Coexpression cluster:C1588

Full id: C1588_Eosinophils_CD14CD16_CD14_Neutrophils_Basophils_Whole_embryonic

Phase1 CAGE Peaks

Hg19::chr10:60027628..60027641,-	p2@IPMK
Hg19::chr5:176730629..176730638,-	p5@RAB24
Hg19::chr5:176730640..176730649,-	p4@RAB24
Hg19::chr5:176730651..176730666,-	p3@RAB24
Hg19::chr5:176730676..176730730,-	p1@RAB24

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:0050516	inositol polyphosphate multikinase activity	0.0044742070763476
GO:0046853	inositol and derivative phosphorylation	0.0044742070763476
GO:0046835	carbohydrate phosphorylation	0.00760447274511088
GO:0008440	inositol trisphosphate 3-kinase activity	0.00760447274511088
GO:0006020	inositol metabolic process	0.00760447274511088
GO:0051766	inositol trisphosphate kinase activity	0.00760447274511088
GO:0001839	neural plate morphogenesis	0.00760447274511088
GO:0001841	neural tube formation	0.00760447274511088
GO:0001840	neural plate development	0.00760447274511088
GO:0001838	embryonic epithelial tube formation	0.00760447274511088
GO:0021915	neural tube development	0.00772624213739308
GO:0016331	morphogenesis of embryonic epithelium	0.00820029831559406
GO:0006914	autophagy	0.00894525314623864
GO:0005793	ER-Golgi intermediate compartment	0.0137339145107121
GO:0005770	late endosome	0.0152013327330055
GO:0002009	morphogenesis of an epithelium	0.0173540881453391
GO:0004428	inositol or phosphatidylinositol kinase activity	0.0173540881453391
GO:0035239	tube morphogenesis	0.0202127547381958
GO:0048598	embryonic morphogenesis	0.0202127547381958
GO:0009792	embryonic development ending in birth or egg hatching	0.0202127547381958
GO:0043009	chordate embryonic development	0.0202127547381958
GO:0035295	tube development	0.0237543708322871
GO:0005768	endosome	0.0374388860274241
GO:0009790	embryonic development	0.0436597004450281
GO:0019318	hexose metabolic process	0.046962490367732
GO:0005996	monosaccharide metabolic process	0.046962490367732

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
CD14-positive, CD16-negative classical monocyte	5.76e-27	42
myeloid leukocyte	1.28e-23	76
classical monocyte	1.62e-23	45
leukocyte	9.54e-23	140
granulocyte monocyte progenitor cell	1.32e-20	71
macrophage dendritic cell progenitor	4.80e-19	65
nongranular leukocyte	2.91e-18	119
hematopoietic lineage restricted progenitor cell	3.51e-18	124
hematopoietic stem cell	6.52e-18	172
angioblastic mesenchymal cell	6.52e-18	172
monopoietic cell	7.17e-18	63
monocyte	7.17e-18	63
monoblast	7.17e-18	63
promonocyte	7.17e-18	63
myeloid lineage restricted progenitor cell	2.20e-17	70
hematopoietic cell	6.65e-17	182
hematopoietic oligopotent progenitor cell	3.74e-16	165
hematopoietic multipotent progenitor cell	3.74e-16	165
myeloid cell	1.08e-14	112
common myeloid progenitor	1.08e-14	112
connective tissue cell	2.61e-12	365
mesenchymal cell	2.65e-11	358
motile cell	7.89e-10	390
multi fate stem cell	1.22e-09	430
somatic stem cell	1.45e-08	436
stem cell	2.87e-08	444
intermediate monocyte	2.01e-07	9
CD14-positive, CD16-positive monocyte	2.01e-07	9

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.15e-22	102
blood island	4.15e-22	102
hemolymphoid system	8.07e-22	112
bone element	2.59e-18	86
bone marrow	6.68e-18	80
skeletal element	4.47e-15	101
skeletal system	4.47e-15	101
immune system	4.89e-14	115
connective tissue	1.72e-12	375
musculoskeletal system	1.75e-09	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
ATF3#467	4	17.970539620807	1.89252338486495e-05	0.000428841939231742
CCNT2#905	5	6.33620157696263	9.78880505817628e-05	0.00138828491508809
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239195979560142
CTCFL#140690	4	15.7971794871795	3.15350622350688e-05	0.000633607226773442
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.0035208753307893
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00322397349756637
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00330282904936694
ELF1#1997	4	3.40647836704603	0.0123506610529955	0.0447211000836873
ELK4#2005	4	12.9885453267744	6.83810524411663e-05	0.00109049453899877
ETS1#2113	4	7.78300873776187	0.000512103594768887	0.00443884034642441
GABPB1#2553	4	5.65414706894574	0.00177669650209667	0.0109035377824935
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00673553034407126
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00880605967998362
MAX#4149	5	6.45255550900712	8.93743970843928e-05	0.00130529613440035
MXI1#4601	5	9.9615716287593	1.01894348670516e-05	0.000266376567729662
MYC#4609	5	5.2222818716094	0.000257394484885061	0.00276223002537103
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247735488032968
SMARCB1#6598	3	10.9516294686944	0.00151187284834318	0.00964913764410374
SRF#6722	4	11.0377426097342	0.000129925581484675	0.00170962552660678
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135110555856512
USF1#7391	5	6.36149927720796	9.59569864925045e-05	0.00136683738574614
USF2#7392	4	10.3937579080557	0.000164617972868753	0.00202598827108646
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352425133485247
ZBTB7A#51341	5	7.3519093078759	4.65425347594289e-05	0.000814896192412404
ZNF143#7702	4	10.8007012417823	0.000141522343086319	0.00184363876632057

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.