Coexpression cluster:C3792

Full id: C3792_Renal_Alveolar_anaplastic_acute_testicular_lymphoma_diffuse

Phase1 CAGE Peaks

Hg19::chr19:41256764..41256825,+	p3@SNRPA
Hg19::chr20:42295713..42295738,+	p2@MYBL2
Hg19::chr20:42295745..42295765,+	p1@MYBL2

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:0005685	snRNP U1	0.00847744498676387
GO:0005684	U2-dependent spliceosome	0.0211911169354966
GO:0030532	small nuclear ribonucleoprotein complex	0.0353107296901619
GO:0000375	RNA splicing, via transesterification reactions	0.0494022677164302
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0494022677164302
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0494022677164302

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	4.37e-26	253
animal cell	7.64e-18	679
eukaryotic cell	7.64e-18	679
embryonic cell	1.52e-12	250
native cell	1.35e-09	722
squamous epithelial cell	1.66e-07	63
meso-epithelial cell	6.43e-07	45
lining cell	7.75e-07	58
barrier cell	7.75e-07	58

Uber Anatomy

Ontology term	p-value	n
trunk region element	4.23e-07	101

Disease

Ontology term	p-value	n
cancer	2.60e-44	235
disease of cellular proliferation	6.50e-42	239
organ system cancer	6.84e-22	137
cell type cancer	1.05e-21	143
hematologic cancer	7.94e-20	51
immune system cancer	7.94e-20	51
carcinoma	4.70e-18	106
leukemia	8.58e-16	39
myeloid leukemia	3.68e-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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325340322035394
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437057220005837
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322158512004836
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462215243365209
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128049741006651
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186468847230574
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720186609343816
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294442396902279
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269581578530994
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172883016559574
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00882148935118511
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276683745606011
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246434573663487
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190238387372175
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329317976333761
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0378160021957942

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.