Coexpression cluster:C303

Full id: C303_CD14_Basophils_Peripheral_Eosinophils_CD14CD16_Neutrophils_Whole

Phase1 CAGE Peaks

Hg19::chr10:135073029..135073042,+	p@chr10:135073029..135073042 +
Hg19::chr11:64163297..64163310,-	p1@ENST00000457725
Hg19::chr11:65220998..65221001,+	p@chr11:65220998..65221001 +
Hg19::chr11:66888450..66888468,-	p@chr11:66888450..66888468 -
Hg19::chr12:69747591..69747611,-	p1@ENST00000548626
Hg19::chr13:99922932..99922946,-	p@chr13:99922932..99922946 -
Hg19::chr13:99930136..99930140,+	p1@AF339795
Hg19::chr13:99932682..99932704,+	p@chr13:99932682..99932704 +
Hg19::chr13:99932706..99932716,+	p@chr13:99932706..99932716 +
Hg19::chr13:99934075..99934096,-	p@chr13:99934075..99934096 -
Hg19::chr14:75754624..75754635,+	p@chr14:75754624..75754635 +
Hg19::chr17:7024749..7024764,-	p@chr17:7024749..7024764 -
Hg19::chr17:7077590..7077615,-	p@chr17:7077590..7077615 -
Hg19::chr17:7077620..7077625,-	p@chr17:7077620..7077625 -
Hg19::chr17:72524949..72524975,+	p@chr17:72524949..72524975 +
Hg19::chr17:72774120..72774160,-	p@chr17:72774120..72774160 -
Hg19::chr17:72776484..72776500,+	p@chr17:72776484..72776500 +
Hg19::chr17:72776516..72776526,+	p@chr17:72776516..72776526 +
Hg19::chr17:81060279..81060283,-	p@chr17:81060279..81060283 -
Hg19::chr17:81101323..81101338,+	p@chr17:81101323..81101338 +
Hg19::chr17:81103271..81103285,-	p@chr17:81103271..81103285 -
Hg19::chr17:81103526..81103542,+	p@chr17:81103526..81103542 +
Hg19::chr17:81147900..81147911,+	p@chr17:81147900..81147911 +
Hg19::chr1:10057123..10057149,+	p3@RBP7
Hg19::chr22:37976067..37976079,-	p3@LGALS2
Hg19::chr2:230162106..230162117,-	p@chr2:230162106..230162117 -
Hg19::chr2:230162122..230162143,-	p@chr2:230162122..230162143 -
Hg19::chr5:139631154..139631161,-	p@chr5:139631154..139631161 -
Hg19::chr5:139725653..139725678,-	p@chr5:139725653..139725678 -
Hg19::chr6:11537600..11537651,-	p@chr6:11537600..11537651 -
Hg19::chr6:163826254..163826261,+	p@chr6:163826254..163826261 +
Hg19::chr6:163827012..163827025,-	p@chr6:163827012..163827025 -
Hg19::chr7:2774708..2774727,-	p@chr7:2774708..2774727 -
Hg19::chr7:2797828..2797848,-	p@chr7:2797828..2797848 -
Hg19::chr8:48273366..48273391,+	p3@KIAA0146
Hg19::chr8:48273416..48273419,+	p15@KIAA0146
Hg19::chr8:48282088..48282092,-	p@chr8:48282088..48282092 -
Hg19::chr8:48513543..48513562,+	p@chr8:48513543..48513562 +
Hg19::chr8:48540690..48540694,+	p@chr8:48540690..48540694 +
Hg19::chr9:27701766..27701787,-	p@chr9:27701766..27701787 -

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:0019841	retinol binding	0.00425250120614753
GO:0016918	retinal binding	0.00425250120614753
GO:0005501	retinoid binding	0.00425250120614753
GO:0019840	isoprenoid binding	0.00425250120614753
GO:0005625	soluble fraction	0.0407202229474492
GO:0019842	vitamin binding	0.0407202229474492
GO:0005529	sugar binding	0.0493596312651508

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
classical monocyte	3.31e-141	42
CD14-positive, CD16-negative classical monocyte	3.31e-141	42
defensive cell	1.50e-122	48
phagocyte	1.50e-122	48
monopoietic cell	2.00e-96	59
monocyte	2.00e-96	59
monoblast	2.00e-96	59
promonocyte	2.00e-96	59
macrophage dendritic cell progenitor	4.71e-93	61
myeloid leukocyte	5.84e-92	72
myeloid lineage restricted progenitor cell	1.67e-85	66
granulocyte monocyte progenitor cell	3.97e-84	67
stuff accumulating cell	5.64e-64	87
nongranular leukocyte	1.27e-60	115
myeloid cell	8.24e-59	108
common myeloid progenitor	8.24e-59	108
leukocyte	1.43e-58	136
hematopoietic lineage restricted progenitor cell	7.45e-49	120
hematopoietic stem cell	7.82e-46	168
angioblastic mesenchymal cell	7.82e-46	168
hematopoietic cell	4.49e-43	177
hematopoietic oligopotent progenitor cell	5.64e-41	161
hematopoietic multipotent progenitor cell	5.64e-41	161
intermediate monocyte	1.14e-39	9
CD14-positive, CD16-positive monocyte	1.14e-39	9
mesenchymal cell	3.70e-17	354
connective tissue cell	1.19e-16	361
motile cell	7.27e-15	386
basophil	3.45e-14	3
single nucleate cell	3.77e-14	3
mononuclear cell	3.77e-14	3
non-classical monocyte	9.89e-14	3
CD14-low, CD16-positive monocyte	9.89e-14	3
multi fate stem cell	1.12e-12	427
somatic stem cell	2.24e-12	433
stem cell	5.52e-12	441
circulating cell	2.77e-07	6

Uber Anatomy

Ontology term	p-value	n
bone marrow	2.42e-73	76
bone element	1.88e-67	82
hematopoietic system	1.38e-65	98
blood island	1.38e-65	98
skeletal element	8.37e-61	90
hemolymphoid system	8.52e-59	108
immune system	1.33e-58	93
skeletal system	5.67e-54	100
musculoskeletal system	3.68e-29	167
lateral plate mesoderm	1.93e-27	203
connective tissue	5.84e-16	371
mesoderm	1.16e-15	315
mesoderm-derived structure	1.16e-15	315
presumptive mesoderm	1.16e-15	315

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
BATF#10538	6	3.65367026884555	0.0055224974640936	0.0250027792895991
IRF4#3662	7	3.83503972018022	0.00203047490418992	0.0117949145402242

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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