Coexpression cluster:C150

Full id: C150_merkel_carcinoid_nonsmall_gastrointestinal_argyrophil_pineal_small

Phase1 CAGE Peaks

Hg19::chr11:31312303..31312307,-	p@chr11:31312303..31312307 -
Hg19::chr11:31312513..31312524,-	p@chr11:31312513..31312524 -
Hg19::chr12:54779280..54779298,-	p10@ZNF385A
Hg19::chr12:54786411..54786421,-	p@chr12:54786411..54786421 -
Hg19::chr12:65175253..65175283,-	p@chr12:65175253..65175283 -
Hg19::chr12:660023..660044,+	p@chr12:660023..660044 +
Hg19::chr12:70093235..70093242,-	p6@BEST3
Hg19::chr13:79169067..79169071,-	p@chr13:79169067..79169071 -
Hg19::chr13:79177629..79177636,-	p4@POU4F1
Hg19::chr13:79177674..79177701,-	p1@POU4F1
Hg19::chr14:106331164..106331201,-	p2@IGHJ2P
Hg19::chr15:46610951..46610964,+	p@chr15:46610951..46610964 +
Hg19::chr15:68114974..68114985,+	p@chr15:68114974..68114985 +
Hg19::chr15:68117844..68117858,+	p3@SKOR1
Hg19::chr15:68124190..68124195,-	p@chr15:68124190..68124195 -
Hg19::chr16:3005195..3005202,-	p@chr16:3005195..3005202 -
Hg19::chr16:53653257..53653264,-	p@chr16:53653257..53653264 -
Hg19::chr16:67429759..67429769,-	p@chr16:67429759..67429769 -
Hg19::chr16:70207349..70207353,-	p1@ENST00000502126 p1@uc002eyi.1
Hg19::chr16:70207686..70207690,+	p1@CLEC18C
Hg19::chr17:18012062..18012075,+	p1@MYO15A
Hg19::chr17:48049323..48049330,+	p6@DLX4
Hg19::chr17:61554829..61554849,+	p@chr17:61554829..61554849 +
Hg19::chr17:61573742..61573786,+	p@chr17:61573742..61573786 +
Hg19::chr17:61600483..61600515,+	p2@KCNH6
Hg19::chr17:61600682..61600740,+	p1@KCNH6
Hg19::chr17:61603769..61603773,+	p@chr17:61603769..61603773 +
Hg19::chr18:5197501..5197504,-	p3@C18orf42
Hg19::chr18:77543021..77543032,-	p@chr18:77543021..77543032 -
Hg19::chr18:77543062..77543072,-	p@chr18:77543062..77543072 -
Hg19::chr19:39401676..39401683,-	p@chr19:39401676..39401683 -
Hg19::chr19:39402817..39402833,-	p1@LOC643669
Hg19::chr19:47138167..47138185,-	p1@GNG8
Hg19::chr19:47139424..47139443,-	p@chr19:47139424..47139443 -
Hg19::chr19:49928618..49928665,+	p@chr19:49928618..49928665 +
Hg19::chr19:49928666..49928692,+	p@chr19:49928666..49928692 +
Hg19::chr19:57599766..57599777,+	p@chr19:57599766..57599777 +
Hg19::chr1:155048200..155048207,+	p@chr1:155048200..155048207 +
Hg19::chr1:160342039..160342041,+	p@chr1:160342039..160342041 +
Hg19::chr1:17026663..17026700,-	p@chr1:17026663..17026700 -
Hg19::chr1:216196797..216196801,-	p@chr1:216196797..216196801 -
Hg19::chr1:216595350..216595395,-	p@chr1:216595350..216595395 -
Hg19::chr1:242843433..242843446,-	p@chr1:242843433..242843446 -
Hg19::chr1:40769918..40769923,-	p@chr1:40769918..40769923 -
Hg19::chr1:40770344..40770353,-	p29@COL9A2
Hg19::chr1:92949195..92949210,-	p7@GFI1
Hg19::chr1:92949213..92949223,-	p9@GFI1
Hg19::chr20:31116333..31116338,-	p@chr20:31116333..31116338 -
Hg19::chr20:49727833..49727839,-	p@chr20:49727833..49727839 -
Hg19::chr20:49727891..49727898,-	p@chr20:49727891..49727898 -
Hg19::chr20:49727900..49727904,-	p@chr20:49727900..49727904 -
Hg19::chr20:7391944..7391948,+	p@chr20:7391944..7391948 +
Hg19::chr2:194367490..194367523,+	p@chr2:194367490..194367523 +
Hg19::chr2:197078770..197078778,+	p@chr2:197078770..197078778 +
Hg19::chr2:197080808..197080817,-	p@chr2:197080808..197080817 -
Hg19::chr2:197081754..197081790,-	p@chr2:197081754..197081790 -
Hg19::chr2:200325452..200325462,-	p33@SATB2
