Coexpression cluster:C294

Full id: C294_CD14_Macrophage_Monocytederived_CD14CD16_Neutrophils_Basophils_Peripheral

Phase1 CAGE Peaks

Hg19::chr11:117059709..117059733,+	p11@SIDT2
Hg19::chr11:59950486..59950515,-	p2@MS4A6A
Hg19::chr11:59950519..59950605,-	p1@MS4A6A
Hg19::chr11:72433267..72433292,-	p4@ARAP1
Hg19::chr11:72433293..72433345,-	p3@ARAP1
Hg19::chr12:111127201..111127221,-	p3@HVCN1
Hg19::chr12:96429349..96429381,-	p1@LTA4H
Hg19::chr14:103587794..103587823,+	p@chr14:103587794..103587823 +
Hg19::chr16:50308028..50308093,+	p2@ADCY7
Hg19::chr17:29248896..29248906,+	p5@ADAP2
Hg19::chr17:29248918..29248949,+	p2@ADAP2
Hg19::chr17:29248955..29248978,+	p1@ADAP2
Hg19::chr17:72542265..72542277,-	p4@CD300C
Hg19::chr17:7462261..7462266,+	p13@TNFSF13
Hg19::chr17:7462268..7462279,+	p7@TNFSF13
Hg19::chr17:7462297..7462342,+	p1@TNFSF13
Hg19::chr1:150738211..150738260,-	p1@CTSS
Hg19::chr1:153330728..153330829,+	p2@S100A9
Hg19::chr1:182758900..182758918,+	p1@NPL
Hg19::chr1:182767386..182767390,+	p@chr1:182767386..182767390 +
Hg19::chr1:183559693..183559704,-	p5@NCF2
Hg19::chr20:1517945..1517963,-	p@chr20:1517945..1517963 -
Hg19::chr22:17700260..17700331,-	p1@CECR1
Hg19::chr2:68962023..68962095,+	p5@ARHGAP25
Hg19::chr2:68962229..68962279,+	p6@ARHGAP25
Hg19::chr2:74782818..74782845,-	p3@LOXL3
Hg19::chr5:140012392..140012432,-	p5@CD14
Hg19::chr5:140013191..140013202,-	p10@CD14
Hg19::chr5:140013224..140013235,-	p12@CD14
Hg19::chr5:140013241..140013270,-	p3@CD14
Hg19::chr5:140013275..140013296,-	p4@CD14
Hg19::chr5:149466042..149466143,-	p1@CSF1R
Hg19::chr5:180230830..180230903,-	p2@MGAT1
Hg19::chr5:39274617..39274636,-	p7@FYB
Hg19::chr5:39274655..39274666,-	p12@FYB
Hg19::chr6:25452404..25452424,-	p@chr6:25452404..25452424 -
Hg19::chr7:157647472..157647497,+	p1@ENST00000443338
Hg19::chr8:67624963..67625045,+	p3@SGK3
Hg19::chr9:115983523..115983565,-	p1@FKBP15
Hg19::chrX:37639279..37639290,+	p2@CYBB
Hg19::chrX:80457922..80457946,+	p4@SH3BGRL
Hg19::chrX:80457962..80457977,+	p6@SH3BGRL
Hg19::chrX:80458001..80458016,+	p8@SH3BGRL

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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p.value	FDR	nGenes	nPathway	Name
8.37369675774424e-06	0.0053005500476521	4	156	Phagosome (KEGG):04145

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:0006952	defense response	0.000349565744672719
GO:0006954	inflammatory response	0.00448776427999258
GO:0009611	response to wounding	0.0127504247667843
GO:0009605	response to external stimulus	0.0246489756269869
GO:0045113	regulation of integrin biosynthetic process	0.0246489756269869
GO:0004218	cathepsin S activity	0.0246489756269869
GO:0008747	N-acetylneuraminate lyase activity	0.0246489756269869
GO:0045112	integrin biosynthetic process	0.0246489756269869
GO:0006950	response to stress	0.026619015725701
GO:0006968	cellular defense response	0.0289096751976543
GO:0005011	macrophage colony stimulating factor receptor activity	0.0358425014391679

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
myeloid leukocyte	1.74e-60	72
macrophage dendritic cell progenitor	6.60e-59	61
monopoietic cell	6.04e-58	59
monocyte	6.04e-58	59
monoblast	6.04e-58	59
promonocyte	6.04e-58	59
granulocyte monocyte progenitor cell	7.19e-53	67
defensive cell	2.78e-52	48
phagocyte	2.78e-52	48
myeloid lineage restricted progenitor cell	1.12e-50	66
myeloid cell	3.34e-45	108
common myeloid progenitor	3.34e-45	108
classical monocyte	4.15e-45	42
CD14-positive, CD16-negative classical monocyte	4.15e-45	42
leukocyte	3.62e-36	136
hematopoietic stem cell	1.59e-32	168
angioblastic mesenchymal cell	1.59e-32	168
nongranular leukocyte	1.92e-31	115
hematopoietic cell	3.17e-29	177
hematopoietic oligopotent progenitor cell	3.40e-29	161
hematopoietic multipotent progenitor cell	3.40e-29	161
hematopoietic lineage restricted progenitor cell	3.88e-28	120
stuff accumulating cell	7.18e-20	87
intermediate monocyte	2.37e-11	9
CD14-positive, CD16-positive monocyte	2.37e-11	9
macrophage	2.12e-08	6
granulocyte	2.58e-08	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.26e-54	98
blood island	4.26e-54	98
hemolymphoid system	2.31e-49	108
adult organism	1.49e-45	114
bone marrow	4.89e-45	76
immune system	1.35e-40	93
bone element	6.08e-40	82
skeletal element	3.04e-34	90
skeletal system	1.62e-29	100
lateral plate mesoderm	7.33e-20	203
musculoskeletal system	9.01e-12	167
neural tube	1.19e-11	56
neural rod	1.19e-11	56
future spinal cord	1.19e-11	56
neural keel	1.19e-11	56
regional part of nervous system	4.17e-10	53
regional part of brain	4.17e-10	53
tissue	3.91e-09	773
blood	4.08e-09	15
haemolymphatic fluid	4.08e-09	15
organism substance	4.08e-09	15
organ	1.12e-08	503
regional part of forebrain	1.19e-08	41
forebrain	1.19e-08	41
anterior neural tube	1.19e-08	41
future forebrain	1.19e-08	41
mesoderm	1.24e-08	315
mesoderm-derived structure	1.24e-08	315
presumptive mesoderm	1.24e-08	315
germ layer	4.82e-08	560
germ layer / neural crest	4.82e-08	560
embryonic tissue	4.82e-08	560
presumptive structure	4.82e-08	560
germ layer / neural crest derived structure	4.82e-08	560
epiblast (generic)	4.82e-08	560
embryonic structure	4.99e-08	564
developing anatomical structure	2.90e-07	581
brain grey matter	4.07e-07	34
gray matter	4.07e-07	34
telencephalon	4.69e-07	34
neural plate	5.10e-07	82
presumptive neural plate	5.10e-07	82
embryo	5.50e-07	592
central nervous system	5.87e-07	81

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
SPI1#6688	19	3.62516620144027	1.80912235243461e-07	9.89748189449547e-06

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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