Coexpression cluster:C125

Full id: C125_mucinous_alveolar_mesothelioma_Smooth_lung_CD14_Nucleus

Phase1 CAGE Peaks

Hg19::chr10:32872106..32872117,+	p@chr10:32872106..32872117 +
Hg19::chr10:34987997..34988013,-	p@chr10:34987997..34988013 -
Hg19::chr10:34988014..34988029,-	p@chr10:34988014..34988029 -
Hg19::chr10:34988093..34988129,-	p@chr10:34988093..34988129 -
Hg19::chr10:44801889..44801898,-	p@chr10:44801889..44801898 -
Hg19::chr10:5060201..5060211,-	p5@AKR1C2
Hg19::chr10:5136509..5136521,+	p4@AKR1C3
Hg19::chr10:70992187..70992196,-	p3@ENST00000450995
Hg19::chr10:70992213..70992241,-	p1@ENST00000450995
Hg19::chr10:70992318..70992353,+	p2@HKDC1
Hg19::chr10:70992359..70992379,+	p5@HKDC1
Hg19::chr10:76969764..76969775,+	p9@VDAC2
Hg19::chr11:108800179..108800190,+	p9@DDX10
Hg19::chr11:76480789..76480811,-	p@chr11:76480789..76480811 -
Hg19::chr11:76480816..76480852,-	p@chr11:76480816..76480852 -
Hg19::chr11:93465296..93465301,-	p1@SNORA1
Hg19::chr12:104671230..104671232,-	p@chr12:104671230..104671232 -
Hg19::chr12:104674641..104674651,-	p6@ENST00000549807
Hg19::chr12:104982622..104982628,+	p13@CHST11
Hg19::chr12:10771068..10771102,-	p@chr12:10771068..10771102 -
Hg19::chr12:13025302..13025313,+	p@chr12:13025302..13025313 +
Hg19::chr12:15815689..15815698,-	p29@EPS8
Hg19::chr12:15815728..15815729,-	p37@EPS8
Hg19::chr12:15815732..15815744,-	p21@EPS8
Hg19::chr12:1609586..1609598,+	p5@LOC100292680
Hg19::chr12:21791511..21791535,-	p8@LDHB
Hg19::chr12:21791552..21791567,-	p7@LDHB
Hg19::chr12:21791577..21791608,-	p6@LDHB
Hg19::chr12:50641120..50641132,+	p@chr12:50641120..50641132 +
Hg19::chr12:60015797..60015821,+	p@chr12:60015797..60015821 +
Hg19::chr12:61513089..61513090,+	p@chr12:61513089..61513090 +
Hg19::chr12:75214368..75214385,+	p@chr12:75214368..75214385 +
Hg19::chr12:88693740..88693754,+	p@chr12:88693740..88693754 +
Hg19::chr12:88693779..88693791,+	p@chr12:88693779..88693791 +
Hg19::chr12:88739033..88739034,+	p@chr12:88739033..88739034 +
Hg19::chr12:95571339..95571343,-	p@chr12:95571339..95571343 -
Hg19::chr12:98416778..98416782,-	p@chr12:98416778..98416782 -
Hg19::chr13:37363331..37363344,-	p@chr13:37363331..37363344 -
Hg19::chr13:37363350..37363364,-	p@chr13:37363350..37363364 -
Hg19::chr13:73458552..73458595,+	p6@PIBF1
Hg19::chr14:29706068..29706072,-	p@chr14:29706068..29706072 -
Hg19::chr14:55913197..55913206,-	p@chr14:55913197..55913206 -
Hg19::chr14:80683203..80683212,-	p@chr14:80683203..80683212 -
Hg19::chr14:80683293..80683297,-	p@chr14:80683293..80683297 -
Hg19::chr14:89297734..89297738,+	p@chr14:89297734..89297738 +
Hg19::chr17:79881409..79881423,-	p8@MAFG
