Coexpression cluster:C3766

Full id: C3766_Alveolar_Renal_chronic_Placental_nonsmall_acute_carcinoid

Phase1 CAGE Peaks

Hg19::chr19:18433875..18433909,-	p1@LSM4
Hg19::chr19:18433910..18433944,-	p2@LSM4
Hg19::chr7:100303728..100303787,+	p1@POP7

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:0005688	snRNP U6	0.00312021664900506
GO:0006396	RNA processing	0.00445686189516397
GO:0030681	multimeric ribonuclease P complex	0.00445686189516397
GO:0005655	nucleolar ribonuclease P complex	0.00445686189516397
GO:0030677	ribonuclease P complex	0.00445686189516397
GO:0005684	U2-dependent spliceosome	0.00445686189516397
GO:0004526	ribonuclease P activity	0.00445686189516397
GO:0004549	tRNA-specific ribonuclease activity	0.00584920069324615
GO:0044428	nuclear part	0.0059422257858873
GO:0030529	ribonucleoprotein complex	0.0059422257858873
GO:0030532	small nuclear ribonucleoprotein complex	0.00708889649082795
GO:0016891	endoribonuclease activity, producing 5'-phosphomonoesters	0.00983488969882731
GO:0044452	nucleolar part	0.00983488969882731
GO:0016893	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0122482513790345
GO:0004521	endoribonuclease activity	0.0149613887740454
GO:0008033	tRNA processing	0.0179172156272548
GO:0004540	ribonuclease activity	0.0183274711924229
GO:0005681	spliceosome	0.0240460659124371
GO:0004519	endonuclease activity	0.0247427641746072
GO:0005730	nucleolus	0.0256796512216183
GO:0006399	tRNA metabolic process	0.0293575749978811
GO:0032991	macromolecular complex	0.0293575749978811
GO:0008380	RNA splicing	0.0293575749978811
GO:0004518	nuclease activity	0.0293575749978811
GO:0044446	intracellular organelle part	0.0293575749978811
GO:0044422	organelle part	0.0293575749978811
GO:0016070	RNA metabolic process	0.0293575749978811
GO:0006397	mRNA processing	0.0303003199967942
GO:0016071	mRNA metabolic process	0.0366123538767712
GO:0010467	gene expression	0.0455277092838167

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	1.49e-27	254
embryonic cell	3.07e-21	248
animal cell	1.16e-18	679
eukaryotic cell	1.16e-18	679
mesodermal cell	3.38e-09	119
native cell	2.20e-08	722
ectodermal cell	1.08e-07	71
squamous epithelial cell	1.13e-07	62
epithelial cell of nephron	2.58e-07	16
kidney cell	9.47e-07	18
kidney epithelial cell	9.47e-07	18

Uber Anatomy

Ontology term	p-value	n
mesenchyme	1.52e-09	238
entire embryonic mesenchyme	1.52e-09	238
segment of respiratory tract	1.61e-07	46
trunk	2.38e-07	216
nephron epithelium	2.58e-07	16
nephron	2.58e-07	16
uriniferous tubule	2.58e-07	16
metanephric mesenchyme	2.58e-07	16
nephrogenic mesenchyme	2.58e-07	16
trunk mesenchyme	4.18e-07	143
cell layer	4.81e-07	312
respiratory primordium	7.16e-07	38
endoderm of foregut	7.16e-07	38

Disease

Ontology term	p-value	n
cancer	1.76e-24	235
disease of cellular proliferation	1.89e-24	239
cell type cancer	7.92e-14	143
organ system cancer	2.21e-11	137
hematologic cancer	7.77e-11	51
immune system cancer	7.77e-11	51
carcinoma	5.47e-10	106
leukemia	6.53e-09	39
myeloid leukemia	4.67e-07	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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259558342760005
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.018997806607675
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660231427200687
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325292416226886
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.004369828526041
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322120863470069
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00914921090177978
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462167865828988
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401934986675065
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00761970391920095
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154059101705089
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108676431353651
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128028761856249
IRF3#3661	2	31.3213014743264	0.00133951467332011	0.008876749553736
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186442015893738
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294418751658601
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324730262146692
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381270068059665
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471126893954931
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172866035613051
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268324866358562
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276648949913836
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.032986549080874
SMC3#9126	2	10.0299552299552	0.012665637976747	0.045745834992858
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246402296705574
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203180779654732
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.015867406652914
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329293375581038

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.