Coexpression cluster:C722

Full id: C722_Mast_Natural_CD8_CD4_CD19_mature_Basophils

Phase1 CAGE Peaks

Hg19::chr10:3934617..3934629,-	p@chr10:3934617..3934629 -
Hg19::chr11:9594422..9594446,+	p@chr11:9594422..9594446 +
Hg19::chr14:50101898..50101922,-	p3@DNAAF2
Hg19::chr19:14529156..14529170,+	p@chr19:14529156..14529170 +
Hg19::chr1:59249645..59249656,-	p4@JUN
Hg19::chr1:59249688..59249703,-	p3@JUN
Hg19::chr1:59249707..59249727,-	p1@JUN
Hg19::chr1:59249732..59249749,-	p2@JUN
Hg19::chr6:170122964..170122975,+	p@chr6:170122964..170122975 +
Hg19::chr6:31830554..31830563,-	p4@NEU1
Hg19::chr9:123346608..123346621,+	p@chr9:123346608..123346621 +

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
2.38818258532104e-05	0.0151171957650822	2	140	Regulation of toll-like receptor signaling pathway (Wikipathways):WP1449

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:0035026	leading edge cell differentiation	0.00284936345388452
GO:0043202	lysosomal lumen	0.00284936345388452
GO:0031953	negative regulation of protein amino acid autophosphorylation	0.00284936345388452
GO:0031952	regulation of protein amino acid autophosphorylation	0.00284936345388452
GO:0005775	vacuolar lumen	0.00284936345388452
GO:0016997	alpha-sialidase activity	0.00508792435269485
GO:0004308	exo-alpha-sialidase activity	0.00508792435269485
GO:0001933	negative regulation of protein amino acid phosphorylation	0.00569822364226741
GO:0045763	negative regulation of amino acid metabolic process	0.00569822364226741
GO:0033239	negative regulation of amine metabolic process	0.00569822364226741
GO:0031974	membrane-enclosed lumen	0.0082293520490518
GO:0043233	organelle lumen	0.0082293520490518
GO:0030855	epithelial cell differentiation	0.0181924770505665
GO:0046777	protein amino acid autophosphorylation	0.0181924770505665
GO:0001932	regulation of protein amino acid phosphorylation	0.0181924770505665
GO:0033238	regulation of amine metabolic process	0.0181924770505665
GO:0006521	regulation of amino acid metabolic process	0.0181924770505665
GO:0016540	protein autoprocessing	0.0181924770505665
GO:0005765	lysosomal membrane	0.0191069383036046
GO:0005774	vacuolar membrane	0.0196412195283527
GO:0002009	morphogenesis of an epithelium	0.0196412195283527
GO:0042325	regulation of phosphorylation	0.0196412195283527
GO:0044437	vacuolar part	0.0196412195283527
GO:0051174	regulation of phosphorus metabolic process	0.0196412195283527
GO:0019220	regulation of phosphate metabolic process	0.0196412195283527
GO:0016485	protein processing	0.02608187441823
GO:0000228	nuclear chromosome	0.02608187441823
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0352913285426469
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	0.0462804105238576
GO:0005764	lysosome	0.0462804105238576
GO:0000323	lytic vacuole	0.0462804105238576
GO:0005667	transcription factor complex	0.0465692044661635
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.0465692044661635
GO:0045893	positive regulation of transcription, DNA-dependent	0.0465692044661635
GO:0005773	vacuole	0.0472603152259916
GO:0044446	intracellular organelle part	0.0483224709928153
GO:0044422	organelle part	0.0483224709928153

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><br><br>

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Cell Type

Ontology term	p-value	n
leukocyte	1.63e-11	136
hematopoietic lineage restricted progenitor cell	7.62e-10	120
CD4-positive, alpha-beta T cell	9.94e-10	6
nongranular leukocyte	5.42e-09	115
hematopoietic stem cell	2.03e-07	168
angioblastic mesenchymal cell	2.03e-07	168
hematopoietic cell	2.21e-07	177

