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
myeloid leukocyte	6.29e-35	76
leukocyte	3.14e-34	140
granulocyte monocyte progenitor cell	2.35e-31	71
macrophage dendritic cell progenitor	4.98e-31	65
monopoietic cell	4.86e-30	63
monocyte	4.86e-30	63
monoblast	4.86e-30	63
promonocyte	4.86e-30	63
hematopoietic stem cell	1.35e-29	172
angioblastic mesenchymal cell	1.35e-29	172
myeloid lineage restricted progenitor cell	2.09e-29	70
CD14-positive, CD16-negative classical monocyte	7.82e-28	42
myeloid cell	3.63e-27	112
common myeloid progenitor	3.63e-27	112
hematopoietic lineage restricted progenitor cell	4.00e-27	124
nongranular leukocyte	6.15e-27	119
hematopoietic cell	7.34e-27	182
hematopoietic oligopotent progenitor cell	1.63e-26	165
hematopoietic multipotent progenitor cell	1.63e-26	165
classical monocyte	5.83e-24	45
intermediate monocyte	1.64e-07	9
CD14-positive, CD16-positive monocyte	1.64e-07	9

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	8.39e-35	102
blood island	8.39e-35	102
hemolymphoid system	7.06e-32	112
bone marrow	2.41e-28	80
bone element	8.15e-26	86
adult organism	1.32e-25	115
immune system	9.76e-25	115
skeletal element	2.57e-19	101
skeletal system	2.57e-19	101
lateral plate mesoderm	1.87e-14	216
neural tube	1.42e-08	57
neural rod	1.42e-08	57
future spinal cord	1.42e-08	57
neural keel	1.42e-08	57
musculoskeletal system	2.98e-07	167
tissue	5.78e-07	787
anterior neural tube	9.73e-07	42

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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