Coexpression cluster:C1017

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0005381	iron ion transmembrane transporter activity	0.0126732839990412
GO:0006032	chitin catabolic process	0.0126732839990412
GO:0006046	N-acetylglucosamine catabolic process	0.0126732839990412
GO:0006043	glucosamine catabolic process	0.0126732839990412
GO:0006030	chitin metabolic process	0.0126732839990412
GO:0004568	chitinase activity	0.0126732839990412
GO:0046348	amino sugar catabolic process	0.0126732839990412
GO:0044247	cellular polysaccharide catabolic process	0.0137973605797099
GO:0000272	polysaccharide catabolic process	0.0137973605797099
GO:0046915	transition metal ion transmembrane transporter activity	0.0172395925919889
GO:0006044	N-acetylglucosamine metabolic process	0.0172395925919889
GO:0006041	glucosamine metabolic process	0.0172395925919889
GO:0006040	amino sugar metabolic process	0.0186382001077193
GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity	0.0224461786782998
GO:0006826	iron ion transport	0.0224461786782998
GO:0044264	cellular polysaccharide metabolic process	0.0298563934301294
GO:0005976	polysaccharide metabolic process	0.0298563934301294
GO:0000041	transition metal ion transport	0.0334280270378697

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>

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Cell Type

Ontology term	p-value	n
leukocyte	6.70e-43	140
hematopoietic lineage restricted progenitor cell	2.54e-40	124
hematopoietic stem cell	8.46e-40	172
angioblastic mesenchymal cell	8.46e-40	172
hematopoietic oligopotent progenitor cell	5.56e-38	165
hematopoietic multipotent progenitor cell	5.56e-38	165
nongranular leukocyte	1.05e-36	119
hematopoietic cell	4.66e-35	182
myeloid leukocyte	1.06e-34	76
granulocyte monocyte progenitor cell	1.33e-33	71
myeloid lineage restricted progenitor cell	1.39e-33	70
macrophage dendritic cell progenitor	2.32e-31	65
monopoietic cell	1.54e-30	63
monocyte	1.54e-30	63
monoblast	1.54e-30	63
promonocyte	1.54e-30	63
myeloid cell	4.29e-30	112
common myeloid progenitor	4.29e-30	112
CD14-positive, CD16-negative classical monocyte	2.56e-26	42
classical monocyte	1.91e-24	45
lymphoid lineage restricted progenitor cell	4.03e-08	52
lymphocyte	1.19e-07	53
common lymphoid progenitor	1.19e-07	53

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.59e-35	102
blood island	7.59e-35	102
adult organism	1.64e-32	115
hemolymphoid system	1.26e-30	112
bone marrow	3.57e-29	80
bone element	2.74e-25	86
immune system	2.08e-21	115
skeletal element	5.51e-18	101
skeletal system	5.51e-18	101
neural tube	1.10e-10	57
neural rod	1.10e-10	57
future spinal cord	1.10e-10	57
neural keel	1.10e-10	57
anterior neural tube	6.52e-09	42
regional part of forebrain	9.75e-09	41
forebrain	9.75e-09	41
future forebrain	9.75e-09	41
regional part of brain	2.54e-08	59
lateral plate mesoderm	5.43e-08	216
brain	3.30e-07	69
future brain	3.30e-07	69
central nervous system	3.81e-07	82
gray matter	4.19e-07	34
brain grey matter	4.19e-07	34
telencephalon	5.16e-07	34
regional part of telencephalon	9.05e-07	33

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	6	16.8473808945066	2.0128920133559e-07	1.08811816243725e-05
EBF1#1879	6	6.67985013492675	4.58015900243755e-05	0.000805298360362921
ELF1#1997	7	3.7258357139566	0.000250341272551272	0.00269818288585989
FOS#2353	6	6.7484664816708	4.31702653902356e-05	0.000769921336593376
MAX#4149	6	4.83941663175534	0.000291750431370536	0.00309687196888987
MYC#4609	7	4.56949663765823	6.28392411465611e-05	0.00102657085970682
NFE2#4778	6	57.9031954887218	1.28513996806255e-10	1.37660239102036e-08
PAX5#5079	6	5.00217414838337	0.000241608451547577	0.00262902115765549
POU2F2#5452	6	6.82959304330689	4.02833503357943e-05	0.000738356059269923
SP1#6667	7	4.98608370587328	3.46905874958224e-05	0.000680385026756092
SPI1#6688	6	6.15324263139204	7.3612205654473e-05	0.00114848896718666
TBP#6908	6	2.78007801532229	0.00639018112126301	0.0278018798635113
USF1#7391	7	5.56631186755696	1.63553159235289e-05	0.000377905495517132
USF2#7392	6	9.7441480388022	5.07489102954454e-06	0.000156531761439634

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

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This analysis result is provided for C0 - C305 clusters.