Hg19::chr2:219846948..219846958,-	p@chr2:219846948..219846958 -
Hg19::chr2:239149300..239149321,-	p2@HES6
Hg19::chr2:96782288..96782301,-	p2@ADRA2B
Hg19::chr2:96782304..96782315,-	p1@ADRA2B
Hg19::chr3:181980650..181980653,-	p@chr3:181980650..181980653 -
Hg19::chr3:182129789..182129798,-	p@chr3:182129789..182129798 -
Hg19::chr3:182129807..182129809,-	p@chr3:182129807..182129809 -
Hg19::chr3:182129895..182129901,-	p@chr3:182129895..182129901 -
Hg19::chr3:182129918..182129932,-	p@chr3:182129918..182129932 -
Hg19::chr3:182262882..182262922,-	p@chr3:182262882..182262922 -
Hg19::chr3:192232532..192232549,-	p@chr3:192232532..192232549 -
Hg19::chr3:85827683..85827691,+	p@chr3:85827683..85827691 +
Hg19::chr3:85829954..85829989,-	p@chr3:85829954..85829989 -
Hg19::chr4:132456095..132456124,-	p@chr4:132456095..132456124 -
Hg19::chr4:173606828..173606840,-	p@chr4:173606828..173606840 -
Hg19::chr4:17783004..17783015,-	p3@FAM184B
Hg19::chr4:17783228..17783250,-	p1@FAM184B
Hg19::chr4:6356121..6356152,-	p@chr4:6356121..6356152 -
Hg19::chr4:77155662..77155702,-	p@chr4:77155662..77155702 -
Hg19::chr4:94749897..94749909,+	p1@ATOH1
Hg19::chr4:94750014..94750025,+	p2@ATOH1
Hg19::chr4:94751839..94751843,+	p@chr4:94751839..94751843 +
Hg19::chr4:94997408..94997423,-	p@chr4:94997408..94997423 -
Hg19::chr5:145718398..145718410,+	p1@POU4F3
Hg19::chr5:145718596..145718607,+	p2@POU4F3
Hg19::chr5:145722450..145722456,+	p@chr5:145722450..145722456 +
Hg19::chr5:145724630..145724641,+	p@chr5:145724630..145724641 +
Hg19::chr5:145724642..145724652,+	p@chr5:145724642..145724652 +
Hg19::chr5:145808948..145808956,+	p@chr5:145808948..145808956 +
Hg19::chr5:168853885..168853910,-	p@chr5:168853885..168853910 -
Hg19::chr5:50674304..50674338,-	p@chr5:50674304..50674338 -
Hg19::chr5:63986233..63986261,+	p2@FAM159B
Hg19::chr5:63986324..63986342,+	p1@FAM159B
Hg19::chr5:64369050..64369067,+	p@chr5:64369050..64369067 +
Hg19::chr5:64369069..64369083,+	p@chr5:64369069..64369083 +
Hg19::chr5:64369097..64369105,+	p@chr5:64369097..64369105 +
Hg19::chr6:112466463..112466468,+	p@chr6:112466463..112466468 +
Hg19::chr6:129930311..129930322,-	p@chr6:129930311..129930322 -
Hg19::chr6:129930348..129930359,-	p@chr6:129930348..129930359 -
Hg19::chr6:133414003..133414011,-	p@chr6:133414003..133414011 -
Hg19::chr6:152793691..152793718,-	p8@SYNE1
Hg19::chr6:168502185..168502196,-	p@chr6:168502185..168502196 -
Hg19::chr6:32862645..32862655,+	p4@ENST00000499196 p4@uc003oci.1
Hg19::chr6:34507199..34507208,-	p@chr6:34507199..34507208 -
Hg19::chr6:35773169..35773180,+	p3@LHFPL5
Hg19::chr6:50807829..50807852,+	p@chr6:50807829..50807852 +
Hg19::chr6:91865192..91865202,-	p@chr6:91865192..91865202 -
Hg19::chr7:119914647..119914684,+	p1@AB384090
Hg19::chr7:126173903..126173915,-	p@chr7:126173903..126173915 -
Hg19::chr8:137528469..137528506,+	p@chr8:137528469..137528506 +
Hg19::chr9:104302091..104302134,+	p@chr9:104302091..104302134 +
Hg19::chr9:107573173..107573188,-	p@chr9:107573173..107573188 -
Hg19::chr9:139089234..139089236,-	p@chr9:139089234..139089236 -
Hg19::chr9:139096224..139096231,-	p@chr9:139096224..139096231 -
Hg19::chr9:14346413..14346451,+	p@chr9:14346413..14346451 +
Hg19::chr9:20236750..20236767,+	p@chr9:20236750..20236767 +
Hg19::chrX:130021517..130021528,-	p@chrX:130021517..130021528 -

