Coexpression cluster:C1488

Full id: C1488_CD4_CD19_CD14CD16_CD8_Neutrophils_Basophils_Natural

Phase1 CAGE Peaks

Hg19::chr21:43482969..43482994,+	p2@UMODL1
Hg19::chr4:83295323..83295348,+	p@chr4:83295323..83295348 +
Hg19::chr5:1386528..1386539,-	p2@AK127466
Hg19::chr7:144533055..144533069,-	p2@TPK1
Hg19::chr8:132916684..132916697,-	p@chr8:132916684..132916697 -
Hg19::chr9:115095363..115095398,+	p@chr9:115095363..115095398 +

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:0042357	thiamin diphosphate metabolic process	0.00144820886924134
GO:0004788	thiamin diphosphokinase activity	0.00144820886924134
GO:0009229	thiamin diphosphate biosynthetic process	0.00144820886924134
GO:0042724	thiamin and derivative biosynthetic process	0.00144820886924134
GO:0006772	thiamin metabolic process	0.00144820886924134
GO:0042723	thiamin and derivative metabolic process	0.00201134199617551
GO:0016778	diphosphotransferase activity	0.00482658131089662
GO:0006767	water-soluble vitamin metabolic process	0.0192921145785954
GO:0006766	vitamin metabolic process	0.0230358905860548
GO:0009108	coenzyme biosynthetic process	0.0469337764260271
GO:0051188	cofactor biosynthetic process	0.0481194432595581

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	6.91e-57	136
hematopoietic stem cell	1.65e-48	168
angioblastic mesenchymal cell	1.65e-48	168
hematopoietic lineage restricted progenitor cell	7.52e-47	120
nongranular leukocyte	1.26e-46	115
hematopoietic cell	2.45e-45	177
hematopoietic oligopotent progenitor cell	2.60e-44	161
hematopoietic multipotent progenitor cell	2.60e-44	161
myeloid leukocyte	4.26e-28	72
granulocyte monocyte progenitor cell	1.57e-24	67
macrophage dendritic cell progenitor	1.17e-22	61
lymphoid lineage restricted progenitor cell	1.54e-22	52
classical monocyte	2.44e-22	42
CD14-positive, CD16-negative classical monocyte	2.44e-22	42
myeloid lineage restricted progenitor cell	2.49e-22	66
lymphocyte	5.03e-22	53
common lymphoid progenitor	5.03e-22	53
monopoietic cell	8.84e-22	59
monocyte	8.84e-22	59
monoblast	8.84e-22	59
promonocyte	8.84e-22	59
myeloid cell	1.50e-21	108
common myeloid progenitor	1.50e-21	108
nucleate cell	4.68e-21	55
defensive cell	1.63e-20	48
phagocyte	1.63e-20	48
mature alpha-beta T cell	4.64e-12	18
alpha-beta T cell	4.64e-12	18
immature T cell	4.64e-12	18
mature T cell	4.64e-12	18
immature alpha-beta T cell	4.64e-12	18
T cell	9.31e-12	25
pro-T cell	9.31e-12	25
lymphocyte of B lineage	3.71e-10	24
pro-B cell	3.71e-10	24
CD8-positive, alpha-beta T cell	1.23e-08	11
B cell	4.63e-08	14
intermediate monocyte	3.09e-07	9
CD14-positive, CD16-positive monocyte	3.09e-07	9
mesenchymal cell	3.36e-07	354

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	5.07e-30	108
hematopoietic system	7.31e-30	98
blood island	7.31e-30	98
immune system	8.91e-25	93
bone marrow	2.71e-23	76
bone element	4.11e-20	82
skeletal element	1.53e-15	90
skeletal system	4.70e-12	100
lateral plate mesoderm	7.25e-10	203
adult organism	1.45e-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
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205330768269639
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380513657505277
SRF#6722	3	6.8985891310839	0.0064424516893037	0.0280036297489986
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573475660696918

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.