Coexpression cluster:C3964

Full id: C3964_chronic_Mesenchymal_hepatocellular_hereditary_acute_rhabdomyosarcoma_Skeletal

Phase1 CAGE Peaks

Hg19::chr1:28844730..28844776,+	p2@RCC1
Hg19::chr1:28844778..28844807,+	p3@RCC1
Hg19::chr22:20105012..20105085,+	p1@RANBP1

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
4.59498110789263e-05	0.0290862304129603	2	194	HIV Infection (Reactome):REACT_6185

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:0005083	small GTPase regulator activity	0.00884912319659774
GO:0005087	Ran guanyl-nucleotide exchange factor activity	0.00884912319659774
GO:0030695	GTPase regulator activity	0.00884912319659774
GO:0007090	regulation of S phase of mitotic cell cycle	0.00884912319659774
GO:0007052	mitotic spindle organization and biogenesis	0.00884912319659774
GO:0008536	Ran GTPase binding	0.00884912319659774
GO:0033261	regulation of progression through S phase	0.00904970673294687
GO:0042393	histone binding	0.00904970673294687
GO:0000084	S phase of mitotic cell cycle	0.00911647317396334
GO:0007051	spindle organization and biogenesis	0.00916982948411652
GO:0051320	S phase	0.00921343297182372
GO:0000790	nuclear chromatin	0.00924972184269641
GO:0005092	GDP-dissociation inhibitor activity	0.0102534655193447
GO:0000794	condensed nuclear chromosome	0.0102534655193447
GO:0007346	regulation of progression through mitotic cell cycle	0.0102534655193447
GO:0000082	G1/S transition of mitotic cell cycle	0.0102534655193447
GO:0000793	condensed chromosome	0.0147554015762654
GO:0044454	nuclear chromosome part	0.0170067703933241
GO:0007088	regulation of mitosis	0.0170067703933241
GO:0017016	Ras GTPase binding	0.0185651040629841
GO:0051329	interphase of mitotic cell cycle	0.018628663845914
GO:0031267	small GTPase binding	0.018628663845914
GO:0051325	interphase	0.0188654918799131
GO:0051020	GTPase binding	0.0189105199641022
GO:0000228	nuclear chromosome	0.0189105199641022
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0189105199641022
GO:0003682	chromatin binding	0.0210616528993315
GO:0016043	cellular component organization and biogenesis	0.0272424842678321
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0274005387140235
GO:0007067	mitosis	0.0368278486951195
GO:0000087	M phase of mitotic cell cycle	0.0368278486951195
GO:0051301	cell division	0.0368278486951195
GO:0019899	enzyme binding	0.0412168034622221
GO:0000279	M phase	0.0412168034622221
GO:0005085	guanyl-nucleotide exchange factor activity	0.0412168034622221
GO:0007017	microtubule-based process	0.0412168034622221
GO:0000785	chromatin	0.0412168034622221
GO:0000278	mitotic cell cycle	0.0412168034622221
GO:0005096	GTPase activator activity	0.0420473751475497
GO:0000074	regulation of progression through cell cycle	0.0420473751475497
GO:0051726	regulation of cell cycle	0.0420473751475497
GO:0022403	cell cycle phase	0.0421833541290076
GO:0008047	enzyme activator activity	0.0494377287556743
GO:0006323	DNA packaging	0.0494377287556743
GO:0044427	chromosomal part	0.0494377287556743

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
animal cell	1.74e-27	679
eukaryotic cell	1.74e-27	679
epithelial cell	8.27e-26	253
native cell	1.37e-16	722
embryonic cell	6.05e-15	250
squamous epithelial cell	6.34e-08	63
kidney cell	1.84e-07	17
kidney epithelial cell	1.84e-07	17
epithelial cell of nephron	2.07e-07	15
somatic cell	3.27e-07	588

Uber Anatomy

Ontology term	p-value	n
nephron epithelium	2.07e-07	15
renal tubule	2.07e-07	15
nephron tubule	2.07e-07	15
nephron	2.07e-07	15
uriniferous tubule	2.07e-07	15
nephrogenic mesenchyme	2.07e-07	15
segment of respiratory tract	5.58e-07	47
larynx	6.22e-07	9

Disease

Ontology term	p-value	n
cancer	9.68e-34	235
disease of cellular proliferation	2.83e-32	239
hematologic cancer	8.99e-18	51
immune system cancer	8.99e-18	51
organ system cancer	1.20e-17	137
cell type cancer	1.37e-16	143
carcinoma	1.88e-16	106
leukemia	5.91e-15	39
myeloid leukemia	3.49e-12	31

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279697716392251
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306814772942665
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322560644645816
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462721208807951
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762995717079107
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00581782458216022
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225919714992376
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.01542438730113
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434386203706726
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186728615524261
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720776281785965
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294785680230661
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000738180828833083
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471436667535242
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277090343040457
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457569118493715
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543578587219885
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190452750548706
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329736752232155
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389387251106232

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.