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:0042491	auditory receptor cell differentiation	3.448801044842e-09
GO:0042490	mechanoreceptor differentiation	3.448801044842e-09
GO:0060113	inner ear receptor cell differentiation	3.448801044842e-09
GO:0042472	inner ear morphogenesis	3.31530321747534e-08
GO:0042471	ear morphogenesis	4.75021866280329e-08
GO:0048839	inner ear development	9.26960517688193e-08
GO:0043583	ear development	1.20355517019841e-07
GO:0007423	sensory organ development	1.97531279678092e-06
GO:0048598	embryonic morphogenesis	2.40976491361931e-06
GO:0006357	regulation of transcription from RNA polymerase II promoter	2.44749855030467e-05
GO:0032990	cell part morphogenesis	3.8893567802266e-05
GO:0048858	cell projection morphogenesis	3.8893567802266e-05
GO:0030030	cell projection organization and biogenesis	3.8893567802266e-05
GO:0007275	multicellular organismal development	4.0111506662543e-05
GO:0048731	system development	4.80974703124171e-05
GO:0032502	developmental process	4.80974703124171e-05
GO:0009790	embryonic development	5.21588078337726e-05
GO:0048869	cellular developmental process	8.44270344712617e-05
GO:0030154	cell differentiation	8.44270344712617e-05
GO:0048513	organ development	8.44270344712617e-05
GO:0006366	transcription from RNA polymerase II promoter	8.8279020785022e-05
GO:0032501	multicellular organismal process	0.000106438416945446
GO:0048856	anatomical structure development	0.000140090819149837
GO:0009887	organ morphogenesis	0.000200968586353601
GO:0007409	axonogenesis	0.000200968586353601
GO:0048667	neuron morphogenesis during differentiation	0.000210154693008892
GO:0048812	neurite morphogenesis	0.000210154693008892
GO:0001708	cell fate specification	0.000210154693008892
GO:0000904	cellular morphogenesis during differentiation	0.000233770238907642
GO:0050954	sensory perception of mechanical stimulus	0.000250333507452838
GO:0007605	sensory perception of sound	0.000250333507452838
GO:0003700	transcription factor activity	0.000250333507452838
GO:0031175	neurite development	0.00025199268930492
GO:0050885	neuromuscular process controlling balance	0.00025199268930492
GO:0006355	regulation of transcription, DNA-dependent	0.000270991047338285
GO:0006351	transcription, DNA-dependent	0.000308548976568433
GO:0032774	RNA biosynthetic process	0.000308548976568433
GO:0048666	neuron development	0.000324737421023006
GO:0050905	neuromuscular process	0.000352076630921378
GO:0032989	cellular structure morphogenesis	0.000352076630921378
GO:0000902	cell morphogenesis	0.000352076630921378
GO:0045449	regulation of transcription	0.000418666594506109
GO:0009653	anatomical structure morphogenesis	0.000448975509715475
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.000448975509715475
GO:0006350	transcription	0.000522258809055618
GO:0010468	regulation of gene expression	0.000540803525951619
GO:0031323	regulation of cellular metabolic process	0.000637519357924391
GO:0030182	neuron differentiation	0.00064564947869513
GO:0016477	cell migration	0.000859842311100581
GO:0019222	regulation of metabolic process	0.000871800303826359
GO:0016070	RNA metabolic process	0.000871800303826359
GO:0048699	generation of neurons	0.000906070976962741
GO:0022008	neurogenesis	0.00111274255393528
GO:0045597	positive regulation of cell differentiation	0.00111274255393528
GO:0007399	nervous system development	0.00124687473016944
GO:0007411	axon guidance	0.00152510102005092
GO:0003677	DNA binding	0.00193362723345703
GO:0051094	positive regulation of developmental process	0.00193362723345703
GO:0045633	positive regulation of mechanoreceptor differentiation	0.00193362723345703
GO:0045609	positive regulation of auditory receptor cell differentiation	0.00193362723345703
GO:0019230	proprioception	0.00193362723345703
GO:0051355	proprioception during equilibrioception	0.00193362723345703
GO:0048934	peripheral nervous system neuron differentiation	0.00193362723345703
GO:0042660	positive regulation of cell fate specification	0.00193362723345703
GO:0042667	auditory receptor cell fate specification	0.00193362723345703
GO:0042659	regulation of cell fate specification	0.00193362723345703
GO:0010453	regulation of cell fate commitment	0.00193362723345703
GO:0009996	negative regulation of cell fate specification	0.00193362723345703
GO:0021535	cell migration in hindbrain	0.00193362723345703
GO:0010454	negative regulation of cell fate commitment	0.00193362723345703
GO:0045165	cell fate commitment	0.00193362723345703
GO:0043565	sequence-specific DNA binding	0.00201455786858099
GO:0006928	cell motility	0.00244243515136125
GO:0051674	localization of cell	0.00244243515136125
GO:0007600	sensory perception	0.00267080380076567
