Coexpression cluster:C473

Full id: C473_immature_Eosinophils_cord_CD14_CD4_CD8_Natural

Phase1 CAGE Peaks

Hg19::chr10:106028656..106028685,-	p1@MIR4482-1
Hg19::chr10:3827776..3827787,+	p@chr10:3827776..3827787 +
Hg19::chr11:18548217..18548243,+	p@chr11:18548217..18548243 +
Hg19::chr11:58346354..58346370,-	p@chr11:58346354..58346370 -
Hg19::chr12:25539298..25539317,+	p@chr12:25539298..25539317 +
Hg19::chr13:45151945..45151990,-	p@chr13:45151945..45151990 -
Hg19::chr14:24583688..24583704,-	p@chr14:24583688..24583704 -
Hg19::chr16:20912197..20912222,-	p4@DCUN1D3
Hg19::chr19:49376263..49376332,-	p@chr19:49376263..49376332 -
Hg19::chr1:171455122..171455146,-	p1@BC007549
Hg19::chr2:96811170..96811186,-	p1@DUSP2
Hg19::chr3:150126416..150126437,+	p3@TSC22D2
Hg19::chr3:5020939..5020952,+	p2@BHLHE40
Hg19::chr4:103461950..103461953,+	p@chr4:103461950..103461953 +
Hg19::chr6:108879688..108879712,-	p@chr6:108879688..108879712 -
Hg19::chr7:151216229..151216250,+	p@chr7:151216229..151216250 +
Hg19::chr7:73508557..73508570,-	p@chr7:73508557..73508570 -
Hg19::chr8:102218439..102218455,-	p3@ZNF706
Hg19::chr8:81397846..81397860,+	p3@ZBTB10
Hg19::chr8:81397876..81397898,+	p5@ZBTB10

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:0051019	mitogen-activated protein kinase binding	0.0135982338777593
GO:0008330	protein tyrosine/threonine phosphatase activity	0.0135982338777593
GO:0033549	MAP kinase phosphatase activity	0.0326141514013656
GO:0017017	MAP kinase tyrosine/serine/threonine phosphatase activity	0.0326141514013656
GO:0000188	inactivation of MAPK activity	0.0326141514013656
GO:0043407	negative regulation of MAP kinase activity	0.0362283455576895

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	4.38e-68	136
hematopoietic stem cell	1.08e-54	168
angioblastic mesenchymal cell	1.08e-54	168
nongranular leukocyte	4.32e-52	115
hematopoietic lineage restricted progenitor cell	1.86e-51	120
hematopoietic cell	7.48e-51	177
hematopoietic oligopotent progenitor cell	5.70e-49	161
hematopoietic multipotent progenitor cell	5.70e-49	161
classical monocyte	3.05e-35	42
CD14-positive, CD16-negative classical monocyte	3.05e-35	42
myeloid leukocyte	5.67e-30	72
defensive cell	1.18e-28	48
phagocyte	1.18e-28	48
lymphocyte	8.77e-27	53
common lymphoid progenitor	8.77e-27	53
lymphoid lineage restricted progenitor cell	2.56e-26	52
granulocyte monocyte progenitor cell	6.94e-26	67
nucleate cell	3.53e-25	55
macrophage dendritic cell progenitor	2.70e-23	61
myeloid lineage restricted progenitor cell	2.01e-22	66
myeloid cell	5.46e-22	108
common myeloid progenitor	5.46e-22	108
monopoietic cell	9.94e-22	59
monocyte	9.94e-22	59
monoblast	9.94e-22	59
promonocyte	9.94e-22	59
mesenchymal cell	4.99e-19	354
connective tissue cell	7.89e-18	361
motile cell	3.28e-15	386
T cell	2.13e-12	25
pro-T cell	2.13e-12	25
lymphocyte of B lineage	2.21e-12	24
pro-B cell	2.21e-12	24
mature alpha-beta T cell	3.29e-12	18
alpha-beta T cell	3.29e-12	18
immature T cell	3.29e-12	18
mature T cell	3.29e-12	18
immature alpha-beta T cell	3.29e-12	18
stuff accumulating cell	6.49e-12	87
B cell	2.28e-10	14
multi fate stem cell	7.99e-10	427
stem cell	1.24e-09	441
somatic stem cell	3.51e-09	433
intermediate monocyte	9.07e-09	9
CD14-positive, CD16-positive monocyte	9.07e-09	9
granulocyte	2.83e-08	8
CD8-positive, alpha-beta T cell	4.36e-07	11
CD4-positive, alpha-beta T cell	9.82e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.08e-23	98
blood island	1.08e-23	98
bone marrow	1.14e-22	76
bone element	2.40e-21	82
hemolymphoid system	4.56e-20	108
immune system	4.45e-19	93
skeletal element	3.59e-17	90
connective tissue	9.97e-17	371
skeletal system	2.31e-14	100

