Coexpression cluster:C1817

Full id: C1817_Alveolar_smallcell_acantholytic_Hepatocyte_squamous_liver_mesothelioma

Phase1 CAGE Peaks

Hg19::chr19:35739597..35739627,+	p4@LSR
Hg19::chr19:35739631..35739674,+	p2@LSR
Hg19::chr19:35739679..35739690,+	p6@LSR
Hg19::chr19:35739871..35739882,+	p3@LSR
Hg19::chr19:35739897..35739920,+	p1@LSR

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	1.65e-24	253
endodermal cell	1.05e-12	58
endo-epithelial cell	1.37e-12	42

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.22e-14	160
endoderm	1.22e-14	160
presumptive endoderm	1.22e-14	160
trunk region element	1.89e-13	101
subdivision of digestive tract	1.21e-11	118
renal system	2.08e-11	48
digestive system	3.59e-11	145
digestive tract	3.59e-11	145
primitive gut	3.59e-11	145
urinary system structure	3.71e-11	47
adult organism	5.50e-11	114
foregut	2.02e-09	87
abdomen element	5.12e-09	54
abdominal segment element	5.12e-09	54
endo-epithelium	1.24e-08	82
organ part	3.66e-08	218
cavitated compound organ	4.20e-08	31
kidney	5.86e-08	26
kidney mesenchyme	5.86e-08	26
upper urinary tract	5.86e-08	26
kidney rudiment	5.86e-08	26
kidney field	5.86e-08	26
subdivision of trunk	1.37e-07	112
respiratory system	3.00e-07	74
immaterial anatomical entity	6.41e-07	117
organ	6.54e-07	503

Disease

Ontology term	p-value	n
carcinoma	6.90e-21	106
cell type cancer	2.27e-12	143
squamous cell carcinoma	5.93e-08	14
adenocarcinoma	2.66e-07	25

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
CCNT2#905	4	5.06896126157011	0.00270999809128077	0.0148978571773488
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239366233382508
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352900355394618
E2F4#1874	4	10.1344482522276	0.000181820150963297	0.00220342477911996
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.0057327611648736
ELK4#2005	5	16.235681658468	8.85705446514576e-07	3.8239847510763e-05
EP300#2033	5	6.7739417262232	7.00901578206049e-05	0.00110844124661208
FOXA1#3169	5	11.0814197493855	5.98116883436141e-06	0.000178987762719734
FOXA2#3170	5	24.6304637526652	1.10174651693954e-07	6.40318889719803e-06
GABPB1#2553	5	7.06768383618217	5.6685482528729e-05	0.00094844202336077
HMGN3#9324	5	8.17854772335059	2.73180911341838e-05	0.000582022464292742
IRF1#3659	5	7.6371637535639	3.84754333311872e-05	0.00072441604140542
IRF4#3662	5	21.9145126867441	1.97628413609567e-07	1.07054532619137e-05
JUND#3727	5	6.99466394187103	5.97069468343598e-05	0.000984175161053298
NANOG#79923	2	11.6979113924051	0.0109116495195608	0.0402273911600625
RDBP#7936	2	61.45536159601	0.000417819102241031	0.00391009043180565
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00248117038839619
SIX5#147912	5	17.086715355459	6.86007756253503e-07	3.10021480118389e-05
SMARCC2#6601	5	94.1553744268976	1.34457127652426e-10	1.43731504144234e-08
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204348515586724
SPI1#6688	5	8.20432350852273	2.68916109982495e-05	0.000574577119690298
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135403161283381
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00918998303817499
TFAP2C#7022	5	10.8092286098602	6.77323239348459e-06	0.000197264254864232
ZEB1#6935	5	16.8884320175439	7.27243686732534e-07	3.23065093146147e-05
ZNF263#10127	5	8.22184163701068	2.6606316672286e-05	0.000571051604384891

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.