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
BCLAF1#9774	4	7.8736900400443	0.00115437508641528	0.00789481891494504
CCNT2#905	6	3.45610995107053	0.00346892417326783	0.017621156212642
CHD2#1106	5	4.70182856096221	0.00236388215455891	0.0133956314888757
E2F4#1874	6	6.90985108106424	7.8773130924702e-05	0.00120718811748275
E2F6#1876	8	3.64884053214355	0.000229244879929919	0.00252820549260832
ETS1#2113	5	4.42216405554652	0.00310836378716529	0.0163412063610065
FOS#2353	8	6.54396749737775	2.80888190396464e-06	9.71058646700306e-05
FOSL2#2355	4	6.15643658347698	0.00286737656398896	0.0155356889897512
GATA1#2623	7	8.62928700060028	2.99493398157953e-06	0.000101422798347012
GATA2#2624	7	8.11041110317072	4.54252138065835e-06	0.000141955831979227
GATA3#2625	5	12.3802347078209	2.5558774340898e-05	0.000553000379819565
GTF2B#2959	4	11.6159381579361	0.000265294844314037	0.00284000904523511
GTF2F1#2962	4	4.6326039551846	0.00798636821974098	0.0322864562398981
HEY1#23462	7	2.57097975470363	0.00712682984021317	0.0296328920169609
HSF1#3297	4	59.7420606060606	4.35491575565215e-07	2.08634425047961e-05
IRF1#3659	5	3.47143806980177	0.00894716207586585	0.0339312487759669
JUN#3725	8	9.10023941260824	2.19796342409383e-07	1.16880398191922e-05
JUNB#3726	7	19.4794935107953	1.16321089188912e-08	8.71481939297044e-07
JUND#3727	7	4.45114978119065	0.000236377425785552	0.00257505183807419
MAFF#23764	4	20.4783114508891	2.96388600973389e-05	0.000614299049356216
MEF2A#4205	5	8.51965041347457	0.000152040353322568	0.00194977191314535
MEF2C#4208	4	15.0223107245906	9.87232765848972e-05	0.00139087552721571
MXI1#4601	8	7.2447793663704	1.28440155682788e-06	5.12969843952378e-05
NFKB1#4790	6	2.99348914046936	0.00728556496302957	0.0301393139180007
NFYA#4800	5	8.37526395446842	0.000164818728564703	0.00202798105473244
NFYB#4801	5	7.61808784251657	0.000257397641240345	0.0027614126608629
POLR2A#5430	10	1.95223016050734	0.0030407318184143	0.016133458158066
POU2F2#5452	5	4.13914729897387	0.00416567688108871	0.0198475879463515
RDBP#7936	4	55.8685105418272	5.6826694055937e-07	2.62375026547657e-05
REST#5978	5	4.3863766891491	0.00322267288154589	0.0167000462972993
RFX5#5993	6	6.5715877239246	0.000104500564341874	0.00145713410404552
SIN3A#25942	7	3.44201755342781	0.00120675394335343	0.0081823135161909
SMARCB1#6598	4	6.63735119314815	0.00217555538509292	0.0125504213910583
SP2#6668	5	11.887968406293	3.10656322491346e-05	0.000628163323614206
TAF7#6879	4	4.1574797836087	0.0116799292229153	0.0426413160454453
TAL1#6886	4	10.8613151554328	0.00034280930934417	0.00346354468981289
TCF12#6938	6	5.80061721937441	0.000210035898573283	0.00244493303734899
TRIM28#10155	4	6.76019092555001	0.00203333593231794	0.0118102203122937
YY1#7528	6	2.67882040901119	0.0127393379134147	0.0459373584345239
ZNF143#7702	4	4.9094096553556	0.00649801564418536	0.0278293387953364

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.