Coexpression cluster:C723

Full id: C723_CD14_CD4_Eosinophils_CD8_Natural_Neutrophils_CD19

Phase1 CAGE Peaks

Hg19::chr10:43633914..43633935,+	p2@CSGALNACT2
Hg19::chr11:82868158..82868179,+	p2@PCF11
Hg19::chr16:21513575..21513614,-	p1@LOC100271836
Hg19::chr16:30346739..30346761,-	p1@LOC595101
Hg19::chr17:18218587..18218624,+	p1@SMCR8
Hg19::chr18:76829385..76829438,+	p1@ATP9B
Hg19::chr2:201729366..201729392,-	p1@CLK1
Hg19::chr5:65440032..65440099,+	p2@SREK1
Hg19::chr7:120590822..120590857,+	p1@ING3
Hg19::chrX:73834345..73834364,-	p4@RLIM
Hg19::chrX:73834386..73834435,-	p2@RLIM

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:0005849	mRNA cleavage factor complex	0.0280344945489482
GO:0015917	aminophospholipid transport	0.0280344945489482
GO:0006379	mRNA cleavage	0.04982443207512

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
hematopoietic stem cell	1.08e-51	172
angioblastic mesenchymal cell	1.08e-51	172
leukocyte	1.17e-50	140
hematopoietic oligopotent progenitor cell	1.03e-47	165
hematopoietic multipotent progenitor cell	1.03e-47	165
hematopoietic cell	1.10e-45	182
hematopoietic lineage restricted progenitor cell	6.85e-42	124
nongranular leukocyte	6.53e-39	119
myeloid cell	7.73e-32	112
common myeloid progenitor	7.73e-32	112
myeloid leukocyte	1.15e-30	76
granulocyte monocyte progenitor cell	2.92e-27	71
myeloid lineage restricted progenitor cell	2.10e-26	70
CD14-positive, CD16-negative classical monocyte	3.39e-26	42
macrophage dendritic cell progenitor	3.34e-24	65
classical monocyte	6.51e-24	45
monopoietic cell	3.69e-23	63
monocyte	3.69e-23	63
monoblast	3.69e-23	63
promonocyte	3.69e-23	63
lymphoid lineage restricted progenitor cell	7.75e-14	52
lymphocyte	8.70e-14	53
common lymphoid progenitor	8.70e-14	53
mature alpha-beta T cell	2.04e-09	18
alpha-beta T cell	2.04e-09	18
immature T cell	2.04e-09	18
mature T cell	2.04e-09	18
immature alpha-beta T cell	2.04e-09	18
T cell	1.28e-08	25
pro-T cell	1.28e-08	25
mesenchymal cell	1.33e-08	358
connective tissue cell	1.80e-07	365

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.17e-30	102
blood island	3.17e-30	102
hemolymphoid system	5.68e-28	112
bone marrow	8.09e-23	80
bone element	7.79e-22	86
adult organism	9.34e-20	115
immune system	7.39e-17	115
skeletal element	7.56e-16	101
skeletal system	7.56e-16	101
neural tube	1.96e-07	57
neural rod	1.96e-07	57
future spinal cord	1.96e-07	57
neural keel	1.96e-07	57
connective tissue	4.55e-07	375

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
CEBPB#1051	8	5.79719827332714	7.09770251647579e-06	0.000204716087577524
E2F1#1869	11	4.90738921487932	2.51269297258347e-08	1.75299359628354e-06
E2F4#1874	8	9.21313477475232	1.99706038053359e-07	1.08011905273199e-05
E2F6#1876	9	4.1049455986615	1.83835844928222e-05	0.000418110448790474
EGR1#1958	7	3.17429578760645	0.00199357209099962	0.0115940904116221
ELF1#1997	11	4.25809795880754	1.19731042846735e-07	6.90479866585873e-06
ELK4#2005	4	5.90388423944292	0.00334112168340882	0.0172573396386515
ETS1#2113	5	4.42216405554652	0.00310836378716529	0.016342028973962
FOS#2353	6	4.90797562303331	0.000528682880176561	0.00457078736115562
GABPB1#2553	9	5.78265041142178	9.50989655291635e-07	4.06550997171523e-05
GTF2F1#2962	5	5.79075494398075	0.000918925041780732	0.00668232923259559
HEY1#23462	11	4.04011104310571	2.1344242734918e-07	1.13675235440699e-05
MAX#4149	7	4.10617168754999	0.000396333145794484	0.00387426407840042
MXI1#4601	5	4.5279871039815	0.00279761876947351	0.0153198671699373
MYC#4609	9	4.27277607677133	1.30375226575527e-05	0.000318658045596103
NFKB1#4790	7	3.49240399721426	0.00110207548522866	0.00769639997337322
NFYB#4801	5	7.61808784251657	0.000257397641240345	0.00276169634821249
PAX5#5079	6	3.63794483518791	0.00264989689588002	0.0146360242164479
POLR2A#5430	11	2.14745317655807	0.000223198342238743	0.00248461006875635
POU2F2#5452	6	4.96697675876865	0.00049515413177051	0.00437841015730931
RFX5#5993	6	6.5715877239246	0.000104500564341874	0.00145732867396194
SIN3A#25942	8	3.93373434677464	0.000131554682498111	0.00172975443603427
SMARCB1#6598	4	6.63735119314815	0.00217555538509292	0.0125511146695973
SPI1#6688	5	3.72923795841942	0.00657139769228244	0.028083730402827
STAT1#6772	3	5.64725113559978	0.0138689600283293	0.048717217691332
STAT3#6774	6	5.73788999844777	0.000223133323888784	0.00248574092945287
TAF1#6872	11	3.34304628574529	1.71447392661505e-06	6.47587495196198e-05
TAF7#6879	7	7.27558962131522	9.39481399808184e-06	0.000250047140455063
TBP#6908	11	3.70677068709639	5.5042384307836e-07	2.54812569801688e-05
TCF7L2#6934	6	5.87464176171128	0.000195714842587612	0.00235405533168347
TFAP2C#7022	5	4.91328573175465	0.00193982427985066	0.0113950901604884
THAP1#55145	3	8.55522125532309	0.004407746242643	0.0208818602783122
USF1#7391	9	5.20486304498833	2.37429471822852e-06	8.40857802906302e-05
USF2#7392	6	7.08665311912887	6.8302134157013e-05	0.00109023484475383
YY1#7528	10	4.46470068168532	1.09711041274109e-06	4.55228901057873e-05
ZNF143#7702	4	4.9094096553556	0.00649801564418536	0.0278304800435954
ZNF263#10127	5	3.73720074409576	0.00651090818209497	0.0278765522744155

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.