Coexpression cluster:C4293

Full id: C4293_Neutrophils_Eosinophils_spinal_CD14_substantia_thalamus_medulla

Phase1 CAGE Peaks

Hg19::chr3:149530983..149531065,+	p1@RNF13
Hg19::chr6:71998492..71998501,+	p3@OGFRL1
Hg19::chr6:71998506..71998522,+	p1@OGFRL1

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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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><br>

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Cell Type

Ontology term	p-value	n
macrophage dendritic cell progenitor	5.84e-29	61
myeloid leukocyte	5.92e-29	72
monopoietic cell	7.38e-28	59
monocyte	7.38e-28	59
monoblast	7.38e-28	59
promonocyte	7.38e-28	59
granulocyte monocyte progenitor cell	2.57e-25	67
defensive cell	2.89e-24	48
phagocyte	2.89e-24	48
myeloid lineage restricted progenitor cell	5.86e-24	66
classical monocyte	3.06e-21	42
CD14-positive, CD16-negative classical monocyte	3.06e-21	42
stuff accumulating cell	1.55e-16	87
myeloid cell	6.41e-15	108
common myeloid progenitor	6.41e-15	108
leukocyte	8.13e-14	136
nongranular leukocyte	1.13e-10	115
hematopoietic lineage restricted progenitor cell	1.85e-09	120
hematopoietic stem cell	5.39e-07	168
angioblastic mesenchymal cell	5.39e-07	168

Uber Anatomy

Ontology term	p-value	n
adult organism	4.96e-29	114
hematopoietic system	1.45e-19	98
blood island	1.45e-19	98
hemolymphoid system	1.65e-19	108
bone marrow	1.53e-18	76
neural tube	4.60e-18	56
neural rod	4.60e-18	56
future spinal cord	4.60e-18	56
neural keel	4.60e-18	56
immune system	1.02e-16	93
bone element	1.40e-16	82
regional part of nervous system	1.85e-16	53
regional part of brain	1.85e-16	53
skeletal element	7.64e-15	90
regional part of forebrain	1.46e-14	41
forebrain	1.46e-14	41
anterior neural tube	1.46e-14	41
future forebrain	1.46e-14	41
skeletal system	2.72e-14	100
brain grey matter	2.14e-12	34
gray matter	2.14e-12	34
brain	2.37e-12	68
future brain	2.37e-12	68
telencephalon	2.89e-12	34
neural plate	4.75e-12	82
presumptive neural plate	4.75e-12	82
central nervous system	2.20e-11	81
regional part of telencephalon	2.98e-11	32
cerebral hemisphere	4.23e-11	32
nervous system	6.53e-10	89
neurectoderm	7.35e-10	86
structure with developmental contribution from neural crest	4.24e-09	132
pre-chordal neural plate	4.85e-09	61
ecto-epithelium	5.60e-09	104
regional part of cerebral cortex	1.05e-08	22
developing anatomical structure	1.46e-08	581
organ	2.83e-08	503
cerebral cortex	6.74e-08	25
pallium	6.74e-08	25
embryonic structure	7.62e-08	564
neocortex	1.30e-07	20
germ layer	1.60e-07	560
germ layer / neural crest	1.60e-07	560
embryonic tissue	1.60e-07	560
presumptive structure	1.60e-07	560
germ layer / neural crest derived structure	1.60e-07	560
epiblast (generic)	1.60e-07	560
embryo	2.09e-07	592

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326578774735877
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769655696200826
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.0061744238341056
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330391678325256

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.