Coexpression cluster:C3287

Full id: C3287_Wilms_brain_duodenum_occipital_temporal_cerebellum_parietal

Phase1 CAGE Peaks

Hg19::chr12:50451133..50451188,+	p2@ACCN2
Hg19::chr12:50451363..50451429,+	p1@ACCN2
Hg19::chr19:36359341..36359352,+	p6@APLP1

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:0009268	response to pH	0.0202716415057658
GO:0006378	mRNA polyadenylation	0.0202716415057658
GO:0015280	amiloride-sensitive sodium channel activity	0.0202716415057658
GO:0043631	RNA polyadenylation	0.0202716415057658
GO:0031124	mRNA 3'-end processing	0.0202716415057658
GO:0031123	RNA 3'-end processing	0.0229245737102913
GO:0005905	coated pit	0.0369863583011517
GO:0030198	extracellular matrix organization and biogenesis	0.0369863583011517
GO:0030900	forebrain development	0.0369863583011517
GO:0005272	sodium channel activity	0.0412411474532464
GO:0005604	basement membrane	0.0427872738164806
GO:0008201	heparin binding	0.0427872738164806
GO:0044459	plasma membrane part	0.0427872738164806
GO:0043062	extracellular structure organization and biogenesis	0.0433944682033477
GO:0031402	sodium ion binding	0.0462792474072028
GO:0005539	glycosaminoglycan binding	0.0469878124796556
GO:0030247	polysaccharide binding	0.0469878124796556
GO:0005507	copper ion binding	0.0469878124796556
GO:0001871	pattern binding	0.04733948380619
GO:0044420	extracellular matrix part	0.04733948380619
GO:0007420	brain development	0.047832875049538
GO:0015276	ligand-gated ion channel activity	0.0478936926355097
GO:0022834	ligand-gated channel activity	0.0478936926355097
GO:0009628	response to abiotic stimulus	0.0478936926355097
GO:0006814	sodium ion transport	0.0478936926355097
GO:0006816	calcium ion transport	0.0478936926355097
GO:0006417	regulation of translation	0.0478936926355097
GO:0010324	membrane invagination	0.0478936926355097
GO:0006897	endocytosis	0.0478936926355097
GO:0031326	regulation of cellular biosynthetic process	0.0478936926355097
GO:0005886	plasma membrane	0.0485554587584505
GO:0009889	regulation of biosynthetic process	0.0485554587584505
GO:0031420	alkali metal ion binding	0.0485554587584505
GO:0007417	central nervous system development	0.0492402134427232
GO:0006810	transport	0.0492402134427232
GO:0015674	di-, tri-valent inorganic cation transport	0.0492402134427232
GO:0051234	establishment of localization	0.0492402134427232

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
non-terminally differentiated cell	1.50e-07	180

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.11e-32	94
nervous system	1.11e-32	94
central nervous system	7.09e-31	82
brain	7.03e-28	69
future brain	7.03e-28	69
neural tube	2.79e-25	57
neural rod	2.79e-25	57
future spinal cord	2.79e-25	57
neural keel	2.79e-25	57
neural plate	1.11e-24	86
presumptive neural plate	1.11e-24	86
neurectoderm	1.13e-24	90
ectoderm	1.13e-23	173
presumptive ectoderm	1.13e-23	173
ectoderm-derived structure	2.19e-23	169
regional part of brain	2.94e-23	59
organism subdivision	4.51e-23	365
head	1.06e-21	123
anterior region of body	6.34e-21	129
craniocervical region	6.34e-21	129
telencephalon	4.92e-20	34
gray matter	5.47e-20	34
brain grey matter	5.47e-20	34
multi-tissue structure	8.84e-20	347
regional part of telencephalon	2.20e-19	33
cerebral hemisphere	7.55e-19	32
regional part of forebrain	7.78e-18	41
forebrain	7.78e-18	41
future forebrain	7.78e-18	41
pre-chordal neural plate	2.40e-17	61
epithelium	3.66e-17	309
cell layer	4.85e-17	312
anterior neural tube	5.15e-17	42
regional part of cerebral cortex	1.14e-14	22
cerebral cortex	1.40e-14	25
pallium	1.40e-14	25
neocortex	1.48e-13	20
organ part	1.66e-13	219
tube	1.50e-10	194
embryo	8.03e-10	612
posterior neural tube	1.23e-09	15
chordal neural plate	1.23e-09	15
embryonic structure	1.83e-09	605
developing anatomical structure	1.83e-09	605
anatomical cluster	2.20e-09	286
organ segment	2.53e-09	97
germ layer	3.13e-09	604
embryonic tissue	3.13e-09	604
presumptive structure	3.13e-09	604
epiblast (generic)	3.13e-09	604
segmental subdivision of nervous system	1.40e-08	13
multi-cellular organism	1.60e-08	659
organ	2.24e-08	511
anatomical system	2.49e-08	625
anatomical group	4.37e-08	626
anatomical conduit	4.94e-08	241
segmental subdivision of hindbrain	5.52e-08	12
hindbrain	5.52e-08	12
presumptive hindbrain	5.52e-08	12
basal ganglion	5.94e-07	9
nuclear complex of neuraxis	5.94e-07	9
aggregate regional part of brain	5.94e-07	9
collection of basal ganglia	5.94e-07	9
cerebral subcortex	5.94e-07	9
nucleus of brain	6.73e-07	9
neural nucleus	6.73e-07	9

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	0.0324087452754469
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109023064025864

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.