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Coexpression cluster:C118

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Full id: C118_cerebellum_parietal_occipital_medial_middle_frontal_insula



Phase1 CAGE Peaks

  Short description
Hg19::chr10:105037220..105037227,+ p12@INA
Hg19::chr10:18689498..18689550,+ p6@CACNB2
Hg19::chr10:24911746..24911793,- p6@ARHGAP21
Hg19::chr10:25463662..25463680,+ p1@GPR158
Hg19::chr10:25463691..25463702,+ p5@GPR158
Hg19::chr10:25463726..25463735,+ p6@GPR158
Hg19::chr10:62149714..62149724,- p34@ANK3
Hg19::chr10:65281549..65281566,- p@chr10:65281549..65281566
-
Hg19::chr11:105480715..105480735,+ p6@GRIA4
Hg19::chr11:105480793..105480845,+ p3@GRIA4
Hg19::chr11:119019778..119019795,+ p2@ABCG4
Hg19::chr11:132714823..132714843,- p@chr11:132714823..132714843
-
Hg19::chr11:132813716..132813736,- p14@OPCML
Hg19::chr11:17172291..17172318,- p@chr11:17172291..17172318
-
Hg19::chr11:17756279..17756367,+ p1@KCNC1
Hg19::chr11:47616210..47616237,- p4@C1QTNF4
Hg19::chr11:66025938..66025957,+ p9@KLC2
Hg19::chr11:66790693..66790733,+ p2@SYT12
Hg19::chr11:94134581..94134594,- p1@GPR83
Hg19::chr12:100378459..100378530,- p6@ANKS1B
Hg19::chr12:108523053..108523101,+ p1@WSCD2
Hg19::chr12:108525551..108525568,+ p4@WSCD2
Hg19::chr12:119419159..119419192,+ p5@SRRM4
Hg19::chr12:132904597..132904617,+ p@chr12:132904597..132904617
+
Hg19::chr12:132906118..132906180,- p1@GALNT9
Hg19::chr12:3601977..3601990,- p1@uc001qmd.1
Hg19::chr12:52214727..52214749,- p@chr12:52214727..52214749
-
Hg19::chr13:103054704..103054731,- p2@FGF14-IT1
Hg19::chr14:24047796..24047818,- p10@JPH4
Hg19::chr14:27067258..27067276,- p3@NOVA1
Hg19::chr15:31658288..31658338,+ p4@KLF13
Hg19::chr15:31658340..31658347,+ p34@KLF13
Hg19::chr15:37391438..37391479,+ p1@ENST00000559509
Hg19::chr15:40650463..40650527,+ p1@DISP2
Hg19::chr16:31004138..31004144,+ p@chr16:31004138..31004144
+
Hg19::chr16:330675..330686,+ p3@PDIA2
p4@ARHGDIG
Hg19::chr16:6069299..6069316,+ p18@RBFOX1
Hg19::chr16:6069333..6069361,+ p10@RBFOX1
Hg19::chr16:6069840..6069851,+ p31@RBFOX1
Hg19::chr16:87636569..87636577,+ p6@JPH3
Hg19::chr17:19314532..19314563,+ p1@RNF112
Hg19::chr17:2658922..2658963,+ p@chr17:2658922..2658963
+
Hg19::chr17:43319081..43319146,- p1@AK096807
Hg19::chr17:48207115..48207152,- p4@SAMD14
Hg19::chr17:50235163..50235180,- p16@CA10
Hg19::chr17:50235879..50235899,- p14@CA10
Hg19::chr17:50237348..50237373,- p5@CA10
Hg19::chr17:50237374..50237388,- p9@CA10
