Coexpression cluster:C1234

Full id: C1234_cerebellum_parietal_pineal_duodenum_occipital_temporal_thalamus

Phase1 CAGE Peaks

Hg19::chr18:32820990..32821031,+	p1@ZNF397
Hg19::chr19:12595586..12595637,-	p2@ZNF709
Hg19::chr19:36870087..36870110,-	p1@ZFP14
Hg19::chr19:37341752..37341816,+	p1@ZNF345
Hg19::chr19:44809143..44809187,-	p1@ZNF235
Hg19::chr19:9434841..9434886,+	p1@ZNF559
Hg19::chr6:28234885..28234960,+	p1@ENST00000437778 p1@ENST00000537979

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	1.28492457308728e-05
GO:0006351	transcription, DNA-dependent	1.28492457308728e-05
GO:0032774	RNA biosynthetic process	1.28492457308728e-05
GO:0003677	DNA binding	1.28492457308728e-05
GO:0045449	regulation of transcription	1.28492457308728e-05
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	1.28492457308728e-05
GO:0006350	transcription	1.28492457308728e-05
GO:0010468	regulation of gene expression	1.28492457308728e-05
GO:0031323	regulation of cellular metabolic process	1.33315034342445e-05
GO:0019222	regulation of metabolic process	1.40038407083747e-05
GO:0016070	RNA metabolic process	1.40038407083747e-05
GO:0008270	zinc ion binding	1.40038407083747e-05
GO:0046914	transition metal ion binding	3.45836035707735e-05
GO:0010467	gene expression	6.10102796453814e-05
GO:0050794	regulation of cellular process	7.45209661201949e-05
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	8.11418631990086e-05
GO:0005634	nucleus	9.43813329104455e-05
GO:0050789	regulation of biological process	9.66298945126734e-05
GO:0003676	nucleic acid binding	0.000114910083150332
GO:0043169	cation binding	0.000122089782962347
GO:0065007	biological regulation	0.00014378886063675
GO:0046872	metal ion binding	0.000151411353560366
GO:0043167	ion binding	0.000160205453538815
GO:0043283	biopolymer metabolic process	0.000339098765258031
GO:0043231	intracellular membrane-bound organelle	0.000591020205429104
GO:0043227	membrane-bound organelle	0.000591020205429104
GO:0043229	intracellular organelle	0.00180918195850643
GO:0043226	organelle	0.00180918195850643
GO:0006359	regulation of transcription from RNA polymerase III promoter	0.0020747978199025
GO:0043170	macromolecule metabolic process	0.0020747978199025
GO:0003709	RNA polymerase III transcription factor activity	0.00313120512504248
GO:0044237	cellular metabolic process	0.00419777458772688
GO:0044238	primary metabolic process	0.00425923366319416
GO:0044424	intracellular part	0.00452565259442613
GO:0006383	transcription from RNA polymerase III promoter	0.0070506184225885
GO:0003704	specific RNA polymerase II transcription factor activity	0.00953998750196115
GO:0005622	intracellular	0.0096374684861231
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0292411412813275
GO:0045892	negative regulation of transcription, DNA-dependent	0.0452875177448344

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
adult organism	9.94e-43	115
central nervous system	5.25e-29	82
regional part of nervous system	1.23e-28	94
nervous system	1.23e-28	94
neural tube	9.01e-28	57
neural rod	9.01e-28	57
future spinal cord	9.01e-28	57
neural keel	9.01e-28	57
brain	4.84e-24	69
future brain	4.84e-24	69
regional part of brain	1.17e-23	59
anterior neural tube	1.25e-23	42
regional part of forebrain	1.26e-23	41
forebrain	1.26e-23	41
future forebrain	1.26e-23	41
neurectoderm	4.47e-20	90
gray matter	1.93e-19	34
brain grey matter	1.93e-19	34
telencephalon	2.02e-19	34
regional part of telencephalon	6.84e-19	33
neural plate	9.32e-19	86
presumptive neural plate	9.32e-19	86
cerebral hemisphere	3.33e-18	32
ectoderm	8.14e-15	173
presumptive ectoderm	8.14e-15	173
pre-chordal neural plate	1.09e-14	61
anterior region of body	1.41e-14	129
craniocervical region	1.41e-14	129
cerebral cortex	4.18e-14	25
pallium	4.18e-14	25
regional part of cerebral cortex	5.54e-14	22
ectoderm-derived structure	9.67e-14	169
head	3.18e-13	123
neocortex	8.34e-13	20
basal ganglion	6.71e-07	9
nuclear complex of neuraxis	6.71e-07	9
aggregate regional part of brain	6.71e-07	9
collection of basal ganglia	6.71e-07	9
cerebral subcortex	6.71e-07	9
nucleus of brain	7.75e-07	9
neural nucleus	7.75e-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
CHD2#1106	4	5.91087019092392	0.00240275446687455	0.013552671946744
E2F6#1876	5	3.58368266549813	0.00459810189782724	0.0217265151385413
EGR1#1958	6	4.27558208126583	0.000376213061986645	0.0037366919620374
ELF1#1997	6	3.64979825040646	0.000937747978262069	0.00679083768559924
ELK4#2005	4	9.27753237626744	0.000432817858966577	0.00404248474088806
ETS1#2113	4	5.55929195554419	0.00302256447530346	0.0160509285216972
GABPB1#2553	4	4.03867647781838	0.0098011349469615	0.0368487250342241
HEY1#23462	7	4.04011104310571	5.68979821988558e-05	0.000950474786127048
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223451285692641
SIN3A#25942	6	4.63618690869869	0.000235167814635783	0.00256588919690206
SIX5#147912	3	7.32287800948243	0.0058666762526916	0.0263327231027531
SP2#6668	3	11.2086559259334	0.00174151533091611	0.0107172305489097
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.00246630801240134
TBP#6908	7	3.70677068709639	0.000103967209750511	0.00145124718245571
TRIM28#10155	4	10.6231571687214	0.000256730100512827	0.00276276506619878
YY1#7528	6	4.20957492844616	0.00041168337886575	0.00392297448954015
ZBTB33#10009	3	13.5705964414205	0.00100139762859007	0.00717761079763356
ZNF143#7702	4	7.71478660127309	0.000877196960661348	0.0065419575388825

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.