Hg19::chr18:21574704..21574720,-	p@chr18:21574704..21574720 -
Hg19::chr18:63273310..63273317,+	p@chr18:63273310..63273317 +
Hg19::chr18:71363277..71363286,-	p@chr18:71363277..71363286 -
Hg19::chr19:39182748..39182750,+	p@chr19:39182748..39182750 +
Hg19::chr1:10480357..10480375,+	p@chr1:10480357..10480375 +
Hg19::chr1:10480469..10480472,+	p@chr1:10480469..10480472 +
Hg19::chr1:246469336..246469344,-	p15@SMYD3
Hg19::chr1:45988542..45988573,-	p2@PRDX1
Hg19::chr1:62072099..62072122,+	p@chr1:62072099..62072122 +
Hg19::chr1:8933951..8933957,-	p@chr1:8933951..8933957 -
Hg19::chr1:94502511..94502519,+	p@chr1:94502511..94502519 +
Hg19::chr21:45671797..45671832,-	p@chr21:45671797..45671832 -
Hg19::chr2:117844646..117844651,+	p@chr2:117844646..117844651 +
Hg19::chr2:117844694..117844699,+	p@chr2:117844694..117844699 +
Hg19::chr2:123150473..123150496,+	p@chr2:123150473..123150496 +
Hg19::chr2:173417533..173417537,-	p@chr2:173417533..173417537 -
Hg19::chr2:19985345..19985386,-	p@chr2:19985345..19985386 -
Hg19::chr2:224873590..224873601,+	p@chr2:224873590..224873601 +
Hg19::chr2:225434513..225434523,-	p29@CUL3
Hg19::chr2:225434538..225434545,-	p43@CUL3
Hg19::chr2:234398623..234398628,-	p20@USP40
Hg19::chr2:235903637..235903654,+	p@chr2:235903637..235903654 +
Hg19::chr2:235903707..235903722,+	p@chr2:235903707..235903722 +
Hg19::chr2:29353400..29353413,+	p28@CLIP4
Hg19::chr2:60642094..60642124,+	p@chr2:60642094..60642124 +
Hg19::chr2:72855783..72855788,+	p@chr2:72855783..72855788 +
Hg19::chr2:75466400..75466410,+	p@chr2:75466400..75466410 +
Hg19::chr2:75466431..75466447,+	p@chr2:75466431..75466447 +
Hg19::chr3:124826952..124826996,-	p7@SLC12A8
Hg19::chr3:139199576..139199582,-	p5@RBP2
Hg19::chr3:139199589..139199596,-	p4@RBP2
Hg19::chr3:139199602..139199615,-	p2@RBP2
Hg19::chr3:139199640..139199652,-	p3@RBP2
Hg19::chr3:153697368..153697372,+	p@chr3:153697368..153697372 +
Hg19::chr3:177364707..177364717,+	p@chr3:177364707..177364717 +
Hg19::chr3:27235576..27235597,-	p5@NEK10
Hg19::chr3:46204959..46204979,+	p3@CCR3
Hg19::chr3:46205262..46205283,+	p5@CCR3
Hg19::chr3:54081801..54081827,+	p@chr3:54081801..54081827 +
Hg19::chr3:54081908..54081914,+	p@chr3:54081908..54081914 +
Hg19::chr3:58631596..58631603,-	p@chr3:58631596..58631603 -
Hg19::chr4:102152036..102152041,-	p@chr4:102152036..102152041 -
Hg19::chr4:116100188..116100192,-	p@chr4:116100188..116100192 -
Hg19::chr4:137426576..137426593,+	p@chr4:137426576..137426593 +
Hg19::chr5:10288678..10288702,-	p@chr5:10288678..10288702 -
Hg19::chr5:13859633..13859640,+	p@chr5:13859633..13859640 +
Hg19::chr5:13860511..13860548,+	p1@ENST00000503244
Hg19::chr5:13986147..13986157,+	p@chr5:13986147..13986157 +
