Coexpression cluster:C3606

Full id: C3606_CD14_Eosinophils_retina_Neutrophils_locus_pons_occipital

Phase1 CAGE Peaks

Hg19::chr17:1466030..1466129,-	p1@PITPNA
Hg19::chr9:135996537..135996544,-	p9@RALGDS
Hg19::chr9:135996616..135996640,-	p1@RALGDS

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
3.91018877356111e-05	0.0247514949366418	2	179	EGFR1 Signaling Pathway (Wikipathways):WP437

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:0008525	phosphatidylcholine transmembrane transporter activity	0.0041209802018991
GO:0008526	phosphatidylinositol transporter activity	0.00618110637118426
GO:0005548	phospholipid transporter activity	0.0219688562324111
GO:0005319	lipid transporter activity	0.049383343269881

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	1.59e-23	72
granulocyte monocyte progenitor cell	2.47e-20	67
defensive cell	3.75e-20	48
phagocyte	3.75e-20	48
macrophage dendritic cell progenitor	4.71e-19	61
myeloid lineage restricted progenitor cell	2.58e-18	66
monopoietic cell	5.77e-18	59
monocyte	5.77e-18	59
monoblast	5.77e-18	59
promonocyte	5.77e-18	59
classical monocyte	6.60e-18	42
CD14-positive, CD16-negative classical monocyte	6.60e-18	42
stuff accumulating cell	2.40e-13	87
myeloid cell	6.96e-13	108
common myeloid progenitor	6.96e-13	108
endothelial cell	1.39e-08	36
leukocyte	2.59e-07	136

Uber Anatomy

Ontology term	p-value	n
adult organism	6.61e-25	114
neural tube	8.21e-20	56
neural rod	8.21e-20	56
future spinal cord	8.21e-20	56
neural keel	8.21e-20	56
regional part of nervous system	1.40e-18	53
regional part of brain	1.40e-18	53
neural plate	4.12e-17	82
presumptive neural plate	4.12e-17	82
hemolymphoid system	3.39e-16	108
immune system	8.29e-16	93
bone marrow	6.64e-15	76
neurectoderm	1.24e-14	86
hematopoietic system	1.59e-14	98
blood island	1.59e-14	98
central nervous system	2.27e-14	81
brain	3.35e-14	68
future brain	3.35e-14	68
regional part of forebrain	3.53e-14	41
forebrain	3.53e-14	41
anterior neural tube	3.53e-14	41
future forebrain	3.53e-14	41
nervous system	4.19e-14	89
bone element	8.76e-14	82
telencephalon	1.59e-13	34
brain grey matter	2.09e-13	34
gray matter	2.09e-13	34
cerebral hemisphere	1.05e-12	32
regional part of telencephalon	1.94e-12	32
ecto-epithelium	6.21e-12	104
anatomical group	1.05e-11	625
lateral plate mesoderm	1.16e-11	203
anatomical system	1.47e-11	624
pre-chordal neural plate	1.67e-11	61
regional part of cerebral cortex	2.79e-11	22
skeletal element	5.81e-11	90
neocortex	1.90e-10	20
organ	1.96e-10	503
germ layer	3.11e-10	560
germ layer / neural crest	3.11e-10	560
embryonic tissue	3.11e-10	560
presumptive structure	3.11e-10	560
germ layer / neural crest derived structure	3.11e-10	560
epiblast (generic)	3.11e-10	560
embryonic structure	6.53e-10	564
embryo	7.20e-10	592
structure with developmental contribution from neural crest	8.39e-10	132
skeletal system	8.77e-10	100
developing anatomical structure	9.73e-10	581
cerebral cortex	1.23e-09	25
pallium	1.23e-09	25
anatomical conduit	1.58e-09	240
multi-cellular organism	4.29e-09	656
ectoderm-derived structure	5.09e-09	171
ectoderm	5.09e-09	171
presumptive ectoderm	5.09e-09	171
tube	4.44e-08	192
anatomical cluster	3.45e-07	373
posterior neural tube	6.16e-07	15
chordal neural plate	6.16e-07	15

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)
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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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189793621352404
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321607213991138
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320123103249197
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461568589950277
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127903031171901
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276255209518798
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457347634980286
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190033408317103

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.