Coexpression cluster:C627

Full id: C627_Mast_Eosinophils_CD14_Neutrophils_Basophils_immature_CD19

Phase1 CAGE Peaks

Hg19::chr12:76477834..76477866,+	p@chr12:76477834..76477866 +
Hg19::chr13:31191097..31191149,-	p@chr13:31191097..31191149 -
Hg19::chr13:31191229..31191249,+	p@chr13:31191229..31191249 +
Hg19::chr14:35874296..35874308,-	p12@NFKBIA
Hg19::chr17:4802892..4802907,+	p6@C17orf107
Hg19::chr17:62972127..62972155,-	p3@AMZ2P1
Hg19::chr17:81147692..81147717,-	p@chr17:81147692..81147717 -
Hg19::chr1:159895503..159895508,+	p@chr1:159895503..159895508 +
Hg19::chr22:37638755..37638764,+	p@chr22:37638755..37638764 +
Hg19::chr2:208394286..208394306,-	p@chr2:208394286..208394306 -
Hg19::chr5:56469337..56469348,-	p@chr5:56469337..56469348 -
Hg19::chr5:56469358..56469387,-	p@chr5:56469358..56469387 -
Hg19::chr5:56469388..56469429,-	p@chr5:56469388..56469429 -
Hg19::chr7:140624061..140624074,-	p@chr7:140624061..140624074 -

