Coexpression cluster:C1775

Full id: C1775_neuroblastoma_iPS_testicular_H9_HES3GFP_skeletal_Melanocyte

Phase1 CAGE Peaks

Hg19::chr17:27370003..27370010,+	p7@PIPOX
Hg19::chr17:27370022..27370051,+	p2@PIPOX
Hg19::chr1:63788080..63788093,-	p2@ENST00000418244
Hg19::chr1:63788098..63788150,-	p1@ENST00000418244 p1@ENST00000449386
Hg19::chr1:63788229..63788250,+	p1@FOXD3

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:0008115	sarcosine oxidase activity	0.00174651065699534
GO:0001829	trophectodermal cell differentiation	0.00174651065699534
GO:0050031	L-pipecolate oxidase activity	0.00174651065699534
GO:0046653	tetrahydrofolate metabolic process	0.00174651065699534
GO:0001825	blastocyst formation	0.00174651065699534
GO:0016647	oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor	0.00174651065699534
GO:0001892	embryonic placenta development	0.0029939301333032
GO:0001824	blastocyst development	0.00873088237650159
GO:0001890	placenta development	0.00873088237650159
GO:0006760	folic acid and derivative metabolic process	0.0226879294561886
GO:0001701	in utero embryonic development	0.0226879294561886
GO:0016645	oxidoreductase activity, acting on the CH-NH group of donors	0.0226879294561886
GO:0009792	embryonic development ending in birth or egg hatching	0.0326998395213866
GO:0043009	chordate embryonic development	0.0326998395213866
GO:0042579	microbody	0.0326998395213866
GO:0005777	peroxisome	0.0326998395213866
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0363413184827587
GO:0046483	heterocycle metabolic process	0.0363413184827587
GO:0006752	group transfer coenzyme metabolic process	0.0363413184827587
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0363413184827587
GO:0048646	anatomical structure formation	0.0380888911765254
GO:0006725	aromatic compound metabolic process	0.0434672701333003
GO:0045892	negative regulation of transcription, DNA-dependent	0.0461077525897228
GO:0045893	positive regulation of transcription, DNA-dependent	0.0485256242130203
GO:0009790	embryonic development	0.0490826948160948

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
melanocyte	2.50e-09	10
melanoblast	2.50e-09	10
neurectodermal cell	3.02e-08	59
migratory neural crest cell	2.90e-07	41
neural cell	4.03e-07	25

Uber Anatomy

Ontology term	p-value	n
adult organism	5.45e-12	115
central nervous system	1.45e-09	82
regional part of nervous system	2.12e-09	94
nervous system	2.12e-09	94
neurectoderm	8.33e-09	90
neural tube	6.57e-08	57
neural rod	6.57e-08	57
future spinal cord	6.57e-08	57
neural keel	6.57e-08	57
neural plate	1.93e-07	86
presumptive neural plate	1.93e-07	86
ectoderm	2.82e-07	173
presumptive ectoderm	2.82e-07	173

Disease

Ontology term	p-value	n
cell type cancer	6.83e-21	143
carcinoma	1.34e-18	106
cancer	2.26e-15	235
disease of cellular proliferation	5.67e-15	239
germ cell and embryonal cancer	5.61e-07	22
germ cell cancer	5.61e-07	22

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
ATF3#467	3	13.4779047156053	0.000824108855140936	0.00627371562956952
CTBP2#1488	2	25.0868001357313	0.00246143859967838	0.0138492719487022
CTCFL#140690	3	11.8478846153846	0.00120177034853823	0.00815010996305092
FOXA1#3169	3	6.64885184963127	0.00638902516656872	0.0278095940389793
FOXA2#3170	3	14.7782782515991	0.000628919285119448	0.00517398197862072
HNF4G#3174	2	11.5013690105787	0.0112743830492105	0.0413806111852572
NANOG#79923	3	17.5468670886076	0.000379420009068183	0.0037606763146125
POU5F1#5460	2	134.175680580762	8.81868530743257e-05	0.00130160355401774
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135329891174461
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00918771963492687
USF2#7392	3	7.79531843104175	0.00404892766172205	0.0193761893357125

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.