Coexpression cluster:C4399

Full id: C4399_Neutrophils_CD14_Whole_Eosinophils_CD19_migratory_spleen

Phase1 CAGE Peaks

Hg19::chr4:185395633..185395651,-	p2@IRF2
Hg19::chr6:32806472..32806481,-	p7@TAP2
Hg19::chr6:32806483..32806503,-	p3@TAP2

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:0004409	homoaconitate hydratase activity	0.00322604381779525
GO:0046967	cytosol to ER transport	0.00322604381779525
GO:0042825	TAP complex	0.00322604381779525
GO:0015433	peptide antigen-transporting ATPase activity	0.00322604381779525
GO:0015440	peptide-transporting ATPase activity	0.00322604381779525
GO:0046980	tapasin binding	0.00322604381779525
GO:0046977	TAP binding	0.00322604381779525
GO:0042824	MHC class I peptide loading complex	0.00322604381779525
GO:0046979	TAP2 binding	0.00322604381779525
GO:0046978	TAP1 binding	0.00322604381779525
GO:0042301	phosphate binding	0.00403243606120116
GO:0015198	oligopeptide transporter activity	0.00403243606120116
GO:0015197	peptide transporter activity	0.00496285212327168
GO:0042288	MHC class I protein binding	0.00518433170739016
GO:0002483	antigen processing and presentation of endogenous peptide antigen	0.00763905561147222
GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	0.00763905561147222
GO:0006857	oligopeptide transport	0.00763905561147222
GO:0042605	peptide antigen binding	0.00763905561147222
GO:0019883	antigen processing and presentation of endogenous antigen	0.00763905561147222
GO:0042287	MHC protein binding	0.00927228213987372
GO:0015833	peptide transport	0.0149703443648315
GO:0005788	endoplasmic reticulum lumen	0.0234414163837479
GO:0016836	hydro-lyase activity	0.0313176878355985
GO:0016835	carbon-oxygen lyase activity	0.0313176878355985
GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	0.0313176878355985
GO:0048002	antigen processing and presentation of peptide antigen	0.0313176878355985
GO:0046982	protein heterodimerization activity	0.0313176878355985
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0365148045338801
GO:0042803	protein homodimerization activity	0.0438413389976883
GO:0003823	antigen binding	0.0474629779509783

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	9.47e-52	136
nongranular leukocyte	1.45e-45	115
hematopoietic stem cell	4.59e-42	168
angioblastic mesenchymal cell	4.59e-42	168
hematopoietic lineage restricted progenitor cell	9.30e-42	120
hematopoietic cell	2.67e-41	177
hematopoietic oligopotent progenitor cell	1.44e-39	161
hematopoietic multipotent progenitor cell	1.44e-39	161
myeloid leukocyte	2.56e-28	72
macrophage dendritic cell progenitor	7.05e-26	61
monopoietic cell	9.83e-26	59
monocyte	9.83e-26	59
monoblast	9.83e-26	59
promonocyte	9.83e-26	59
granulocyte monocyte progenitor cell	2.09e-24	67
myeloid lineage restricted progenitor cell	2.32e-23	66
defensive cell	1.01e-22	48
phagocyte	1.01e-22	48
classical monocyte	4.38e-21	42
CD14-positive, CD16-negative classical monocyte	4.38e-21	42
myeloid cell	6.24e-21	108
common myeloid progenitor	6.24e-21	108
lymphocyte	1.18e-17	53
common lymphoid progenitor	1.18e-17	53
nucleate cell	2.60e-17	55
lymphoid lineage restricted progenitor cell	2.68e-17	52
mesenchymal cell	2.22e-12	354
connective tissue cell	2.96e-12	361
lymphocyte of B lineage	2.13e-11	24
pro-B cell	2.13e-11	24
B cell	5.14e-09	14
motile cell	5.99e-08	386
multi fate stem cell	7.54e-07	427
stuff accumulating cell	9.76e-07	87

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	6.76e-34	108
hematopoietic system	6.03e-33	98
blood island	6.03e-33	98
immune system	9.36e-26	93
bone marrow	4.33e-22	76
bone element	7.23e-18	82
skeletal element	6.79e-17	90
skeletal system	1.60e-14	100
lateral plate mesoderm	2.69e-14	203
connective tissue	1.82e-11	371
blood	2.21e-09	15
haemolymphatic fluid	2.21e-09	15
organism substance	2.21e-09	15

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	2	14.4350984067479	0.00620114743554613	0.0273960083342217
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190728304676291
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464166120962282
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764229755572934
FOSL1#8061	2	26.4757198109153	0.00186983370259098	0.0110279852080923
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108999115898298
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128527119427071
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187178195664687
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00195323817762139
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722106581848048
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270447064528589
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173445265455452
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00884518634848282
PRDM1#639	2	87.8873038516405	0.000171624884802908	0.00209249723837625
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00666759313754767
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00485924039915849
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298367771091295
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027777846199994
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0330069786533311
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457759132315978
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109304359600488
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155182798298328
STAT2#6773	3	65.2637711864407	3.59360517547754e-06	0.000118544703386513
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158754911317711
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330627097109737
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140675148970622
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109806760880237

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.