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:0045746	negative regulation of Notch signaling pathway	0.00210173083716001
GO:0043330	response to exogenous dsRNA	0.00210173083716001
GO:0008593	regulation of Notch signaling pathway	0.00210173083716001
GO:0007253	cytoplasmic sequestering of NF-kappaB	0.00210173083716001
GO:0042347	negative regulation of NF-kappaB import into nucleus	0.00210173083716001
GO:0031663	lipopolysaccharide-mediated signaling pathway	0.00210173083716001
GO:0032496	response to lipopolysaccharide	0.00210173083716001
GO:0043331	response to dsRNA	0.00210173083716001
GO:0043392	negative regulation of DNA binding	0.00210173083716001
GO:0051100	negative regulation of binding	0.00210173083716001
GO:0008139	nuclear localization sequence binding	0.00210173083716001
GO:0042994	cytoplasmic sequestering of transcription factor	0.00210173083716001
GO:0051220	cytoplasmic sequestering of protein	0.00210173083716001
GO:0002237	response to molecule of bacterial origin	0.00210173083716001
GO:0042308	negative regulation of protein import into nucleus	0.00210173083716001
GO:0042992	negative regulation of transcription factor import into nucleus	0.00210173083716001
GO:0051101	regulation of DNA binding	0.00210173083716001
GO:0042345	regulation of NF-kappaB import into nucleus	0.00210173083716001
GO:0042348	NF-kappaB import into nucleus	0.00210173083716001
GO:0046823	negative regulation of nucleocytoplasmic transport	0.00210173083716001
GO:0051224	negative regulation of protein transport	0.00216845245103811
GO:0051059	NF-kappaB binding	0.00256878213430668
GO:0045638	negative regulation of myeloid cell differentiation	0.00256878213430668
GO:0031625	ubiquitin protein ligase binding	0.00256878213430668
GO:0042990	regulation of transcription factor import into nucleus	0.00256878213430668
GO:0005048	signal sequence binding	0.00256878213430668
GO:0042991	transcription factor import into nucleus	0.00256878213430668
GO:0033157	regulation of intracellular protein transport	0.00256878213430668
GO:0000060	protein import into nucleus, translocation	0.00256878213430668
GO:0042306	regulation of protein import into nucleus	0.00256878213430668
GO:0032507	maintenance of cellular protein localization	0.00265370055196971
GO:0051651	maintenance of cellular localization	0.00265370055196971
GO:0032386	regulation of intracellular transport	0.00265370055196971
GO:0045185	maintenance of protein localization	0.00267867655716472
GO:0051223	regulation of protein transport	0.00272446590002224
GO:0051098	regulation of binding	0.00272446590002224
GO:0046822	regulation of nucleocytoplasmic transport	0.00274550424674056
GO:0051051	negative regulation of transport	0.00285761648912107
GO:0045637	regulation of myeloid cell differentiation	0.00305379694288207
GO:0051235	maintenance of localization	0.00359045684681502
GO:0007219	Notch signaling pathway	0.00427181064463418
GO:0045596	negative regulation of cell differentiation	0.00542113112759527
GO:0030099	myeloid cell differentiation	0.00613004827505004
GO:0051093	negative regulation of developmental process	0.00613004827505004
GO:0006606	protein import into nucleus	0.00746266746527831
GO:0051170	nuclear import	0.00746266746527831
GO:0009968	negative regulation of signal transduction	0.00773553710899171
GO:0009617	response to bacterium	0.00773553710899171
GO:0051049	regulation of transport	0.00786361877848985
GO:0017038	protein import	0.00854703873778406
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.00954707798579222
GO:0045595	regulation of cell differentiation	0.00970029617150775
GO:0006913	nucleocytoplasmic transport	0.0101194447715112
GO:0051169	nuclear transport	0.0101194447715112
GO:0030097	hemopoiesis	0.010253898932811
GO:0048534	hemopoietic or lymphoid organ development	0.0108214117508536
GO:0002520	immune system development	0.0111846494843018
GO:0051707	response to other organism	0.0123491529415052
GO:0042277	peptide binding	0.0123491529415052
GO:0006605	protein targeting	0.0127271478472467
GO:0050793	regulation of developmental process	0.0135521441958952
GO:0009607	response to biotic stimulus	0.0163279626865388
GO:0019899	enzyme binding	0.016958410194016
GO:0051704	multi-organism process	0.018225947103497
GO:0042802	identical protein binding	0.0196161544801601
GO:0007243	protein kinase cascade	0.0199558281508122
GO:0008134	transcription factor binding	0.022585764220227
GO:0042127	regulation of cell proliferation	0.0241596020251972
GO:0006886	intracellular protein transport	0.0268554495859335
GO:0005829	cytosol	0.0284234075120688
GO:0042221	response to chemical stimulus	0.0290591423259917
GO:0065009	regulation of a molecular function	0.0326449396234808
GO:0008283	cell proliferation	0.0357486181206441
GO:0009966	regulation of signal transduction	0.0378690240929732
GO:0006915	apoptosis	0.0393960801943847
GO:0012501	programmed cell death	0.0393960801943847
GO:0015031	protein transport	0.0393960801943847
GO:0016265	death	0.0398453137878252
GO:0008219	cell death	0.0398453137878252
GO:0046907	intracellular transport	0.0398453137878252
GO:0045184	establishment of protein localization	0.0398723422193731
GO:0008104	protein localization	0.0410521002949344
GO:0033036	macromolecule localization	0.0427098716306413
GO:0051649	establishment of cellular localization	0.0457877075238432
GO:0051641	cellular localization	0.045940131900375
GO:0048523	negative regulation of cellular process	0.045940131900375
GO:0048513	organ development	0.045940131900375
GO:0048519	negative regulation of biological process	0.047050110786423
GO:0048468	cell development	0.0488829531788902

