Coexpression cluster:C407

Full id: C407_Neutrophils_CD14_Eosinophils_Peripheral_CD19_CD4_Natural

Phase1 CAGE Peaks

Hg19::chr10:14641848..14641853,-	p@chr10:14641848..14641853 -
Hg19::chr10:65028665..65028674,-	p17@JMJD1C
Hg19::chr10:70848483..70848488,+	p@chr10:70848483..70848488 +
Hg19::chr11:78029412..78029415,-	p@chr11:78029412..78029415 -
Hg19::chr11:78127822..78127826,-	p@chr11:78127822..78127826 -
Hg19::chr12:10279509..10279514,-	p4@CLEC7A
Hg19::chr12:65057642..65057645,+	p@chr12:65057642..65057645 +
Hg19::chr12:90064720..90064735,-	p@chr12:90064720..90064735 -
Hg19::chr14:100842126..100842137,+	p@chr14:100842126..100842137 +
Hg19::chr14:70149688..70149690,+	p@chr14:70149688..70149690 +
Hg19::chr15:51047821..51047824,-	p@chr15:51047821..51047824 -
Hg19::chr17:49187745..49187750,-	p@chr17:49187745..49187750 -
Hg19::chr19:10389255..10389259,+	p@chr19:10389255..10389259 +
Hg19::chr20:48315901..48315905,-	p@chr20:48315901..48315905 -
Hg19::chr20:5590491..5590495,-	p@chr20:5590491..5590495 -
Hg19::chr20:5590556..5590620,-	p@chr20:5590556..5590620 -
Hg19::chr2:114691822..114691837,+	p3@ACTR3
Hg19::chr2:114692625..114692632,+	p@chr2:114692625..114692632 +
Hg19::chr2:131867907..131867911,+	p@chr2:131867907..131867911 +
Hg19::chr2:145263063..145263073,-	p@chr2:145263063..145263073 -
Hg19::chr2:201984578..201984581,+	p@chr2:201984578..201984581 +
Hg19::chr2:37876585..37876589,-	p@chr2:37876585..37876589 -
Hg19::chr2:64367919..64367920,-	p@chr2:64367919..64367920 -
Hg19::chr4:103423374..103423399,+	p@chr4:103423374..103423399 +
Hg19::chr5:90679281..90679304,+	p@chr5:90679281..90679304 +

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:0009756	carbohydrate mediated signaling	0.0133550151197745
GO:0006910	phagocytosis, recognition	0.0133550151197745
GO:0042832	defense response to protozoan	0.0133550151197745
GO:0001562	response to protozoan	0.0133550151197745
GO:0005885	Arp2/3 protein complex	0.0149567362972983
GO:0008329	pattern recognition receptor activity	0.0213636212234457
GO:0009743	response to carbohydrate stimulus	0.0274626613699662
GO:0042287	MHC protein binding	0.0296603415103792
GO:0046966	thyroid hormone receptor binding	0.0296603415103792
GO:0005102	receptor binding	0.033105752264889
GO:0008037	cell recognition	0.0336600330303587
GO:0030027	lamellipodium	0.0336600330303587
GO:0006909	phagocytosis	0.0336600330303587
GO:0035257	nuclear hormone receptor binding	0.040537128657825
GO:0051427	hormone receptor binding	0.040537128657825
GO:0010033	response to organic substance	0.0413311162716758
GO:0031252	leading edge	0.0426417620285896
GO:0051213	dioxygenase activity	0.0426417620285896
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	0.0426417620285896
GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	0.0426417620285896
GO:0042110	T cell activation	0.0497223462987851

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	4.76e-57	136
nongranular leukocyte	2.27e-46	115
hematopoietic lineage restricted progenitor cell	2.94e-46	120
hematopoietic stem cell	2.00e-45	168
angioblastic mesenchymal cell	2.00e-45	168
hematopoietic oligopotent progenitor cell	3.63e-44	161
hematopoietic multipotent progenitor cell	3.63e-44	161
myeloid leukocyte	9.19e-44	72
hematopoietic cell	1.16e-43	177
granulocyte monocyte progenitor cell	5.19e-37	67
classical monocyte	5.14e-36	42
CD14-positive, CD16-negative classical monocyte	5.14e-36	42
macrophage dendritic cell progenitor	3.07e-35	61
myeloid lineage restricted progenitor cell	1.09e-34	66
defensive cell	2.60e-34	48
phagocyte	2.60e-34	48
monopoietic cell	7.26e-34	59
monocyte	7.26e-34	59
monoblast	7.26e-34	59
promonocyte	7.26e-34	59
myeloid cell	4.52e-31	108
common myeloid progenitor	4.52e-31	108
stuff accumulating cell	7.15e-13	87
lymphocyte	1.27e-11	53
common lymphoid progenitor	1.27e-11	53
lymphoid lineage restricted progenitor cell	2.67e-11	52
nucleate cell	1.01e-10	55
intermediate monocyte	1.27e-08	9
CD14-positive, CD16-positive monocyte	1.27e-08	9
granulocyte	1.87e-08	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.06e-43	98
blood island	4.06e-43	98
hemolymphoid system	4.53e-38	108
bone marrow	8.01e-32	76
immune system	2.40e-29	93
bone element	2.28e-28	82
skeletal element	1.73e-23	90
skeletal system	6.21e-20	100
lateral plate mesoderm	6.17e-12	203
blood	9.45e-10	15
haemolymphatic fluid	9.45e-10	15
organism substance	9.45e-10	15
adult organism	9.44e-09	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
WRNIP1#56897	3	13.1783957219251	0.00149235823237661	0.0095432525980395

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.