Coexpression cluster:C498

Full id: C498_Eosinophils_Neutrophils_CD19_Burkitt_diffuse_lymphoma_CD14

Phase1 CAGE Peaks

Hg19::chr12:40618919..40618928,+	p9@LRRK2
Hg19::chr13:46960645..46960658,-	p@chr13:46960645..46960658 -
Hg19::chr13:46961337..46961359,-	p2@KIAA0226L
Hg19::chr13:46961366..46961394,-	p1@KIAA0226L
Hg19::chr13:46961530..46961558,-	p6@KIAA0226L
Hg19::chr13:46961580..46961620,-	p4@KIAA0226L
Hg19::chr13:46961859..46961883,-	p5@KIAA0226L
Hg19::chr14:69152139..69152172,-	p1@ENST00000556919
Hg19::chr14:69152180..69152191,-	p3@ENST00000556919
Hg19::chr16:27325202..27325307,+	p1@IL4R
Hg19::chr16:81772633..81772676,+	p1@uc002fgs.2
Hg19::chr16:81812884..81812907,+	p1@PLCG2
Hg19::chr16:81812917..81812933,+	p2@PLCG2
Hg19::chr1:226862756..226862831,-	p1@ITPKB-IT1
Hg19::chr1:244212954..244212968,-	p@chr1:244212954..244212968 -
Hg19::chr2:69001969..69001981,+	p8@ARHGAP25
Hg19::chr3:151923200..151923235,-	p@chr3:151923200..151923235 -
Hg19::chr5:56111170..56111185,+	p9@MAP3K1
Hg19::chr5:56111207..56111219,+	p3@MAP3K1

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:0005057	receptor signaling protein activity	0.00883028193442909
GO:0004913	interleukin-4 receptor activity	0.00883028193442909
GO:0019979	interleukin-4 binding	0.00883028193442909
GO:0005096	GTPase activator activity	0.0230670501762326
GO:0008047	enzyme activator activity	0.0313681190628453
GO:0007165	signal transduction	0.0340275895393832
GO:0004709	MAP kinase kinase kinase activity	0.0340275895393832
GO:0007154	cell communication	0.0350460138096726
GO:0004674	protein serine/threonine kinase activity	0.0366141190724578
GO:0030695	GTPase regulator activity	0.0366141190724578
GO:0004907	interleukin receptor activity	0.0408633383501864
GO:0019965	interleukin binding	0.0424669262345909
GO:0004435	phosphoinositide phospholipase C activity	0.0424669262345909
GO:0004434	inositol or phosphatidylinositol phosphodiesterase activity	0.0424669262345909
GO:0004629	phospholipase C activity	0.0483525701900892
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0483525701900892
GO:0004672	protein kinase activity	0.0483525701900892
GO:0060089	molecular transducer activity	0.0483525701900892
GO:0004871	signal transducer activity	0.0483525701900892
GO:0006468	protein amino acid phosphorylation	0.0483525701900892
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.0483525701900892

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	5.54e-67	136
nongranular leukocyte	2.62e-58	115
hematopoietic lineage restricted progenitor cell	5.29e-52	120
hematopoietic stem cell	6.60e-52	168
angioblastic mesenchymal cell	6.60e-52	168
myeloid leukocyte	2.03e-48	72
hematopoietic cell	1.42e-47	177
hematopoietic oligopotent progenitor cell	1.47e-46	161
hematopoietic multipotent progenitor cell	1.47e-46	161
classical monocyte	3.36e-45	42
CD14-positive, CD16-negative classical monocyte	3.36e-45	42
defensive cell	2.49e-43	48
phagocyte	2.49e-43	48
monopoietic cell	5.94e-40	59
monocyte	5.94e-40	59
monoblast	5.94e-40	59
promonocyte	5.94e-40	59
macrophage dendritic cell progenitor	6.93e-40	61
granulocyte monocyte progenitor cell	7.89e-38	67
myeloid lineage restricted progenitor cell	5.87e-37	66
myeloid cell	6.76e-29	108
common myeloid progenitor	6.76e-29	108
lymphocyte of B lineage	1.34e-20	24
pro-B cell	1.34e-20	24
B cell	2.85e-18	14
stuff accumulating cell	7.63e-17	87
lymphocyte	1.25e-15	53
common lymphoid progenitor	1.25e-15	53
lymphoid lineage restricted progenitor cell	8.20e-15	52
nucleate cell	1.10e-14	55
granulocyte	1.33e-11	8
intermediate monocyte	4.83e-11	9
CD14-positive, CD16-positive monocyte	4.83e-11	9
mesenchymal cell	5.11e-09	354
connective tissue cell	2.26e-08	361
blood cell	8.16e-08	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.61e-47	98
blood island	6.61e-47	98
hemolymphoid system	1.83e-43	108
bone marrow	1.20e-32	76
immune system	1.49e-32	93
bone element	6.24e-29	82
skeletal element	8.87e-25	90
skeletal system	1.62e-21	100
adult organism	2.25e-17	114
lateral plate mesoderm	1.19e-14	203
blood	3.72e-12	15
haemolymphatic fluid	3.72e-12	15
organism substance	3.72e-12	15
connective tissue	7.51e-08	371
musculoskeletal system	3.48e-07	167

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	5.97251686391728	0.00390839570699839	0.0190502141803894
E2F1#1869	10	2.58283642888386	0.00183346537983127	0.0108527142827136
EGR1#1958	12	3.15042890198535	5.09805837530452e-05	0.000868432749402102
PAX5#5079	10	3.51029764798833	0.000142832248088682	0.00185977523477545
POLR2A#5430	18	2.03442932516028	1.12471092130166e-05	0.00028768964954647
TCF12#6938	6	3.35825207437466	0.00637219882280837	0.0277444479449403
ZEB1#6935	6	5.33318905817174	0.00059641743437254	0.00499152499626842

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.