Coexpression cluster:C590

Full id: C590_CD4_CD14CD16_CD14_CD19_Neutrophils_Whole_blood

Phase1 CAGE Peaks

Hg19::chr11:64511549..64511566,-	p5@RASGRP2
Hg19::chr12:51717831..51717874,-	p3@BIN2
Hg19::chr14:100531713..100531724,+	p11@EVL
Hg19::chr15:75074868..75074911,+	p2@CSK
Hg19::chr15:75074915..75074938,+	p5@CSK
Hg19::chr16:30194916..30194955,+	p1@CORO1A
Hg19::chr16:30198468..30198483,+	p3@CORO1A
Hg19::chr17:61775799..61775815,-	p@chr17:61775799..61775815 -
Hg19::chr17:61776662..61776738,-	p2@LIMD2
Hg19::chr17:62097927..62098000,-	p1@ICAM2
Hg19::chr19:3178814..3178835,+	p2@S1PR4
Hg19::chr19:49838937..49838974,+	p@chr19:49838937..49838974 +
Hg19::chr1:167599532..167599568,+	p3@RCSD1
Hg19::chr4:83196097..83196106,+	p1@ENST00000504996
Hg19::chr7:77428066..77428132,+	p2@PHTF2

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
3.01170464246961e-06	0.00190640903868326	3	85	Integrin cell surface interactions (Reactome):REACT_13552
1.95641411763581e-05	0.00619205068231735	4	511	Signaling in Immune system (Reactome):REACT_6900

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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No GOStat results

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	6.59e-97	168
angioblastic mesenchymal cell	6.59e-97	168
hematopoietic cell	5.05e-93	177
hematopoietic oligopotent progenitor cell	6.12e-91	161
hematopoietic multipotent progenitor cell	6.12e-91	161
leukocyte	3.56e-89	136
nongranular leukocyte	8.76e-80	115
hematopoietic lineage restricted progenitor cell	2.52e-75	120
myeloid cell	8.38e-47	108
common myeloid progenitor	8.38e-47	108
myeloid leukocyte	4.77e-42	72
nucleate cell	8.34e-40	55
lymphocyte	2.13e-39	53
common lymphoid progenitor	2.13e-39	53
lymphoid lineage restricted progenitor cell	1.10e-38	52
myeloid lineage restricted progenitor cell	7.11e-36	66
monopoietic cell	8.65e-35	59
monocyte	8.65e-35	59
monoblast	8.65e-35	59
promonocyte	8.65e-35	59
granulocyte monocyte progenitor cell	3.01e-34	67
macrophage dendritic cell progenitor	6.07e-33	61
defensive cell	2.45e-32	48
phagocyte	2.45e-32	48
classical monocyte	1.03e-29	42
CD14-positive, CD16-negative classical monocyte	1.03e-29	42
lymphocyte of B lineage	1.22e-19	24
pro-B cell	1.22e-19	24
mesenchymal cell	1.32e-18	354
T cell	1.00e-17	25
pro-T cell	1.00e-17	25
connective tissue cell	2.25e-17	361
mature alpha-beta T cell	5.49e-16	18
alpha-beta T cell	5.49e-16	18
immature T cell	5.49e-16	18
mature T cell	5.49e-16	18
immature alpha-beta T cell	5.49e-16	18
B cell	9.23e-14	14
motile cell	3.64e-13	386
CD8-positive, alpha-beta T cell	1.04e-10	11
stuff accumulating cell	2.79e-10	87
intermediate monocyte	1.44e-09	9
CD14-positive, CD16-positive monocyte	1.44e-09	9
multi fate stem cell	5.63e-09	427
stem cell	1.44e-08	441
somatic stem cell	2.43e-08	433
granulocyte	5.56e-08	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.73e-46	98
blood island	7.73e-46	98
hemolymphoid system	1.77e-41	108
immune system	2.76e-30	93
bone marrow	7.69e-30	76
bone element	5.49e-26	82
skeletal element	1.04e-21	90
skeletal system	4.71e-18	100
connective tissue	3.69e-16	371
blood	8.05e-13	15
haemolymphatic fluid	8.05e-13	15
organism substance	8.05e-13	15
lateral plate mesoderm	2.72e-10	203

Disease

Ontology term	p-value	n
hematologic cancer	6.16e-14	51
immune system cancer	6.16e-14	51
leukemia	9.12e-11	39
myeloid leukemia	2.60e-07	31

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
EBF1#1879	8	4.75011565150347	7.80369455890836e-05	0.00120243442909093
ELF1#1997	8	2.27098557803069	0.0117859823692146	0.0429414342458889
NFKB1#4790	9	3.2928380545163	0.000380404893577693	0.00376579210240385
POLR2A#5430	14	2.0042896314542	0.000191108900166577	0.00230662457234453
SPI1#6688	7	3.82868430397727	0.00104961345272773	0.00741882643404382
ZEB1#6935	4	4.50358187134503	0.00989309630417724	0.0371183030935468

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.