Coexpression cluster:C569

Full id: C569_CD14_immature_CD19_Basophils_migratory_Dendritic_Peripheral

Phase1 CAGE Peaks

Hg19::chr16:87498643..87498677,+	p@chr16:87498643..87498677 +
Hg19::chr5:149792614..149792625,+	p@chr5:149792614..149792625 +
Hg19::chr6:30227370..30227387,+	p2@HLA-L
Hg19::chr6:32441310..32441322,-	p2@HLA-DRB9
Hg19::chr6:32441341..32441365,-	p1@HLA-DRB9
Hg19::chr6:32572499..32572517,+	p@chr6:32572499..32572517 +
Hg19::chr6:32577605..32577616,-	p@chr6:32577605..32577616 -
Hg19::chr6:32577619..32577667,-	p@chr6:32577619..32577667 -
Hg19::chr6:32577678..32577698,-	p@chr6:32577678..32577698 -
Hg19::chr6:32577917..32577935,+	p@chr6:32577917..32577935 +
Hg19::chr6:32997441..32997457,+	p@chr6:32997441..32997457 +
Hg19::chr6:32997459..32997492,+	p@chr6:32997459..32997492 +
Hg19::chr6:32997495..32997511,+	p@chr6:32997495..32997511 +
Hg19::chr6:33043568..33043579,-	p@chr6:33043568..33043579 -
Hg19::chr7:140017476..140017487,-	p@chr7:140017476..140017487 -
Hg19::chr7:39664276..39664287,-	p@chr7:39664276..39664287 -

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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No GOStat results

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	1.27e-98	136
nongranular leukocyte	6.14e-88	115
hematopoietic lineage restricted progenitor cell	1.38e-83	120
classical monocyte	4.22e-81	42
CD14-positive, CD16-negative classical monocyte	4.22e-81	42
hematopoietic stem cell	6.12e-78	168
angioblastic mesenchymal cell	6.12e-78	168
hematopoietic cell	9.84e-75	177
defensive cell	1.61e-72	48
phagocyte	1.61e-72	48
hematopoietic oligopotent progenitor cell	3.26e-69	161
hematopoietic multipotent progenitor cell	3.26e-69	161
macrophage dendritic cell progenitor	2.56e-62	61
monopoietic cell	2.75e-58	59
monocyte	2.75e-58	59
monoblast	2.75e-58	59
promonocyte	2.75e-58	59
granulocyte monocyte progenitor cell	4.94e-58	67
myeloid leukocyte	1.37e-55	72
myeloid lineage restricted progenitor cell	3.83e-53	66
myeloid cell	2.49e-41	108
common myeloid progenitor	2.49e-41	108
stuff accumulating cell	5.96e-34	87
mesenchymal cell	1.94e-26	354
connective tissue cell	1.69e-25	361
lymphoid lineage restricted progenitor cell	1.45e-24	52
lymphocyte	6.10e-24	53
common lymphoid progenitor	6.10e-24	53
nucleate cell	9.23e-23	55
motile cell	3.44e-22	386
lymphocyte of B lineage	1.34e-21	24
pro-B cell	1.34e-21	24
B cell	5.76e-21	14
intermediate monocyte	1.44e-18	9
CD14-positive, CD16-positive monocyte	1.44e-18	9
stem cell	2.18e-18	441
multi fate stem cell	3.74e-18	427
somatic stem cell	1.35e-17	433
dendritic cell	5.09e-11	10
Langerhans cell	1.28e-10	5
conventional dendritic cell	4.67e-08	8
somatic cell	1.28e-07	588
basophil	1.51e-07	3
single nucleate cell	4.83e-07	3
mononuclear cell	4.83e-07	3
plasmacytoid dendritic cell	8.41e-07	3

Uber Anatomy

Ontology term	p-value	n
bone marrow	5.62e-52	76
hematopoietic system	1.66e-50	98
blood island	1.66e-50	98
immune system	2.33e-47	93
bone element	3.82e-47	82
hemolymphoid system	3.46e-46	108
skeletal element	1.06e-41	90
skeletal system	4.00e-36	100
connective tissue	3.23e-24	371
lateral plate mesoderm	2.69e-17	203
musculoskeletal system	3.58e-16	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
BATF#10538	7	10.6565382841328	1.61542932578931e-06	6.13281800640166e-05
BCL11A#53335	4	7.09236377590176	0.00199672691950642	0.0116104984547815
BCL3#602	3	6.47758177570093	0.010232792362215	0.0380971981148357
EBF1#1879	8	4.4532334232845	0.000140661219814321	0.00183402211438051
FOS#2353	13	7.31083868847671	1.58896378173251e-10	1.67288093145526e-08
FOSL1#8061	4	9.92839492909325	0.000573209667101978	0.0048399583169588
GATA1#2623	6	5.08511555392516	0.000672844599471383	0.00542970306940131
IRF4#3662	4	5.47862817168603	0.00506854601053335	0.0235992098789217
JUN#3725	6	4.69231094712613	0.00103086262074521	0.00729270888356089
JUNB#3726	5	9.5658227061941	0.000119954005334138	0.00162615217589461
MEF2A#4205	4	4.68580772741101	0.00878309993045645	0.033363576548954
NFKB1#4790	12	4.11604756814538	1.1672690224261e-06	4.76204724348277e-05
NFYA#4800	6	6.90959276243645	0.000127235702184565	0.00169278592362469
NFYB#4801	5	5.23743539173014	0.00189213182041166	0.0111469063172368
PAX5#5079	7	2.9179349198903	0.00557036039046474	0.0252096402833881
POLR2A#5430	16	2.14745317655807	4.88536678567824e-06	0.000151087598972298
POU2F2#5452	12	6.82959304330689	3.64282080840165e-09	2.99568946778472e-07
RFX5#5993	13	9.78892754709602	3.88993456139909e-12	5.14254272984759e-10
SP1#6667	10	3.56148836133806	7.84823393273076e-05	0.00120290828250729
SPI1#6688	9	4.61493197354403	3.01826774164688e-05	0.000620765783122998
STAT1#6772	5	6.47080859287475	0.000731766871272107	0.00582774136562357
STAT3#6774	6	3.94479937393284	0.00254423646223763	0.0140874515894198
TAF1#6872	14	2.92516550002713	2.86208202997623e-06	9.84237685639406e-05
TAL1#6886	5	9.33394271170006	0.000134593465396596	0.00176460041834736
TBP#6908	14	3.24342435120934	7.26082897616864e-07	3.23374719591504e-05
TRIM28#10155	4	4.64763126131563	0.00903639042592616	0.0342584427070314
USF2#7392	5	4.06006168283425	0.00573237762379192	0.0258354026949987
YY1#7528	9	2.76253354679279	0.00168671074193619	0.0105408319277809

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.