Coexpression cluster:C2154

Full id: C2154_Eosinophils_Neutrophils_Renal_Endothelial_tridermal_Hepatic_Basophils

Phase1 CAGE Peaks

Hg19::chr11:65381643..65381767,-	p1@MAP3K11
Hg19::chr22:22307182..22307197,-	p2@PPM1F
Hg19::chr22:22307199..22307242,-	p1@PPM1F
Hg19::chr3:50273625..50273655,+	p1@GNAI2

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:0004706	JUN kinase kinase kinase activity	0.0259929336955715
GO:0050790	regulation of catalytic activity	0.0259929336955715
GO:0065009	regulation of a molecular function	0.0259929336955715
GO:0031280	negative regulation of cyclase activity	0.0259929336955715
GO:0007194	negative regulation of adenylate cyclase activity	0.0259929336955715
GO:0051350	negative regulation of lyase activity	0.0259929336955715
GO:0000080	G1 phase of mitotic cell cycle	0.0259929336955715
GO:0004709	MAP kinase kinase kinase activity	0.0259929336955715
GO:0046328	regulation of JNK cascade	0.0259929336955715
GO:0051318	G1 phase	0.0259929336955715
GO:0007257	activation of JNK activity	0.0261157639195323
GO:0043507	positive regulation of JNK activity	0.0262178539814203
GO:0043506	regulation of JNK activity	0.0263039900870814
GO:0015071	protein phosphatase type 2C activity	0.0314401238840169
GO:0045761	regulation of adenylate cyclase activity	0.0314401238840169
GO:0007584	response to nutrient	0.0314401238840169
GO:0031279	regulation of cyclase activity	0.0314401238840169
GO:0051339	regulation of lyase activity	0.0314401238840169
GO:0046777	protein amino acid autophosphorylation	0.0314401238840169
GO:0016540	protein autoprocessing	0.0314401238840169
GO:0000187	activation of MAPK activity	0.0320321372125483
GO:0008287	protein serine/threonine phosphatase complex	0.0320321372125483
GO:0031667	response to nutrient levels	0.0320321372125483
GO:0051259	protein oligomerization	0.0320321372125483
GO:0007254	JNK cascade	0.0320321372125483
GO:0004722	protein serine/threonine phosphatase activity	0.0320321372125483
GO:0009991	response to extracellular stimulus	0.0320321372125483
GO:0043406	positive regulation of MAP kinase activity	0.0320321372125483
GO:0031098	stress-activated protein kinase signaling pathway	0.0320321372125483
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.0329950406170268
GO:0006793	phosphorus metabolic process	0.0329950406170268
GO:0006796	phosphate metabolic process	0.0329950406170268
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0329950406170268
GO:0051329	interphase of mitotic cell cycle	0.0329950406170268
GO:0019933	cAMP-mediated signaling	0.0329950406170268
GO:0043086	negative regulation of catalytic activity	0.0329950406170268
GO:0051325	interphase	0.0332073572743918
GO:0043405	regulation of MAP kinase activity	0.0334083090119861
GO:0016485	protein processing	0.0346456689926608
GO:0007242	intracellular signaling cascade	0.037377126989421
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0389269169469197
GO:0019935	cyclic-nucleotide-mediated signaling	0.0396181824281736
GO:0005813	centrosome	0.0408833829227281
GO:0045860	positive regulation of protein kinase activity	0.0408833829227281
GO:0043687	post-translational protein modification	0.0408833829227281
GO:0033674	positive regulation of kinase activity	0.0408833829227281
GO:0030145	manganese ion binding	0.0408833829227281
GO:0005815	microtubule organizing center	0.0408833829227281
GO:0051347	positive regulation of transferase activity	0.0408833829227281
GO:0000165	MAPKKK cascade	0.0408833829227281
GO:0042803	protein homodimerization activity	0.0422094848719357
GO:0005057	receptor signaling protein activity	0.0463500026719706