Hg19::chr17:72857858..72857869,- p@chr17:72857858..72857869
-
Hg19::chr17:7452189..7452207,+ p3@TNFSF12-TNFSF13
p3@TNFSF12
Hg19::chr17:77090555..77090587,- p@chr17:77090555..77090587
-
Hg19::chr17:79373129..79373161,+ p3@BAHCC1
Hg19::chr17:80656875..80656912,+ p@chr17:80656875..80656912
+
Hg19::chr18:3874247..3874262,- p9@DLGAP1
Hg19::chr18:3874271..3874337,- p3@DLGAP1
Hg19::chr18:44336896..44336907,+ p@chr18:44336896..44336907
+
Hg19::chr19:13106465..13106477,+ p27@NFIX
Hg19::chr19:13616887..13616912,- p10@CACNA1A
Hg19::chr19:13617037..13617069,- p4@CACNA1A
Hg19::chr19:13618233..13618292,- p@chr19:13618233..13618292
-
Hg19::chr19:30019801..30019814,+ p@chr19:30019801..30019814
+
Hg19::chr19:3987889..3987898,- p@chr19:3987889..3987898
-
Hg19::chr19:41036371..41036417,+ p1@SPTBN4
Hg19::chr19:42817511..42817522,+ p6@TMEM145
Hg19::chr19:42817550..42817569,+ p3@TMEM145
Hg19::chr19:44139537..44139540,+ p@chr19:44139537..44139540
+
Hg19::chr1:11714458..11714482,+ p2@FBXO44
Hg19::chr1:174768671..174768682,+ p29@RABGAP1L
Hg19::chr1:174769436..174769459,+ p15@RABGAP1L
Hg19::chr1:205414261..205414293,- p@chr1:205414261..205414293
-
Hg19::chr1:2398876..2398928,+ p1@PLCH2
Hg19::chr1:244211767..244211800,+ p@chr1:244211767..244211800
+
Hg19::chr20:10289444..10289460,+ p@chr20:10289444..10289460
+
Hg19::chr20:3767547..3767623,+ p4@CDC25B
Hg19::chr20:3767689..3767696,+ p8@CDC25B
Hg19::chr20:44036054..44036086,- p1@AK098015
Hg19::chr20:44937047..44937095,- p1@CDH22
Hg19::chr20:44937096..44937105,- p7@CDH22
Hg19::chr20:45980455..45980466,- p24@ZMYND8
Hg19::chr20:9819653..9819663,- p5@PAK7
Hg19::chr22:18958039..18958055,+ p2@DGCR5
Hg19::chr22:37099555..37099599,- p2@CACNG2
Hg19::chr22:51066685..51066719,+ p@chr22:51066685..51066719
+
Hg19::chr2:100721281..100721307,- p5@AFF3
Hg19::chr2:152830428..152830439,- p7@CACNB4
Hg19::chr2:152830441..152830472,- p2@CACNB4
Hg19::chr2:152830479..152830503,- p3@CACNB4
Hg19::chr2:155553962..155553969,+ p@chr2:155553962..155553969
+
Hg19::chr2:155554040..155554063,+ p@chr2:155554040..155554063
+
Hg19::chr2:155555201..155555272,+ p1@KCNJ3
Hg19::chr2:173600040..173600056,+ p20@RAPGEF4
Hg19::chr2:17773946..17773949,+ p@chr2:17773946..17773949
+
Hg19::chr2:183387533..183387548,- p7@PDE1A
Hg19::chr2:197457394..197457421,- p12@HECW2
Hg19::chr2:210636313..210636335,+ p3@UNC80
Hg19::chr2:2328418..2328441,- p13@MYT1L
Hg19::chr2:39893140..39893164,+ p8@TMEM178
Hg19::chr2:39893171..39893182,+ p13@TMEM178