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
BHLHE40#8553	5	11.2179533867444	6.42747363862819e-05	0.00104593162877016
CCNT2#905	10	3.16810078848132	0.000380354293256706	0.00376600512262392
CEBPB#1051	11	4.38413119420365	6.79503322842392e-06	0.000197678683939656
CHD2#1106	6	3.10320685023506	0.00957883741286272	0.0360544996057941
E2F1#1869	13	3.18980298967156	1.87417375144146e-05	0.000425422369977818
E2F6#1876	10	2.50857786584869	0.00252473186887982	0.0139972646594086
EGR1#1958	10	2.49408954740507	0.0026418915002173	0.014594895868352
ELF1#1997	13	2.7677636732249	9.22980427778795e-05	0.00134329923211803
EP300#2033	9	3.04827377680044	0.00118128450666637	0.00801482313985114
FOS#2353	9	4.04907988900248	0.000137120465571173	0.00179210665796367
FOSL2#2355	5	4.23255015114042	0.00526899604893047	0.0244041278262561
FOXA1#3169	6	3.32442592481564	0.00687500193788688	0.0291167204943621
FOXA2#3170	6	7.38913912579957	0.00010583167577042	0.0014753009057377
GABPB1#2553	8	2.82707353447287	0.00410519598610444	0.0195674576054384
GATA3#2625	4	5.4473032714412	0.00548679388819938	0.0248454416792254
GTF2F1#2962	6	3.8218982630273	0.00345300015837971	0.0175513643617569
HEY1#23462	15	3.03008328232928	3.32829050484245e-06	0.000111197483056699
HMGN3#9324	9	3.68034647550777	0.000286847121679929	0.00304947338570135
IRF1#3659	8	3.05486550142556	0.0025022697205526	0.0140351529186248
IRF3#3661	3	7.04729283172344	0.00837752750300273	0.0329222078147992
JUN#3725	6	3.7538487577009	0.00377784860160514	0.0186621289425333
MAX#4149	9	2.90364997905321	0.00168467963301963	0.0105293989343469
MEF2A#4205	7	6.56013081837542	5.13114917567969e-05	0.000873499737178176
MEF2C#4208	3	6.1967031738936	0.0118740797915432	0.0432412922120358
MXI1#4601	9	4.48270723294168	6.16323643311231e-05	0.00101017302234435
MYC#4609	12	3.13336912296564	6.50448960500582e-05	0.00105648894223515
NFKB1#4790	17	4.66485391056476	1.73611812252636e-10	1.8186403269662e-08
NFYA#4800	5	4.60639517495763	0.00366949907423154	0.0185237959211981
NFYB#4801	5	4.18994831338411	0.00549982929407684	0.0249012299667964
PAX5#5079	10	3.33478276558891	0.000247239877718071	0.00268582125951712
POLR2A#5430	18	1.93270785890226	6.29675214552603e-05	0.00102802328798905
POU2F2#5452	10	4.55306202887126	1.65166365444159e-05	0.000381127044644776
REST#5978	8	3.86001148645121	0.000529570002650139	0.00457807809840061
RFX5#5993	8	4.81916433087804	0.000113599007078504	0.00155575225547756
SIN3A#25942	14	3.78621930877059	6.7895687647145e-07	3.07233870111793e-05
SMARCB1#6598	6	5.47581473434722	0.000536533476224363	0.00463597416425881
SP2#6668	4	5.23070609876893	0.0063283015178379	0.0275579152825532
SPI1#6688	7	2.87151322798295	0.00728517203947023	0.0301400761618694
STAT1#6772	5	5.1766468742998	0.00220980226884253	0.012726896391069
TAF1#6872	15	2.50728471430897	4.1297690460894e-05	0.000749972090774701
TAF7#6879	6	3.42992082147717	0.00590337858341472	0.0264803915248572
TBP#6908	16	2.96541654967711	1.18297025119262e-06	4.81857371545654e-05
TCF12#6938	7	3.72206271576525	0.00166685973687412	0.0104217650897627
TCF7L2#6934	7	3.76956179709807	0.00154735260213302	0.00983471022481564
TFAP2A#7020	6	4.95559031191349	0.000909367269260404	0.00661881721613265
TFAP2C#7022	8	4.32369144394409	0.000242797584069214	0.00264085991278949
USF1#7391	11	3.49882460246438	6.03444132472198e-05	0.000990929272818614
USF2#7392	7	4.54726908477436	0.000504082156194133	0.00444156216238582
YY1#7528	11	2.70114391241962	0.000661477878291362	0.00541453782670049
ZBTB33#10009	6	9.49941750899435	2.61702144212769e-05	0.000564126114333072
ZBTB7A#51341	7	2.57316825775656	0.0131732858250138	0.0466137488828941

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.