Coexpression cluster:C1229

Full id: C1229_cerebellum_occipital_parietal_pineal_middle_medial_amygdala

Phase1 CAGE Peaks

Hg19::chr17:5095351..5095419,+	p1@LOC100130950
Hg19::chr19:37998036..37998098,+	p2@ZNF793
Hg19::chr19:52839515..52839572,+	p1@ZNF610
Hg19::chr19:57988878..57988941,-	p1@ZNF772
Hg19::chr1:200708012..200708074,+	p@chr1:200708012..200708074 +
Hg19::chr5:178322893..178322931,+	p1@ZFP2
Hg19::chr5:178368186..178368238,+	p1@ZNF454

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
2.75303467843507e-09	1.7426709514494e-06	5	390	{ASH2L,391} (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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GO ID	GO name	FDR corrected p-value
GO:0006355	regulation of transcription, DNA-dependent	7.7530361604906e-05
GO:0006351	transcription, DNA-dependent	7.7530361604906e-05
GO:0032774	RNA biosynthetic process	7.7530361604906e-05
GO:0003677	DNA binding	7.7530361604906e-05
GO:0045449	regulation of transcription	7.7530361604906e-05
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	7.7530361604906e-05
GO:0006350	transcription	7.7530361604906e-05
GO:0010468	regulation of gene expression	7.7530361604906e-05
GO:0031323	regulation of cellular metabolic process	7.78470640173588e-05
GO:0019222	regulation of metabolic process	7.78470640173588e-05
GO:0016070	RNA metabolic process	7.78470640173588e-05
GO:0008270	zinc ion binding	7.78470640173588e-05
GO:0046914	transition metal ion binding	0.000163152953123399
GO:0010467	gene expression	0.00025861416676931
GO:0050794	regulation of cellular process	0.000302027107601188
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.000320756298776466
GO:0005634	nucleus	0.00036014843875417
GO:0050789	regulation of biological process	0.000363800291165466
GO:0003676	nucleic acid binding	0.000416532099838324
GO:0043169	cation binding	0.000434377092938975
GO:0065007	biological regulation	0.000493781123385218
GO:0046872	metal ion binding	0.000511515697461135
GO:0043167	ion binding	0.000532195466049185
GO:0043283	biopolymer metabolic process	0.000987064155825241
GO:0043231	intracellular membrane-bound organelle	0.00154739567627646
GO:0043227	membrane-bound organelle	0.00154739567627646
GO:0043229	intracellular organelle	0.00388253171397565
GO:0043226	organelle	0.00388253171397565
GO:0043170	macromolecule metabolic process	0.00445060385533282
GO:0044237	cellular metabolic process	0.00816727793047431
GO:0044238	primary metabolic process	0.00820792120921185
GO:0044424	intracellular part	0.00857444245426504
GO:0005622	intracellular	0.0167494844650136

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.86e-40	94
nervous system	1.86e-40	94
ectoderm	6.64e-38	173
presumptive ectoderm	6.64e-38	173
central nervous system	1.19e-37	82
ectoderm-derived structure	2.44e-37	169
neural tube	5.24e-34	57
neural rod	5.24e-34	57
future spinal cord	5.24e-34	57
neural keel	5.24e-34	57
adult organism	2.67e-33	115
regional part of brain	2.87e-32	59
neurectoderm	3.78e-32	90
neural plate	6.54e-32	86
presumptive neural plate	6.54e-32	86
brain	8.52e-32	69
future brain	8.52e-32	69
head	2.88e-30	123
anterior region of body	1.01e-29	129
craniocervical region	1.01e-29	129
anterior neural tube	6.62e-27	42
regional part of forebrain	1.07e-26	41
forebrain	1.07e-26	41
future forebrain	1.07e-26	41
organism subdivision	2.37e-26	365
pre-chordal neural plate	3.34e-24	61
telencephalon	3.20e-22	34
gray matter	3.35e-22	34
brain grey matter	3.35e-22	34
regional part of telencephalon	1.34e-21	33
cerebral hemisphere	4.47e-21	32
multi-cellular organism	1.58e-18	659
multi-tissue structure	5.32e-18	347
cerebral cortex	9.82e-17	25
pallium	9.82e-17	25
regional part of cerebral cortex	1.27e-15	22
neocortex	2.37e-14	20
epithelium	1.09e-13	309
cell layer	1.14e-13	312
anatomical cluster	1.09e-12	286
embryo	1.89e-12	612
anatomical system	2.36e-12	625
anatomical conduit	2.49e-12	241
anatomical group	3.18e-12	626
organ	3.80e-12	511
organ part	4.23e-12	219
embryonic structure	2.19e-10	605
developing anatomical structure	2.19e-10	605
tube	2.37e-10	194
germ layer	4.33e-10	604
embryonic tissue	4.33e-10	604
presumptive structure	4.33e-10	604
epiblast (generic)	4.33e-10	604
posterior neural tube	3.01e-08	15
chordal neural plate	3.01e-08	15
segmental subdivision of nervous system	4.26e-07	13
basal ganglion	4.57e-07	9
nuclear complex of neuraxis	4.57e-07	9
aggregate regional part of brain	4.57e-07	9
collection of basal ganglia	4.57e-07	9
cerebral subcortex	4.57e-07	9
nucleus of brain	6.45e-07	9
neural nucleus	6.45e-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
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.0365670520119168
HEY1#23462	5	2.88579360221836	0.0123136694185303	0.0446273838498762
SETDB1#9869	2	11.5200074794316	0.0118863972798321	0.0432589972996614
TAF1#6872	6	2.86546824492454	0.00372833020747146	0.0185863044648263
ZNF143#7702	3	5.78608995095481	0.011330055887324	0.0415528218146657

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.