Hg19::chr2:47798782..47798832,- p@chr2:47798782..47798832
-
Hg19::chr2:50201327..50201339,- p18@NRXN1
Hg19::chr3:113251885..113251917,+ p4@SIDT1
Hg19::chr3:120627034..120627102,+ p1@STXBP5L
Hg19::chr3:120627517..120627530,+ p2@STXBP5L
Hg19::chr3:120989095..120989099,+ p@chr3:120989095..120989099
+
Hg19::chr3:132843652..132843709,+ p3@TMEM108
Hg19::chr3:138153411..138153433,+ p2@ESYT3
Hg19::chr3:173113898..173113949,+ p4@NLGN1
Hg19::chr3:182833946..182833990,- p5@MCCC1
Hg19::chr3:184098065..184098119,+ p1@CHRD
Hg19::chr3:186080012..186080030,- p1@DGKG
Hg19::chr3:186080056..186080061,- p5@DGKG
Hg19::chr3:35722538..35722559,+ p27@ARPP21
Hg19::chr3:37903001..37903039,+ p6@CTDSPL
Hg19::chr3:52489503..52489540,+ p2@NISCH
Hg19::chr3:96532248..96532290,+ p@chr3:96532248..96532290
+
Hg19::chr4:103998320..103998345,- p10@SLC9B2
Hg19::chr4:114038052..114038059,+ p34@ANK2
Hg19::chr4:118955635..118955655,+ p3@NDST3
Hg19::chr5:110559790..110559803,+ p11@CAMK4
Hg19::chr5:110559929..110559940,+ p8@CAMK4
Hg19::chr5:110559941..110559952,+ p4@CAMK4
Hg19::chr5:138211051..138211072,- p3@LRRTM2
Hg19::chr5:156772748..156772774,- p3@FNDC9
Hg19::chr5:160975364..160975379,- p5@GABRB2
Hg19::chr5:19873309..19873311,- p@chr5:19873309..19873311
-
Hg19::chr5:19988288..19988330,- p1@CDH18
Hg19::chr5:41510865..41510886,- p4@PLCXD3
Hg19::chr5:87981322..87981337,- p@chr5:87981322..87981337
-
Hg19::chr5:94620239..94620258,- p6@MCTP1
Hg19::chr6:101846679..101846702,+ p1@GRIK2
Hg19::chr6:101846725..101846734,+ p17@GRIK2
Hg19::chr6:69345285..69345308,+ p2@BAI3
Hg19::chr6:69345833..69345845,+ p8@BAI3
Hg19::chr6:72596229..72596272,+ p2@RIMS1
Hg19::chr6:72596410..72596454,+ p4@RIMS1
Hg19::chr6:72596604..72596697,+ p1@RIMS1
Hg19::chr7:151511911..151511962,- p9@PRKAG2
Hg19::chr7:28997721..28997738,- p3@TRIL
Hg19::chr7:71801984..71802013,- p3@CALN1
Hg19::chr8:10158687..10158707,+ p4@MSRA
Hg19::chr8:132928997..132929025,+ p@chr8:132928997..132929025
+
Hg19::chr8:15095883..15095918,- p1@SGCZ
Hg19::chr8:15095933..15095945,- p3@SGCZ
Hg19::chr8:85095907..85095910,+ p5@RALYL
Hg19::chr8:9761882..9761897,- p3@ENST00000521863
Hg19::chr8:9776628..9776670,- -
p@chr8:9776628..9776670
Hg19::chr8:9911618..9911629,+ p8@MSRA
Hg19::chr8:9953920..9953944,+ p@chr8:9953920..9953944
+
Hg19::chr9:100264031..100264042,+ p4@TMOD1
Hg19::chr9:15250159..15250231,- p2@TTC39B
Hg19::chr9:79307096..79307129,- p2@PRUNE2
Hg19::chrX:123510693..123510711,- p1@ODZ1
Hg19::chrX:21392356..21392365,+ p7@CNKSR2