GO:0060088	auditory receptor cell stereocilium organization and biogenesis	0.00332701889408755
GO:0045606	positive regulation of epidermal cell differentiation	0.00332701889408755
GO:0045684	positive regulation of epidermis development	0.00332701889408755
GO:0000083	G1/S-specific transcription in mitotic cell cycle	0.00332701889408755
GO:0002093	auditory receptor cell morphogenesis	0.00332701889408755
GO:0060117	auditory receptor cell development	0.00332701889408755
GO:0031290	retinal ganglion cell axon guidance	0.00332701889408755
GO:0010467	gene expression	0.00361483690152535
GO:0050794	regulation of cellular process	0.00444716309051365
GO:0060122	inner ear receptor stereocilium organization and biogenesis	0.00444716309051365
GO:0005594	collagen type IX	0.00444716309051365
GO:0042668	auditory receptor cell fate determination	0.00444716309051365
GO:0001967	suckling behavior	0.00444716309051365
GO:0045607	regulation of auditory receptor cell differentiation	0.00444716309051365
GO:0031490	chromatin DNA binding	0.00444716309051365
GO:0060119	inner ear receptor cell development	0.00444716309051365
GO:0045631	regulation of mechanoreceptor differentiation	0.00444716309051365
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0051878503418388
GO:0007420	brain development	0.00545406274925008
GO:0048468	cell development	0.00545406274925008
GO:0048676	axon extension involved in development	0.00545406274925008
GO:0050884	neuromuscular process controlling posture	0.00545406274925008
GO:0004938	alpha2-adrenergic receptor activity	0.00545406274925008
GO:0060120	inner ear receptor cell fate commitment	0.00545406274925008
GO:0009912	auditory receptor cell fate commitment	0.00545406274925008
GO:0045595	regulation of cell differentiation	0.00552803704992555
GO:0050877	neurological system process	0.00575868598239465
GO:0005634	nucleus	0.00594071659596121
GO:0050789	regulation of biological process	0.00643815187902022
GO:0005521	lamin binding	0.00764273223252338
GO:0007638	mechanosensory behavior	0.00764273223252338
GO:0005593	FACIT collagen	0.00764273223252338
GO:0045604	regulation of epidermal cell differentiation	0.00875111188274745
GO:0021953	central nervous system neuron differentiation	0.00875111188274745
GO:0045682	regulation of epidermis development	0.0098190445325147
GO:0050957	equilibrioception	0.0098190445325147
GO:0003008	system process	0.0105738530424472
GO:0030934	anchoring collagen	0.0106938622956472
GO:0004936	alpha-adrenergic receptor activity	0.0106938622956472
GO:0065007	biological regulation	0.0106938622956472
GO:0007417	central nervous system development	0.0125548743887259
GO:0050793	regulation of developmental process	0.0125548743887259
GO:0051705	behavioral interaction between organisms	0.0138434269449018
GO:0006915	apoptosis	0.0149692882000764
GO:0012501	programmed cell death	0.0151842628104173
GO:0007030	Golgi organization and biogenesis	0.0157437484703259
GO:0004935	adrenoceptor activity	0.0167265920036523
GO:0016265	death	0.0169687109973151
GO:0008219	cell death	0.0169687109973151
GO:0007610	behavior	0.0179851279240935
GO:0048675	axon extension	0.0182029746793254
GO:0009612	response to mechanical stimulus	0.0182029746793254
GO:0048522	positive regulation of cellular process	0.0188364740872973
GO:0044464	cell part	0.0201172655834711
GO:0051179	localization	0.0215191334275471
GO:0030902	hindbrain development	0.0238460910724352
GO:0048518	positive regulation of biological process	0.0244914321799594
GO:0007422	peripheral nervous system development	0.0245036542724781
GO:0016043	cellular component organization and biogenesis	0.0251413212706414
GO:0007416	synaptogenesis	0.0251413212706414
GO:0045664	regulation of neuron differentiation	0.025771456854288
GO:0043283	biopolymer metabolic process	0.025771456854288
GO:0001709	cell fate determination	0.0284373899751289
GO:0003676	nucleic acid binding	0.0284373899751289
GO:0051402	neuron apoptosis	0.0290621776284089
GO:0000082	G1/S transition of mitotic cell cycle	0.0326766313474467
GO:0003779	actin binding	0.0339140597736452
GO:0001764	neuron migration	0.034100852326719
GO:0005834	heterotrimeric G-protein complex	0.0345575661049139
GO:0007631	feeding behavior	0.0345575661049139
GO:0006997	nuclear organization and biogenesis	0.0352412111652633
GO:0050808	synapse organization and biogenesis	0.0359151778143829
GO:0042692	muscle cell differentiation	0.0420147355717764
GO:0006811	ion transport	0.0424420126752048
GO:0009913	epidermal cell differentiation	0.044130865967173
GO:0019897	extrinsic to plasma membrane	0.0447240781727989
GO:0005581	collagen	0.0479447883679032
GO:0048730	epidermis morphogenesis	0.0485035166176686

