Personal tools

Coexpression cluster:C1017

From FANTOM5_SSTAR

Revision as of 16:45, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1017_CD14_Macrophage_Monocytederived_Mast_Dendritic_B_splenic



Phase1 CAGE Peaks

Hg19::chr12:51402984..51403042,-p2@SLC11A2
Hg19::chr14:93651635..93651647,+p4@C14orf109
Hg19::chr1:111742738..111742772,-p4@DENND2D
Hg19::chr1:111742778..111742797,-p7@DENND2D
Hg19::chr1:111742809..111742819,-p12@DENND2D
Hg19::chr1:111742823..111742838,-p5@DENND2D
Hg19::chr1:111742942..111742955,+p5@CHI3L2
Hg19::chr1:111743000..111743011,+p8@CHI3L2


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:0005381iron ion transmembrane transporter activity0.0126732839990412
GO:0006032chitin catabolic process0.0126732839990412
GO:0006046N-acetylglucosamine catabolic process0.0126732839990412
GO:0006043glucosamine catabolic process0.0126732839990412
GO:0006030chitin metabolic process0.0126732839990412
GO:0004568chitinase activity0.0126732839990412
GO:0046348amino sugar catabolic process0.0126732839990412
GO:0044247cellular polysaccharide catabolic process0.0137973605797099
GO:0000272polysaccharide catabolic process0.0137973605797099
GO:0046915transition metal ion transmembrane transporter activity0.0172395925919889
GO:0006044N-acetylglucosamine metabolic process0.0172395925919889
GO:0006041glucosamine metabolic process0.0172395925919889
GO:0006040amino sugar metabolic process0.0186382001077193
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0224461786782998
GO:0006826iron ion transport0.0224461786782998
GO:0044264cellular polysaccharide metabolic process0.0298563934301294
GO:0005976polysaccharide metabolic process0.0298563934301294
GO:0000041transition metal ion transport0.0334280270378697



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
leukocyte6.70e-43140
hematopoietic lineage restricted progenitor cell2.54e-40124
hematopoietic stem cell8.46e-40172
angioblastic mesenchymal cell8.46e-40172
hematopoietic oligopotent progenitor cell5.56e-38165
hematopoietic multipotent progenitor cell5.56e-38165
nongranular leukocyte1.05e-36119
hematopoietic cell4.66e-35182
myeloid leukocyte1.06e-3476
granulocyte monocyte progenitor cell1.33e-3371
myeloid lineage restricted progenitor cell1.39e-3370
macrophage dendritic cell progenitor2.32e-3165
monopoietic cell1.54e-3063
monocyte1.54e-3063
monoblast1.54e-3063
promonocyte1.54e-3063
myeloid cell4.29e-30112
common myeloid progenitor4.29e-30112
CD14-positive, CD16-negative classical monocyte2.56e-2642
classical monocyte1.91e-2445
lymphoid lineage restricted progenitor cell4.03e-0852
lymphocyte1.19e-0753
common lymphoid progenitor1.19e-0753
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.59e-35102
blood island7.59e-35102
adult organism1.64e-32115
hemolymphoid system1.26e-30112
bone marrow3.57e-2980
bone element2.74e-2586
immune system2.08e-21115
skeletal element5.51e-18101
skeletal system5.51e-18101
neural tube1.10e-1057
neural rod1.10e-1057
future spinal cord1.10e-1057
neural keel1.10e-1057
anterior neural tube6.52e-0942
regional part of forebrain9.75e-0941
forebrain9.75e-0941
future forebrain9.75e-0941
regional part of brain2.54e-0859
lateral plate mesoderm5.43e-08216
brain3.30e-0769
future brain3.30e-0769
central nervous system3.81e-0782
gray matter4.19e-0734
brain grey matter4.19e-0734
telencephalon5.16e-0734
regional part of telencephalon9.05e-0733


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


No analysis results for this cluster

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.