Coexpression cluster:C334

Full id: C334_cerebellum_pineal_occipital_pituitary_amygdala_medial_caudate

Phase1 CAGE Peaks

Hg19::chr10:101190668..101190736,+	p1@ENST00000416191
Hg19::chr11:17230061..17230092,+	p@chr11:17230061..17230092 +
Hg19::chr11:57417405..57417423,-	p2@YPEL4
Hg19::chr12:118406777..118406811,-	p1@KSR2
Hg19::chr12:79258463..79258477,+	p10@SYT1
Hg19::chr12:9066766..9066866,+	p1@PHC1
Hg19::chr13:25542609..25542639,-	p1@TPTE2P1
Hg19::chr13:29394076..29394108,+	p@chr13:29394076..29394108 +
Hg19::chr14:100070869..100070889,+	p1@ENST00000502101
Hg19::chr14:103524166..103524207,+	p1@AK057714
Hg19::chr14:58797974..58798011,+	p3@ARID4A
Hg19::chr14:66975213..66975239,+	p2@GPHN
Hg19::chr14:94024982..94024986,+	p@chr14:94024982..94024986 +
Hg19::chr15:61521462..61521482,-	p4@RORA
Hg19::chr15:65204075..65204119,+	p1@ANKDD1A
Hg19::chr17:50235645..50235676,-	p2@CA10
Hg19::chr18:29265423..29265443,-	p@chr18:29265423..29265443 -
Hg19::chr19:28284917..28284960,+	p1@AK095009
Hg19::chr19:44406012..44406044,+	p@chr19:44406012..44406044 +
Hg19::chr1:147719007..147719042,-	p@chr1:147719007..147719042 -
Hg19::chr1:197237324..197237332,+	p5@CRB1
Hg19::chr20:5892037..5892067,+	p2@CHGB
Hg19::chr21:17442799..17442832,+	p17@LINC00478
Hg19::chr21:17443471..17443515,+	p10@LINC00478
Hg19::chr22:20850171..20850221,+	p3@MED15
Hg19::chr4:176987131..176987162,+	p2@WDR17
Hg19::chr4:176987163..176987196,+	p3@WDR17
Hg19::chr4:57276661..57276679,+	p1@ENST00000416157
Hg19::chr5:139487724..139487763,+	p@chr5:139487724..139487763 +
Hg19::chr5:161494464..161494499,+	p4@GABRG2
Hg19::chr6:46620738..46620755,+	p2@SLC25A27
Hg19::chr6:80247381..80247389,+	p@chr6:80247381..80247389 +
Hg19::chrX:46988715..46988759,+	p@chrX:46988715..46988759 +
Hg19::chrX:83443478..83443513,-	p@chrX:83443478..83443513 -

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
6.75939345257143e-05	0.0427869605547771	2	22	{DNM1,22} (Static Module):NA

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
neural cell	9.88e-09	25
neuronal stem cell	1.26e-07	8

Uber Anatomy

Ontology term	p-value	n
nervous system	1.14e-65	89
central nervous system	5.13e-62	81
adult organism	4.59e-61	114
neural tube	6.06e-60	56
neural rod	6.06e-60	56
future spinal cord	6.06e-60	56
neural keel	6.06e-60	56
regional part of nervous system	1.22e-56	53
regional part of brain	1.22e-56	53
brain	6.10e-50	68
future brain	6.10e-50	68
regional part of forebrain	2.47e-48	41
forebrain	2.47e-48	41
anterior neural tube	2.47e-48	41
future forebrain	2.47e-48	41
neural plate	2.62e-48	82
presumptive neural plate	2.62e-48	82
neurectoderm	1.01e-47	86
brain grey matter	8.22e-40	34
gray matter	8.22e-40	34
telencephalon	8.96e-40	34
ectoderm-derived structure	1.29e-39	171
ectoderm	1.29e-39	171
presumptive ectoderm	1.29e-39	171
pre-chordal neural plate	3.41e-38	61
cerebral hemisphere	9.91e-38	32
regional part of telencephalon	1.36e-37	32
organ system subdivision	3.70e-37	223
ecto-epithelium	4.06e-37	104
structure with developmental contribution from neural crest	5.81e-34	132
cerebral cortex	1.74e-29	25
pallium	1.74e-29	25
regional part of cerebral cortex	1.02e-27	22
neocortex	2.28e-25	20
anatomical cluster	1.12e-23	373
organ part	9.67e-15	218
multi-tissue structure	4.03e-14	342
embryo	4.74e-14	592
tube	1.13e-12	192
posterior neural tube	1.37e-12	15
chordal neural plate	1.37e-12	15
developing anatomical structure	4.88e-12	581
basal ganglion	7.48e-12	9
nuclear complex of neuraxis	7.48e-12	9
aggregate regional part of brain	7.48e-12	9
collection of basal ganglia	7.48e-12	9
cerebral subcortex	7.48e-12	9
embryonic structure	9.47e-12	564
multi-cellular organism	1.06e-11	656
anatomical conduit	1.12e-11	240
neural nucleus	1.24e-11	9
nucleus of brain	1.24e-11	9
germ layer	1.26e-11	560
germ layer / neural crest	1.26e-11	560
embryonic tissue	1.26e-11	560
presumptive structure	1.26e-11	560
germ layer / neural crest derived structure	1.26e-11	560
epiblast (generic)	1.26e-11	560
segmental subdivision of nervous system	1.38e-10	13
diencephalon	8.35e-10	7
future diencephalon	8.35e-10	7
organ	1.21e-09	503
segmental subdivision of hindbrain	1.24e-09	12
hindbrain	1.24e-09	12
presumptive hindbrain	1.24e-09	12
epithelium	1.44e-09	306
telencephalic nucleus	1.66e-09	7
anatomical system	1.86e-09	624
anatomical group	2.26e-09	625
cell layer	3.07e-09	309
temporal lobe	4.14e-09	6
gyrus	1.23e-08	6
brainstem	6.10e-08	6
limbic system	2.08e-07	5
parietal lobe	2.13e-07	5
occipital lobe	2.30e-07	5

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
NFE2#4778	4	9.0828541943093	0.000955074056277887	0.00687530875128248
NFYB#4801	7	3.45054566984574	0.00346435537471603	0.0176005161735646
NR2C2#7182	5	4.79626630959425	0.003585427593585	0.0181608454554743
POLR2A#5430	25	1.57900968864564	0.00131139902386779	0.0087846323297882
TBP#6908	17	1.85338534354819	0.00353755986200671	0.0179497262026002
YY1#7528	13	1.87780058082647	0.0126118953453923	0.0456021928395452
ZEB1#6935	7	3.47703012125903	0.00332015686360625	0.017172833928198

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.