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	1.87e-25	76
CD14-positive, CD16-negative classical monocyte	3.13e-23	42
macrophage dendritic cell progenitor	2.89e-22	65
granulocyte monocyte progenitor cell	5.05e-22	71
monopoietic cell	1.31e-21	63
monocyte	1.31e-21	63
monoblast	1.31e-21	63
promonocyte	1.31e-21	63
myeloid cell	1.38e-21	112
common myeloid progenitor	1.38e-21	112
endothelial cell	1.69e-20	35
classical monocyte	2.40e-19	45
myeloid lineage restricted progenitor cell	9.17e-19	70
endothelial cell of vascular tree	4.61e-16	24
meso-epithelial cell	5.17e-16	44
mesodermal cell	5.64e-15	119
blood vessel endothelial cell	6.97e-13	18
embryonic blood vessel endothelial progenitor cell	6.97e-13	18
somatic cell	3.37e-12	591
lining cell	1.54e-09	57
barrier cell	1.54e-09	57
hematopoietic cell	2.51e-08	182
multi fate stem cell	7.20e-08	430
hematopoietic stem cell	9.13e-08	172
angioblastic mesenchymal cell	9.13e-08	172
somatic stem cell	1.42e-07	436
contractile cell	1.84e-07	59
hematopoietic oligopotent progenitor cell	2.88e-07	165
hematopoietic multipotent progenitor cell	2.88e-07	165
leukocyte	3.36e-07	140
endothelial cell of artery	3.52e-07	9
stem cell	4.49e-07	444
vascular associated smooth muscle cell	9.58e-07	32

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.59e-48	216
circulatory system	2.30e-27	113
cardiovascular system	3.36e-27	110
hemolymphoid system	6.60e-27	112
hematopoietic system	8.04e-23	102
blood island	8.04e-23	102
vasculature	1.60e-22	79
vascular system	1.60e-22	79
vessel	5.67e-22	69
splanchnic layer of lateral plate mesoderm	2.32e-20	84
bone marrow	2.38e-20	80
immune system	7.02e-20	115
blood vessel	4.45e-19	60
epithelial tube open at both ends	4.45e-19	60
blood vasculature	4.45e-19	60
vascular cord	4.45e-19	60
musculoskeletal system	4.58e-19	167
bone element	6.81e-17	86
epithelial tube	1.15e-15	118
skeletal element	2.58e-13	101
skeletal system	2.58e-13	101
mesoderm	3.47e-13	448
mesoderm-derived structure	3.47e-13	448
presumptive mesoderm	3.47e-13	448
endothelium	6.97e-13	18
blood vessel endothelium	6.97e-13	18
cardiovascular system endothelium	6.97e-13	18
artery	2.89e-12	42
arterial blood vessel	2.89e-12	42
arterial system	2.89e-12	42
simple squamous epithelium	2.02e-10	22
anatomical system	8.07e-10	625
anatomical group	1.44e-09	626
systemic artery	6.11e-09	33
systemic arterial system	6.11e-09	33
squamous epithelium	4.53e-08	25
tissue	1.95e-07	787
endothelial tube	3.52e-07	9
arterial system endothelium	3.52e-07	9
endothelium of artery	3.52e-07	9
embryonic structure	5.17e-07	605
developing anatomical structure	5.17e-07	605
germ layer	5.92e-07	604
embryonic tissue	5.92e-07	604
presumptive structure	5.92e-07	604
epiblast (generic)	5.92e-07	604

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
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106271127297709
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160577236156418
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185589209162296
JUNB#3726	2	15.3053163299106	0.00612694714847562	0.0270934132119419
MAFK#7975	3	20.3255498533724	0.000195321368893111	0.00235040539760659
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00766650819214201
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00443153074812447
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321306446989279
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243527517213288
TFAP2A#7020	3	12.3889757797837	0.00084694130358843	0.00637917948979317
TFAP2C#7022	3	8.10692145739517	0.00294701173986644	0.0157152391677259

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.