Hg19::chr2:217259800..217259818,+p@chr2:217259800..217259818
+
Hg19::chr2:85636928..85636947,-p4@CAPG
Hg19::chr2:85637459..85637495,-p2@CAPG
Hg19::chr2:85637502..85637513,-p5@CAPG
Hg19::chr3:188664953..188664966,+p12@TPRG1
Hg19::chr3:188664988..188665018,+p6@TPRG1
Hg19::chr7:47520822..47520831,-p@chr7:47520822..47520831
-
Hg19::chr7:47520869..47520899,-p3@TNS3
Hg19::chr7:47520910..47520921,-p15@TNS3
Hg19::chr8:16050142..16050168,-p1@MSR1
Hg19::chr8:16050214..16050227,-p2@MSR1
Hg19::chr8:87111104..87111113,+p3@ATP6V0D2
Hg19::chr8:87111117..87111122,+p4@ATP6V0D2


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
macrophage dendritic cell progenitor4.72e-8461
monopoietic cell8.96e-8459
monocyte8.96e-8459
monoblast8.96e-8459
promonocyte8.96e-8459
granulocyte monocyte progenitor cell2.32e-7867
defensive cell9.54e-7748
phagocyte9.54e-7748
myeloid lineage restricted progenitor cell1.67e-7666
myeloid leukocyte5.99e-7572
classical monocyte1.29e-6242
CD14-positive, CD16-negative classical monocyte1.29e-6242
myeloid cell4.47e-49108
common myeloid progenitor4.47e-49108
nongranular leukocyte1.19e-39115
hematopoietic lineage restricted progenitor cell4.65e-39120
leukocyte1.95e-37136
stuff accumulating cell1.64e-3687
hematopoietic oligopotent progenitor cell3.20e-29161
hematopoietic multipotent progenitor cell3.20e-29161
hematopoietic stem cell1.19e-28168
angioblastic mesenchymal cell1.19e-28168
hematopoietic cell2.07e-26177
macrophage1.31e-156
adult endothelial progenitor cell1.49e-083
immature conventional dendritic cell9.97e-075
common dendritic progenitor9.97e-075
Uber Anatomy
Ontology termp-valuen
bone marrow3.35e-7076
immune system4.81e-6793
bone element5.35e-6482
hematopoietic system9.32e-6398
blood island9.32e-6398
hemolymphoid system9.37e-58108
skeletal element5.27e-5790
skeletal system7.90e-50100
musculoskeletal system2.76e-26167
lateral plate mesoderm2.08e-25203
mesoderm1.46e-15315
mesoderm-derived structure1.46e-15315
presumptive mesoderm1.46e-15315
organ3.50e-11503
adult organism7.08e-09114
developing anatomical structure1.55e-08581
germ layer1.66e-08560
germ layer / neural crest1.66e-08560
embryonic tissue1.66e-08560
presumptive structure1.66e-08560
germ layer / neural crest derived structure1.66e-08560
epiblast (generic)1.66e-08560
embryonic structure2.63e-08564
embryo5.26e-08592
anatomical system4.22e-07624
anatomical group4.66e-07625


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
POU5F1#5460367.08784029038111.16739030186779e-050.000297006274632814



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.