Coexpression cluster:C344

Full id: C344_Neutrophils_CD14_Eosinophils_Whole_blood_CD14CD16_gall

Phase1 CAGE Peaks

Hg19::chr12:40618649..40618678,-	p@chr12:40618649..40618678 -
Hg19::chr12:40618680..40618710,-	p@chr12:40618680..40618710 -
Hg19::chr14:95652006..95652032,+	p@chr14:95652006..95652032 +
Hg19::chr15:45018966..45018983,-	p@chr15:45018966..45018983 -
Hg19::chr15:45019081..45019115,+	p@chr15:45019081..45019115 +
Hg19::chr15:55581954..55582018,-	p1@RAB27A
Hg19::chr15:86087074..86087082,+	p48@AKAP13
Hg19::chr15:86087098..86087118,+	p12@AKAP13
Hg19::chr15:86087125..86087141,+	p18@AKAP13
Hg19::chr16:74734672..74734722,-	p2@MLKL
Hg19::chr17:76384663..76384707,-	p@chr17:76384663..76384707 -
Hg19::chr17:76409198..76409218,-	p@chr17:76409198..76409218 -
Hg19::chr17:76413038..76413051,-	p@chr17:76413038..76413051 -
Hg19::chr19:1132472..1132486,+	p@chr19:1132472..1132486 +
Hg19::chr1:154580616..154580695,-	p1@ADAR
Hg19::chr1:221054774..221054789,-	p@chr1:221054774..221054789 -
Hg19::chr1:245214949..245214973,+	p@chr1:245214949..245214973 +
Hg19::chr1:28270172..28270184,+	p@chr1:28270172..28270184 +
Hg19::chr1:40840377..40840413,+	p7@SMAP2
Hg19::chr20:3993560..3993585,+	p@chr20:3993560..3993585 +
Hg19::chr20:48909087..48909099,-	p@chr20:48909087..48909099 -
Hg19::chr21:34602680..34602705,+	p4@IFNAR2
Hg19::chr22:31626561..31626578,-	p4@ENST00000365149
Hg19::chr2:152146385..152146435,-	p2@NMI
Hg19::chr3:187463154..187463172,-	p@chr3:187463154..187463172 -
Hg19::chr3:46150615..46150632,+	p@chr3:46150615..46150632 +
Hg19::chr4:15661474..15661499,-	p5@FBXL5
Hg19::chr7:134832793..134832807,+	p3@TMEM140
Hg19::chr7:134832808..134832879,+	p1@TMEM140
Hg19::chr9:114423841..114423900,+	p1@GNG10
Hg19::chrX:12924732..12924745,+	p1@TLR8
Hg19::chrX:12924771..12924776,+	p2@TLR8
Hg19::chrX:48554974..48554979,-	p@chrX:48554974..48554979 -

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:0007259	JAK-STAT cascade	0.00887448671705014
GO:0003725	double-stranded RNA binding	0.00887448671705014
GO:0007242	intracellular signaling cascade	0.00887448671705014
GO:0007243	protein kinase cascade	0.00887448671705014
GO:0009615	response to virus	0.0149020786189561
GO:0019962	interferon-alpha/beta binding	0.0149020786189561
GO:0004905	interferon-alpha/beta receptor activity	0.0149020786189561
GO:0005121	Toll binding	0.0149020786189561
GO:0003726	double-stranded RNA adenosine deaminase activity	0.0149020786189561
GO:0009597	detection of virus	0.0149020786189561
GO:0045359	positive regulation of interferon-beta biosynthetic process	0.0149020786189561
GO:0032608	interferon-beta production	0.0149020786189561
GO:0045357	regulation of interferon-beta biosynthetic process	0.0149020786189561
GO:0016553	base conversion or substitution editing	0.0149020786189561
GO:0003969	RNA editase activity	0.0149020786189561
GO:0045356	positive regulation of interferon-alpha biosynthetic process	0.0149020786189561
GO:0045350	interferon-beta biosynthetic process	0.0149020786189561
GO:0007165	signal transduction	0.0149020786189561
GO:0045354	regulation of interferon-alpha biosynthetic process	0.0149020786189561
GO:0019961	interferon binding	0.0149020786189561
GO:0032607	interferon-alpha production	0.0149020786189561
GO:0045349	interferon-alpha biosynthetic process	0.0149020786189561
GO:0004904	interferon receptor activity	0.0149020786189561
GO:0051707	response to other organism	0.0154822736543798
GO:0045416	positive regulation of interleukin-8 biosynthetic process	0.0164497156937845
GO:0007154	cell communication	0.0182726205744676
GO:0032606	interferon type I production	0.0182726205744676
GO:0045414	regulation of interleukin-8 biosynthetic process	0.0182726205744676
GO:0004691	cAMP-dependent protein kinase activity	0.0182726205744676
GO:0045351	interferon type I biosynthetic process	0.0182726205744676
GO:0042228	interleukin-8 biosynthetic process	0.0198275305357204
GO:0003924	GTPase activity	0.0198275305357204
GO:0045078	positive regulation of interferon-gamma biosynthetic process	0.0198275305357204
GO:0045089	positive regulation of innate immune response	0.0198275305357204
GO:0009607	response to biotic stimulus	0.0198275305357204
GO:0006954	inflammatory response	0.0198275305357204
GO:0032637	interleukin-8 production	0.0198275305357204
GO:0045088	regulation of innate immune response	0.0198275305357204
GO:0004690	cyclic nucleotide-dependent protein kinase activity	0.0200446930089062
GO:0045072	regulation of interferon-gamma biosynthetic process	0.0200446930089062
GO:0031047	RNA-mediated gene silencing	0.0200446930089062
GO:0042095	interferon-gamma biosynthetic process	0.0211952510192287
GO:0051704	multi-organism process	0.021785239839871
GO:0009595	detection of biotic stimulus	0.021785239839871
GO:0004000	adenosine deaminase activity	0.023808613748567
GO:0051607	defense response to virus	0.023808613748567
GO:0032609	interferon-gamma production	0.0262078614030427
GO:0003727	single-stranded RNA binding	0.0285056322417812
GO:0009611	response to wounding	0.0309794943871959
GO:0005834	heterotrimeric G-protein complex	0.0498755017895259
GO:0030425	dendrite	0.0498755017895259
GO:0016458	gene silencing	0.0498755017895259