Hg19::chr5:173822039..173822053,+	p@chr5:173822039..173822053 +
Hg19::chr5:179246687..179246707,+	p@chr5:179246687..179246707 +
Hg19::chr5:29793807..29793849,+	p@chr5:29793807..29793849 +
Hg19::chr5:34526058..34526105,+	p@chr5:34526058..34526105 +
Hg19::chr5:34728676..34728679,+	p26@RAI14
Hg19::chr5:72141549..72141572,+	p@chr5:72141549..72141572 +
Hg19::chr5:72141725..72141727,+	p@chr5:72141725..72141727 +
Hg19::chr5:72141969..72142012,+	p@chr5:72141969..72142012 +
Hg19::chr5:78439900..78439935,-	p@chr5:78439900..78439935 -
Hg19::chr5:84591097..84591104,-	p@chr5:84591097..84591104 -
Hg19::chr5:91690025..91690036,+	p@chr5:91690025..91690036 +
Hg19::chr6:113330168..113330197,-	p@chr6:113330168..113330197 -
Hg19::chr6:125589278..125589288,+	p@chr6:125589278..125589288 +
Hg19::chr6:135196569..135196573,-	p@chr6:135196569..135196573 -
Hg19::chr6:141742789..141742801,+	p@chr6:141742789..141742801 +
Hg19::chr6:141743015..141743025,+	p@chr6:141743015..141743025 +
Hg19::chr6:14777773..14777808,-	p@chr6:14777773..14777808 -
Hg19::chr6:158461610..158461622,+	p@chr6:158461610..158461622 +
Hg19::chr6:161724933..161724947,+	p@chr6:161724933..161724947 +
Hg19::chr6:83673328..83673334,-	p@chr6:83673328..83673334 -
Hg19::chr7:134212226..134212234,+	p5@AKR1B10
Hg19::chr7:39636570..39636595,-	p@chr7:39636570..39636595 -
Hg19::chr7:83045406..83045430,+	p@chr7:83045406..83045430 +
Hg19::chr8:103549284..103549319,-	p@chr8:103549284..103549319 -
Hg19::chr8:117415998..117416010,-	p1@ENST00000523110
Hg19::chr8:117416058..117416064,-	p2@ENST00000523110
Hg19::chr8:17663434..17663445,-	p@chr8:17663434..17663445 -
Hg19::chr8:23918084..23918100,-	p@chr8:23918084..23918100 -
Hg19::chr8:32579302..32579316,+	p9@NRG1
Hg19::chr8:32579321..32579340,+	p10@NRG1
Hg19::chr8:32579341..32579372,+	p2@NRG1
Hg19::chr8:62789354..62789363,-	p@chr8:62789354..62789363 -
Hg19::chr8:74573966..74573994,-	p@chr8:74573966..74573994 -
Hg19::chr9:123163075..123163103,-	p17@CDK5RAP2
Hg19::chr9:123163148..123163176,-	p18@CDK5RAP2
Hg19::chr9:123165453..123165477,-	p6@CDK5RAP2
Hg19::chr9:123165478..123165498,-	p2@CDK5RAP2
Hg19::chr9:123165508..123165509,-	p20@CDK5RAP2
Hg19::chr9:123165545..123165560,-	p3@CDK5RAP2
Hg19::chr9:123165695..123165711,-	p11@CDK5RAP2
Hg19::chr9:123165748..123165770,-	p5@CDK5RAP2
Hg19::chr9:123165778..123165799,-	p8@CDK5RAP2
Hg19::chr9:33233082..33233096,+	p@chr9:33233082..33233096 +
Hg19::chr9:98577619..98577666,+	p@chr9:98577619..98577666 +
Hg19::chrX:153770412..153770420,+	p22@IKBKG
Hg19::chrX:38429930..38429939,+	p12@TSPAN7
Hg19::chrX:38429941..38429957,+	p6@TSPAN7
Hg19::chrX:38429964..38429975,+	p11@TSPAN7