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	1.54e-62	136
hematopoietic lineage restricted progenitor cell	9.11e-50	120
nongranular leukocyte	3.59e-46	115
hematopoietic stem cell	7.56e-46	168
angioblastic mesenchymal cell	7.56e-46	168
hematopoietic cell	1.82e-45	177
hematopoietic oligopotent progenitor cell	2.35e-43	161
hematopoietic multipotent progenitor cell	2.35e-43	161
classical monocyte	2.90e-43	42
CD14-positive, CD16-negative classical monocyte	2.90e-43	42
myeloid leukocyte	5.42e-43	72
defensive cell	7.01e-36	48
phagocyte	7.01e-36	48
granulocyte monocyte progenitor cell	4.26e-35	67
myeloid lineage restricted progenitor cell	4.80e-32	66
macrophage dendritic cell progenitor	9.67e-31	61
monopoietic cell	1.71e-28	59
monocyte	1.71e-28	59
monoblast	1.71e-28	59
promonocyte	1.71e-28	59
myeloid cell	4.89e-27	108
common myeloid progenitor	4.89e-27	108
stuff accumulating cell	4.52e-18	87
lymphoid lineage restricted progenitor cell	4.98e-15	52
lymphocyte	1.49e-14	53
common lymphoid progenitor	1.49e-14	53
nucleate cell	1.16e-13	55
intermediate monocyte	3.58e-12	9
CD14-positive, CD16-positive monocyte	3.58e-12	9
granulocyte	1.17e-11	8
mesenchymal cell	3.85e-10	354
blood cell	7.88e-10	11
connective tissue cell	1.93e-09	361
CD4-positive, alpha-beta T cell	7.38e-08	6
motile cell	9.84e-08	386
T cell	1.75e-07	25
pro-T cell	1.75e-07	25
circulating cell	2.11e-07	6
histamine secreting cell	4.77e-07	5
biogenic amine secreting cell	4.77e-07	5
granulocytopoietic cell	4.77e-07	5
mast cell	4.77e-07	5
mast cell progenitor	4.77e-07	5
basophil mast progenitor cell	4.77e-07	5

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.01e-33	98
blood island	6.01e-33	98
bone marrow	1.01e-31	76
hemolymphoid system	5.92e-30	108
immune system	1.81e-29	93
bone element	4.42e-28	82
skeletal element	5.15e-24	90
skeletal system	6.77e-20	100
connective tissue	7.20e-09	371
lateral plate mesoderm	3.78e-08	203
musculoskeletal system	8.09e-07	167

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
BCL11A#53335	5	10.1319482512882	8.32782329868578e-05	0.00125107816094857
BCL3#602	7	17.2735514018692	4.86650874441473e-08	3.15098144301259e-06
CTCF#10664	7	2.68012818653751	0.0078548724880142	0.0322580719506003
EBF1#1879	8	5.08940962661086	4.04144399024511e-05	0.000739979608866075
EGR1#1958	7	2.49408954740507	0.0117605194461907	0.042859128007562
HEY1#23462	11	3.1743729624402	3.59719932856811e-05	0.000696492214824481
HMGN3#9324	6	3.50509188143597	0.00417154685841666	0.0198710231400765
HSF1#3297	3	35.2051428571429	7.78651961638345e-05	0.00119996506155448
MEF2A#4205	4	5.35520883132687	0.00526133968973413	0.0243719088022773
MEF2C#4208	3	8.8524331055623	0.00422365328590312	0.0201045588408202
MXI1#4601	5	3.55770415312832	0.00937782304330066	0.0353884398330422
NANOG#79923	3	6.26673824593128	0.0109602307927629	0.0403239350324221
NFKB1#4790	10	3.9200453029956	1.9593663942264e-05	0.000438752716223438
PAX5#5079	9	4.28757784147146	3.71976426636989e-05	0.000718226031087826
PBX3#5090	4	6.26128933906975	0.00299894388765468	0.0159400834995556
POLR2A#5430	12	1.84067415133549	0.00308514162916731	0.0162616890384882
POU2F2#5452	6	3.90262459617537	0.00240286007908887	0.013551072077324
SIN3A#25942	7	2.70444236340757	0.00746246190599541	0.0307808870063292
TAF1#6872	11	2.62667922451416	0.000239368378315676	0.00260600375929437
TAL1#6886	4	8.53389047926863	0.000959305563636706	0.00690196429874993
TBP#6908	10	2.64769334792599	0.000666552966265281	0.00544839361695075
TCF12#6938	6	4.55762781522275	0.00106427627976311	0.00751941214870648
THAP1#55145	3	6.72195955775386	0.00905312049031581	0.034268379213805
ZBTB7A#51341	6	3.15081827480396	0.00712763978868938	0.0296350798953354

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.