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.20e-27	115
regional part of nervous system	1.62e-26	94
nervous system	1.62e-26	94
central nervous system	2.80e-26	82
neural tube	1.06e-22	57
neural rod	1.06e-22	57
future spinal cord	1.06e-22	57
neural keel	1.06e-22	57
brain	7.37e-21	69
future brain	7.37e-21	69
regional part of brain	1.11e-20	59
anterior neural tube	2.52e-18	42
regional part of forebrain	5.88e-18	41
forebrain	5.88e-18	41
future forebrain	5.88e-18	41
neurectoderm	4.11e-14	90
telencephalon	4.35e-14	34
gray matter	4.58e-14	34
brain grey matter	4.58e-14	34
neural plate	1.08e-13	86
presumptive neural plate	1.08e-13	86
regional part of telencephalon	1.29e-13	33
cerebral hemisphere	2.33e-13	32
ectoderm	2.99e-13	173
presumptive ectoderm	2.99e-13	173
ectoderm-derived structure	8.70e-13	169
regional part of cerebral cortex	2.10e-11	22
neocortex	1.88e-10	20
cerebral cortex	2.53e-10	25
pallium	2.53e-10	25
pre-chordal neural plate	5.93e-10	61
anterior region of body	1.89e-08	129
craniocervical region	1.89e-08	129
head	4.23e-08	123

Disease

Ontology term	p-value	n
cell type cancer	2.60e-10	143
cancer	2.70e-09	235
disease of cellular proliferation	7.22e-09	239
carcinoma	3.31e-08	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
SUZ12#23512	12	5.27534535905925	3.30230218822868e-06	0.000110399852188353

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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FF samples	Score

FF samples	Score
merkel cell carcinoma cell line:MKL-1 CNhs12838	1.31
merkel cell carcinoma cell line:MS-1 CNhs12839	0.60
carcinoid cell line:NCI-H1770 CNhs11834	0.13
Adipocyte - breast, donor1 CNhs11051	0.00
Adipocyte - breast, donor2 CNhs11969	0.00
Adipocyte - omental, donor1 CNhs11054	0.00
Adipocyte - omental, donor2 CNhs12067	0.00
Adipocyte - omental, donor3 CNhs12068	0.00
Adipocyte - perirenal, donor1 CNhs12069	0.00
Adipocyte - subcutaneous, donor1 CNhs12494	0.00

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