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
3.08879411926494e-05	0.00977603338747354	2	9	Benzo(a)pyrene metabolism (Wikipathways):WP696
2.14511302572539e-05	0.00977603338747354	4	175	metapathway biotransformation (Wikipathways):WP702
0.000178921968614274	0.0377525353776118	2	21	{POU2F1,21} (Static Module):NA

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:0047026	3-alpha-hydroxysteroid dehydrogenase (A-specific) activity	0.000196426050335292
GO:0047115	trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity	0.000294517646387335
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.000495130272441399
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	0.000495130272441399
GO:0004033	aldo-keto reductase activity	0.00258215931067551
GO:0016628	oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor	0.00331866359094554
GO:0006693	prostaglandin metabolic process	0.00331866359094554
GO:0006692	prostanoid metabolic process	0.00331866359094554
GO:0005737	cytoplasm	0.00908720129811135
GO:0016229	steroid dehydrogenase activity	0.00962304248041086
GO:0044265	cellular macromolecule catabolic process	0.0158728621380326
GO:0006690	icosanoid metabolic process	0.0196592456954908
GO:0047017	prostaglandin-F synthase activity	0.0233314313144762
GO:0009057	macromolecule catabolic process	0.0243425548611502
GO:0032052	bile acid binding	0.0384079954882468
GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	0.0384079954882468
GO:0008283	cell proliferation	0.0384079954882468
GO:0007586	digestion	0.0395363767192471
GO:0044248	cellular catabolic process	0.0395363767192471
GO:0042808	neuronal Cdc2-like kinase binding	0.0395363767192471
GO:0030297	transmembrane receptor protein tyrosine kinase activator activity	0.0395363767192471
GO:0047045	testosterone 17-beta-dehydrogenase (NADP+) activity	0.0395363767192471
GO:0047756	chondroitin 4-sulfotransferase activity	0.0395363767192471
GO:0032501	multicellular organismal process	0.046617552219066
GO:0050327	testosterone 17-beta-dehydrogenase activity	0.046617552219066
GO:0030971	receptor tyrosine kinase binding	0.046617552219066

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	8.22e-23	679
eukaryotic cell	8.22e-23	679
native cell	3.13e-16	722
non-terminally differentiated cell	8.41e-10	180
classical monocyte	4.35e-09	45
fibroblast	6.50e-09	75
multi fate stem cell	1.93e-08	430
monopoietic cell	2.13e-08	63
monocyte	2.13e-08	63
monoblast	2.13e-08	63
promonocyte	2.13e-08	63
somatic cell	2.88e-08	591
CD14-positive, CD16-negative classical monocyte	6.88e-08	42
somatic stem cell	8.84e-08	436
macrophage dendritic cell progenitor	1.63e-07	65
myeloid lineage restricted progenitor cell	2.01e-07	70
stem cell	6.73e-07	444
mesothelial cell	9.63e-07	19

Uber Anatomy

Ontology term	p-value	n
mesoderm	9.86e-12	448
mesoderm-derived structure	9.86e-12	448
presumptive mesoderm	9.86e-12	448
musculoskeletal system	6.72e-09	167
multi-cellular organism	3.82e-07	659
bone marrow	4.37e-07	80

Disease

Ontology term	p-value	n
carcinoma	1.16e-10	106

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
CEBPB#1051	46	2.58220275202776	5.9558087765293e-10	5.71183391011886e-08
EP300#2033	49	2.33748693369674	3.79787354777007e-09	3.11583751339795e-07
FOS#2353	38	2.40790353336611	1.9390957584687e-07	1.05477719749329e-05
FOSL1#8061	11	3.07640406253594	0.000997151674183716	0.0071491400906208
FOSL2#2355	16	1.90762823713371	0.00997744027680398	0.037426689356696
JUN#3725	33	2.90791100948661	2.03666225375693e-08	1.45093430504856e-06
JUNB#3726	13	2.80238186322306	0.000824549589131977	0.00627524116733619
JUND#3727	54	2.65994262578194	2.55805097394752e-12	3.44722949249168e-10
MAFF#23764	15	5.94880526302238	4.40808559252356e-08	2.88999404392698e-06
MAFK#7975	36	6.87060840113998	3.18013373121331e-20	8.18054154566962e-18
NFE2#4778	17	9.24276359913869	6.73642927467144e-12	8.59030448128707e-10
NR3C1#2908	40	4.21775305103466	3.38099307939824e-15	6.04636192156288e-13
STAT3#6774	35	2.59282587958027	1.17357416348617e-07	6.77165260001836e-06
TFAP2C#7022	22	1.67466922124595	0.0114525610452804	0.04189911454822

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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