Coexpression cluster:C3280

Full id: C3280_acute_somatostatinoma_neuroblastoma_small_choriocarcinoma_bile_signet

Phase1 CAGE Peaks

Hg19::chr12:46662478..46662504,-	p6@SLC38A1
Hg19::chr12:46662513..46662549,-	p2@SLC38A1
Hg19::chr12:46662553..46662572,-	p8@SLC38A1

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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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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	3.84e-26	254
animal cell	9.74e-18	679
eukaryotic cell	9.74e-18	679
native cell	2.35e-11	722
endo-epithelial cell	3.73e-10	43
endodermal cell	2.08e-09	59

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	5.68e-09	169
endoderm	5.68e-09	169
presumptive endoderm	5.68e-09	169
digestive system	2.39e-07	155
digestive tract	2.39e-07	155
primitive gut	2.39e-07	155

Disease

Ontology term	p-value	n
disease of cellular proliferation	8.48e-31	239
cancer	8.58e-31	235
cell type cancer	1.13e-22	143
carcinoma	3.63e-21	106
organ system cancer	4.84e-15	137

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	22.4631745260087	8.81932387510763e-05	0.00129329032040489
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00163997674892676
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189434545237991
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.011499923133877
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278628851844894
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171342777214756
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324063682221041
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436092413780659
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032090828493248
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460578470396773
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255176335837418
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153714844501258
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000626336606722705
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108435668980168
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185995961020554
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718765543026135
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293487792589556
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268858839714557
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00308187785237999
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172467941454894
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.0088029591698618
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662298600035985
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765800823859237
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275735802632012
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308279379728753
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541136861843588
USF1#7391	3	6.36149927720796	0.0038840405729056	0.018968684283081
USF2#7392	3	12.9921973850696	0.000455897939342781	0.0042072567718495
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328300124541265
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109010413403443

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.