Coexpression cluster:C1047

Full id: C1047_Whole_blood_CD14_Neutrophils_Eosinophils_Reticulocytes_Mast

Phase1 CAGE Peaks

Hg19::chr17:21188012..21188031,+	p1@MAP2K3
Hg19::chr17:21188043..21188069,+	p2@MAP2K3
Hg19::chr17:21188075..21188079,+	p4@MAP2K3
Hg19::chr4:2801321..2801334,+	p@chr4:2801321..2801334 +
Hg19::chr6:108882109..108882173,+	p2@FOXO3
Hg19::chr6:108882364..108882391,+	p4@FOXO3
Hg19::chr7:35469..35507,-	p1@ENST00000469418
Hg19::chrX:67718803..67718831,-	p@chrX:67718803..67718831 -

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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p.value	FDR	nGenes	nPathway	Name
2.92938943019595e-05	0.0101306962986864	2	155	TGF-beta Receptor Signaling Pathway (Wikipathways):WP366
3.20085191111734e-05	0.0101306962986864	2	162	Insulin Signaling (Wikipathways):WP481

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:0045893	positive regulation of transcription, DNA-dependent	0.002668471739994
GO:0045941	positive regulation of transcription	0.002668471739994
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.002668471739994
GO:0031325	positive regulation of cellular metabolic process	0.00293335680241988
GO:0009893	positive regulation of metabolic process	0.00293335680241988
GO:0045648	positive regulation of erythrocyte differentiation	0.00544534052623127
GO:0045646	regulation of erythrocyte differentiation	0.0079495422567252
GO:0004708	MAP kinase kinase activity	0.0079495422567252
GO:0004712	protein serine/threonine/tyrosine kinase activity	0.0079495422567252
GO:0045639	positive regulation of myeloid cell differentiation	0.0079495422567252
GO:0048522	positive regulation of cellular process	0.0079495422567252
GO:0048518	positive regulation of biological process	0.00903133988169789
GO:0030218	erythrocyte differentiation	0.0158625041483939
GO:0045637	regulation of myeloid cell differentiation	0.0158625041483939
GO:0045597	positive regulation of cell differentiation	0.0204618228353415
GO:0051094	positive regulation of developmental process	0.027745483969377
GO:0030099	myeloid cell differentiation	0.0295656607028872
GO:0019901	protein kinase binding	0.0300962908074367
GO:0019900	kinase binding	0.0340005992307244
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0393274420359954
GO:0045860	positive regulation of protein kinase activity	0.0393274420359954
GO:0045595	regulation of cell differentiation	0.0393274420359954
GO:0033674	positive regulation of kinase activity	0.0393274420359954
GO:0051347	positive regulation of transferase activity	0.0393274420359954
GO:0030097	hemopoiesis	0.0393274420359954
GO:0006355	regulation of transcription, DNA-dependent	0.0393274420359954
GO:0048534	hemopoietic or lymphoid organ development	0.0393274420359954
GO:0006351	transcription, DNA-dependent	0.0393274420359954
GO:0032774	RNA biosynthetic process	0.0393274420359954
GO:0002520	immune system development	0.0395387988639219
GO:0045449	regulation of transcription	0.0396816272126048
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0396816272126048
GO:0006350	transcription	0.0396816272126048
GO:0010468	regulation of gene expression	0.0396816272126048
GO:0031323	regulation of cellular metabolic process	0.0396816272126048
GO:0050793	regulation of developmental process	0.0396816272126048
GO:0045859	regulation of protein kinase activity	0.0396816272126048
GO:0043549	regulation of kinase activity	0.0396816272126048
GO:0051338	regulation of transferase activity	0.0396816272126048
GO:0019222	regulation of metabolic process	0.0396816272126048
GO:0016070	RNA metabolic process	0.0396816272126048
GO:0043085	positive regulation of catalytic activity	0.0396816272126048
GO:0019899	enzyme binding	0.0446688293427135
GO:0004713	protein-tyrosine kinase activity	0.0446688293427135
GO:0016563	transcription activator activity	0.0446688293427135

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
defensive cell	2.81e-27	48
phagocyte	2.81e-27	48
classical monocyte	2.06e-26	42
CD14-positive, CD16-negative classical monocyte	2.06e-26	42
myeloid leukocyte	3.39e-25	72
myeloid lineage restricted progenitor cell	1.81e-21	66
granulocyte monocyte progenitor cell	3.37e-21	67
macrophage dendritic cell progenitor	7.95e-20	61
monopoietic cell	7.74e-19	59
monocyte	7.74e-19	59
monoblast	7.74e-19	59
promonocyte	7.74e-19	59
stuff accumulating cell	7.21e-18	87
myeloid cell	1.40e-08	108
common myeloid progenitor	1.40e-08	108

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.45e-21	98
blood island	2.45e-21	98
hemolymphoid system	7.53e-20	108
bone marrow	1.67e-19	76
bone element	1.74e-17	82
lateral plate mesoderm	2.78e-17	203
musculoskeletal system	6.35e-16	167
skeletal system	7.40e-16	100
immune system	1.60e-15	93
multi-cellular organism	3.65e-15	656
skeletal element	6.39e-15	90
mesoderm	3.66e-14	315
mesoderm-derived structure	3.66e-14	315
presumptive mesoderm	3.66e-14	315
anatomical system	4.78e-14	624
anatomical group	5.77e-14	625
germ layer	4.83e-10	560
germ layer / neural crest	4.83e-10	560
embryonic tissue	4.83e-10	560
presumptive structure	4.83e-10	560
germ layer / neural crest derived structure	4.83e-10	560
epiblast (generic)	4.83e-10	560
embryonic structure	1.03e-09	564
developing anatomical structure	1.19e-09	581
embryo	1.69e-09	592
adult organism	5.63e-07	114

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
CHD2#1106	5	6.46501427132304	0.000367624325807319	0.00366078537023175
FOSL2#2355	3	6.34882522671063	0.00921194665864107	0.0348266605278485
HEY1#23462	6	3.03008328232928	0.00400172346648327	0.0191854570839169
MAFK#7975	3	10.1627749266862	0.00244557310713952	0.0137681639661767
NFYA#4800	3	6.90959276243645	0.00727972723713068	0.030122323015796
NFYB#4801	3	6.28492247007617	0.00947376901248262	0.0356963331371193
PBX3#5090	3	8.21794225752905	0.00447320658280844	0.0211670165512179
REST#5978	4	4.82501435806401	0.00572073539826954	0.0257873833251272
SIN3A#25942	5	3.38055295425946	0.00734222696117028	0.0303652968596865
SP2#6668	3	9.80757393519174	0.00270718466508561	0.0148863085998461
TAF1#6872	6	2.50728471430897	0.0111173447561386	0.0408832524290973
TBP#6908	6	2.78007801532229	0.00639018112126301	0.0278030380821358

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.