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	2.39e-74	72
defensive cell	1.65e-72	48
phagocyte	1.65e-72	48
classical monocyte	9.71e-68	42
CD14-positive, CD16-negative classical monocyte	9.71e-68	42
monopoietic cell	3.24e-65	59
monocyte	3.24e-65	59
monoblast	3.24e-65	59
promonocyte	3.24e-65	59
macrophage dendritic cell progenitor	1.52e-62	61
myeloid lineage restricted progenitor cell	1.06e-58	66
granulocyte monocyte progenitor cell	1.41e-57	67
leukocyte	3.76e-49	136
nongranular leukocyte	2.89e-44	115
myeloid cell	3.45e-43	108
common myeloid progenitor	3.45e-43	108
hematopoietic lineage restricted progenitor cell	4.34e-38	120
hematopoietic stem cell	8.39e-37	168
angioblastic mesenchymal cell	8.39e-37	168
hematopoietic oligopotent progenitor cell	5.57e-34	161
hematopoietic multipotent progenitor cell	5.57e-34	161
hematopoietic cell	8.26e-34	177
stuff accumulating cell	9.12e-33	87
intermediate monocyte	1.47e-14	9
CD14-positive, CD16-positive monocyte	1.47e-14	9
granulocyte	1.57e-14	8
blood cell	4.90e-10	11
mesenchymal cell	5.15e-07	354
neutrophil	5.79e-07	3

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.49e-68	98
blood island	2.49e-68	98
hemolymphoid system	3.88e-64	108
bone marrow	8.57e-51	76
immune system	5.29e-49	93
bone element	7.74e-46	82
skeletal element	2.91e-40	90
skeletal system	1.46e-34	100
lateral plate mesoderm	9.99e-26	203
blood	1.02e-15	15
haemolymphatic fluid	1.02e-15	15
organism substance	1.02e-15	15
adult organism	5.12e-15	114
musculoskeletal system	2.36e-14	167
mesoderm	3.58e-13	315
mesoderm-derived structure	3.58e-13	315
presumptive mesoderm	3.58e-13	315

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
BATF#10538	5	3.69057602913691	0.0105877801731713	0.0391024142828895
BRF2#55290	2	65.1257928118393	0.000446047377681331	0.00415193779658293
CEBPB#1051	14	3.38169899277416	1.86072005286264e-05	0.000422644066117705
CTCF#10664	12	1.94918413566365	0.0126933349909202	0.0457999382662539
EP300#2033	12	2.46325153680844	0.00181435430642365	0.0108989617743345
FOXA1#3169	11	3.69380658312848	9.47506033378001e-05	0.00137325260366313
FOXA2#3170	7	5.22464382632293	0.000304975524063399	0.00314581123532418
GTF2F1#2962	7	2.70235230719102	0.012713866635593	0.0458676817007393
HDAC2#3066	8	3.25227157251546	0.00243107558424595	0.0136931885957859
HNF4A#3172	5	3.50489247923541	0.0130261333416483	0.046218323087087
HNF4G#3174	5	4.35657917067376	0.005348952993327	0.0245739366414498
JUNB#3726	6	5.56556957451293	0.000628229309272852	0.00516993466481344
MAFF#23764	7	11.9456816796853	1.5762538789157e-06	6.00154498213915e-05
MAFK#7975	9	7.39110903758998	2.17305616749095e-06	7.82053111911051e-05
MAX#4149	11	2.15085183633571	0.00866384909560058	0.0329753547993961
MEF2A#4205	6	3.40786016538983	0.00734385656973354	0.0303672263644297
RXRA#6256	6	3.64993038893332	0.00528674748968454	0.0244841745853915
SPI1#6688	12	2.98339036673554	0.000317621998396855	0.00325312581058833
STAT1#6772	12	7.5296681807997	2.18515375642827e-08	1.54722219096686e-06
STAT2#6773	9	17.7992103235747	1.27255403713315e-09	1.15468523965377e-07
STAT3#6774	16	5.1003466652869	1.05453466606223e-08	7.94621543931266e-07
TAL1#6886	5	4.52554798143033	0.00455848305149365	0.0215461355636742

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.