Coexpression cluster:C2643

Full id: C2643_Eosinophils_acute_Neutrophils_CD14_Whole_Monocytederived_Macrophage

Phase1 CAGE Peaks

Hg19::chr22:37257002..37257013,+	p4@NCF4
Hg19::chr22:37257015..37257065,+	p1@NCF4
Hg19::chr22:37257072..37257091,+	p2@NCF4
Hg19::chr22:37257098..37257115,+	p3@NCF4

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	6.92e-75	172
angioblastic mesenchymal cell	6.92e-75	172
hematopoietic oligopotent progenitor cell	4.92e-72	165
hematopoietic multipotent progenitor cell	4.92e-72	165
hematopoietic cell	4.85e-70	182
leukocyte	2.23e-59	140
myeloid cell	9.71e-55	112
common myeloid progenitor	9.71e-55	112
hematopoietic lineage restricted progenitor cell	1.87e-50	124
nongranular leukocyte	2.87e-47	119
myeloid leukocyte	7.69e-40	76
granulocyte monocyte progenitor cell	1.19e-35	71
myeloid lineage restricted progenitor cell	1.96e-34	70
macrophage dendritic cell progenitor	2.52e-32	65
monopoietic cell	3.92e-31	63
monocyte	3.92e-31	63
monoblast	3.92e-31	63
promonocyte	3.92e-31	63
CD14-positive, CD16-negative classical monocyte	2.45e-27	42
classical monocyte	4.98e-24	45
lymphocyte	1.28e-14	53
common lymphoid progenitor	1.28e-14	53
lymphoid lineage restricted progenitor cell	2.27e-14	52
lymphocyte of B lineage	1.31e-10	24
pro-B cell	1.31e-10	24
mesenchymal cell	3.97e-09	358
connective tissue cell	4.20e-08	365
granulocyte	3.11e-07	8
B cell	5.67e-07	14

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.67e-42	102
blood island	3.67e-42	102
hemolymphoid system	2.92e-38	112
bone marrow	1.83e-30	80
adult organism	4.78e-27	115
bone element	4.65e-26	86
immune system	2.54e-22	115
skeletal element	1.07e-18	101
skeletal system	1.07e-18	101
blood	7.99e-10	15
haemolymphatic fluid	7.99e-10	15
organism substance	7.99e-10	15
lateral plate mesoderm	5.64e-08	216
connective tissue	2.99e-07	375

Disease

Ontology term	p-value	n
hematologic cancer	3.32e-13	51
immune system cancer	3.32e-13	51
myeloid leukemia	9.66e-13	31
leukemia	1.27e-12	39

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
BCL11A#53335	4	28.3694551036071	1.542446414682e-06	5.8964700257311e-05
BCL3#602	4	34.5471028037383	7.01262157705428e-07	3.15142506405324e-05
EBF1#1879	4	8.906466846569	0.0001588790747201	0.0019977331669507
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101529035126975
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161057591930551
IRF4#3662	4	21.9145126867441	4.33289161192893e-06	0.000136548843409247
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076844205944601
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444309742768933
REST#5978	4	9.65002871612802	0.000115282561421917	0.00157262218290799
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00684844682150208
SPI1#6688	4	8.20432350852273	0.00022066188152768	0.00249601497290906
SRF#6722	4	13.7971782621678	2.75840773062708e-05	0.000584944862901444
TCF12#6938	4	10.6344649021864	7.8163066689251e-05	0.00120136460955978
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106941453051368
ZEB1#6935	4	16.8884320175439	1.22862303393937e-05	0.000304499670245833

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.