Coexpression cluster:C4512

Full id: C4512_CD4_Neutrophils_CD14_plasma_CD8_Peripheral_Eosinophils

Phase1 CAGE Peaks

Hg19::chr5:64859206..64859218,+	p3@PPWD1
Hg19::chr5:64859227..64859241,+	p2@PPWD1
Hg19::chrX:11778228..11778347,+	p2@MSL3

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:0003755	peptidyl-prolyl cis-trans isomerase activity	0.0406216884493112
GO:0016859	cis-trans isomerase activity	0.0406216884493112
GO:0005681	spliceosome	0.0406216884493112
GO:0008380	RNA splicing	0.0406216884493112
GO:0006397	mRNA processing	0.0406216884493112
GO:0016853	isomerase activity	0.0406216884493112
GO:0016071	mRNA metabolic process	0.0406216884493112
GO:0006457	protein folding	0.0406216884493112

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	4.81e-47	136
hematopoietic stem cell	1.08e-46	168
angioblastic mesenchymal cell	1.08e-46	168
hematopoietic cell	2.73e-44	177
hematopoietic oligopotent progenitor cell	7.56e-43	161
hematopoietic multipotent progenitor cell	7.56e-43	161
nongranular leukocyte	1.96e-38	115
hematopoietic lineage restricted progenitor cell	1.71e-36	120
myeloid cell	8.76e-23	108
common myeloid progenitor	8.76e-23	108
myeloid leukocyte	1.01e-21	72
classical monocyte	1.08e-21	42
CD14-positive, CD16-negative classical monocyte	1.08e-21	42
granulocyte monocyte progenitor cell	6.79e-19	67
lymphocyte	8.52e-19	53
common lymphoid progenitor	8.52e-19	53
macrophage dendritic cell progenitor	1.48e-18	61
lymphoid lineage restricted progenitor cell	2.68e-18	52
nucleate cell	7.21e-18	55
defensive cell	1.31e-17	48
phagocyte	1.31e-17	48
monopoietic cell	1.32e-17	59
monocyte	1.32e-17	59
monoblast	1.32e-17	59
promonocyte	1.32e-17	59
myeloid lineage restricted progenitor cell	6.92e-17	66
mature alpha-beta T cell	2.53e-11	18
alpha-beta T cell	2.53e-11	18
immature T cell	2.53e-11	18
mature T cell	2.53e-11	18
immature alpha-beta T cell	2.53e-11	18
mesenchymal cell	1.28e-10	354
T cell	4.14e-10	25
pro-T cell	4.14e-10	25
motile cell	1.04e-09	386
connective tissue cell	2.79e-09	361
B cell	3.91e-08	14
lymphocyte of B lineage	5.76e-08	24
pro-B cell	5.76e-08	24
CD8-positive, alpha-beta T cell	1.04e-07	11

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.13e-24	108
hematopoietic system	3.93e-23	98
blood island	3.93e-23	98
immune system	4.08e-19	93
bone marrow	3.34e-15	76
bone element	1.61e-14	82
skeletal element	3.36e-12	90
skeletal system	8.16e-10	100
connective tissue	3.34e-09	371
lateral plate mesoderm	6.45e-07	203
blood	8.22e-07	15
haemolymphatic fluid	8.22e-07	15
organism substance	8.22e-07	15

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	2	14.9754496840058	0.00576829454079388	0.0259692608649871
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296426389499763
IRF3#3661	2	31.3213014743264	0.00133951467332011	0.00887900310782429
MAFK#7975	2	18.0671554252199	0.00398367474493681	0.0191173554512914
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324908203037033
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381514541600028
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.046074045639538
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370886165833825

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.