Enriched pathways on this co-expression cluster
Summary:


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.
Analyst: Emmanuel Dimont

link to source dataset


data

p.valueFDRnGenesnPathwayName
3.21588558482119e-050.006785518583972715126Glutamatergic synapse (KEGG):04724
9.77861502511732e-050.0123824018731482483Hypertrophic cardiomyopathy (HCM) (KEGG):05410
0.0001066964919002110.0123824018731482332Hypothetical Network for Drug Addiction (Wikipathways):WP666
2.70775915789819e-101.71401154694955e-0710197Synaptic Transmission (Reactome):REACT_13685
0.0004706991269927620.04256464962663124125Integration of energy metabolism (Reactome):REACT_1505
0.0001173687381341060.01238240187314826265Axon guidance (Reactome):REACT_18266
9.00885823625835e-070.000285130363177577426{RASGRF1,26} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster
Summary: 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.
Analyst: Erik Arner



link to source dataset


data

GO IDGO nameFDR corrected p-value
GO:0005886plasma membrane2.52069622669271e-06
GO:0030054cell junction1.17290317297813e-05
GO:0044425membrane part1.73607675976265e-05
GO:0044459plasma membrane part1.96924833961766e-05
GO:0016021integral to membrane2.96607884633392e-05
GO:0031224intrinsic to membrane2.96607884633392e-05
GO:0016020membrane2.96607884633392e-05
GO:0019226transmission of nerve impulse5.52398222233686e-05
GO:0005891voltage-gated calcium channel complex9.62884579184354e-05
GO:0044456synapse part0.000100003913961408
GO:0022836gated channel activity0.000100003913961408
GO:0007268synaptic transmission0.000195909142086055
GO:0005245voltage-gated calcium channel activity0.000735829937860229
GO:0005216ion channel activity0.000774514386210364
GO:0045211postsynaptic membrane0.000774514386210364
GO:0022838substrate specific channel activity0.000774514386210364
GO:0022843voltage-gated cation channel activity0.000774514386210364
GO:0022803passive transmembrane transporter activity0.000774514386210364
GO:0015267channel activity0.000774514386210364
GO:0005509calcium ion binding0.00232511436195309
GO:0022832voltage-gated channel activity0.00232511436195309
GO:0005244voltage-gated ion channel activity0.00232511436195309
GO:0007267cell-cell signaling0.00232511436195309
GO:0050808synapse organization and biogenesis0.00235257978902726
GO:0016079synaptic vesicle exocytosis0.00325202505564878
GO:0007154cell communication0.00325202505564878
GO:0005262calcium channel activity0.00336573353867295
GO:0007528neuromuscular junction development0.00483663614046024
GO:0005261cation channel activity0.00737641660664985
GO:0048489synaptic vesicle transport0.015006921745046
GO:0006816calcium ion transport0.015006921745046
GO:0046873metal ion transmembrane transporter activity0.0164919554253955
GO:0043062extracellular structure organization and biogenesis0.0166120175719292
GO:0005200structural constituent of cytoskeleton0.0166869234776399
GO:0006790sulfur metabolic process0.0166902838132157
GO:0005515protein binding0.0166902838132157
GO:0007215glutamate signaling pathway0.0168140216446291
GO:0044464cell part0.0192693977562345
GO:0008066glutamate receptor activity0.0194643442025702
GO:0006887exocytosis0.0305731989543396
GO:0006810transport0.0318329478143315
GO:0048172regulation of short-term neuronal synaptic plasticity0.0318329478143315
GO:0031557induction of programmed cell death in response to chemical stimulus0.0318329478143315
GO:0015674di-, tri-valent inorganic cation transport0.0318329478143315
GO:0015075ion transmembrane transporter activity0.0348655253979806
GO:0004970ionotropic glutamate receptor activity0.0399196833593958
GO:0006811ion transport0.0399196833593958
GO:0051234establishment of localization0.0399196833593958
GO:0005230extracellular ligand-gated ion channel activity0.0399196833593958
GO:0051179localization0.0414994901283276
GO:0005234extracellular-glutamate-gated ion channel activity0.0419511124508003
GO:0007269neurotransmitter secretion0.042722762846028
GO:0008081phosphoric diester hydrolase activity0.042722762846028
GO:0048741skeletal muscle fiber development0.0443533759491619
GO:0048747muscle fiber development0.0443533759491619
GO:0005856cytoskeleton0.0443533759491619
GO:0030001metal ion transport0.0443533759491619
GO:0006552leucine catabolic process0.0457689282451179
GO:0006768biotin metabolic process0.0457689282451179
GO:0016080synaptic vesicle targeting0.0457689282451179
GO:0004485methylcrotonoyl-CoA carboxylase activity0.0457689282451179



Enriched sample ontology terms on this co-expression cluster
Summary: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. Analyst: Hideya Kawaji



links to source dataset


uberon_data



Uber Anatomy
Ontology termp-valuen
neural tube2.41e-12856
neural rod2.41e-12856
future spinal cord2.41e-12856
neural keel2.41e-12856
regional part of nervous system3.00e-11953
regional part of brain3.00e-11953
central nervous system1.25e-10481
brain1.90e-9868
future brain1.90e-9868
regional part of forebrain1.43e-9741
forebrain1.43e-9741
anterior neural tube1.43e-9741
future forebrain1.43e-9741
nervous system6.51e-9789
neural plate2.65e-8882
presumptive neural plate2.65e-8882
telencephalon3.64e-8834
brain grey matter4.11e-8834
gray matter4.11e-8834
neurectoderm1.01e-8386
cerebral hemisphere1.81e-8232
regional part of telencephalon5.08e-8232
regional part of cerebral cortex1.25e-6922
ecto-epithelium2.05e-67104
pre-chordal neural plate1.08e-6661
adult organism6.26e-64114
neocortex2.02e-6320
cerebral cortex6.92e-6125
pallium6.92e-6125
structure with developmental contribution from neural crest1.17e-55132
ectoderm-derived structure1.26e-47171
ectoderm1.26e-47171
presumptive ectoderm1.26e-47171
organ system subdivision1.97e-35223
tube1.89e-31192
posterior neural tube6.07e-3015
chordal neural plate6.07e-3015
basal ganglion1.29e-289
nuclear complex of neuraxis1.29e-289
aggregate regional part of brain1.29e-289
collection of basal ganglia1.29e-289
cerebral subcortex1.29e-289
neural nucleus3.24e-289
nucleus of brain3.24e-289
anatomical conduit6.63e-23240
telencephalic nucleus2.39e-227
segmental subdivision of hindbrain9.06e-2212
hindbrain9.06e-2212
presumptive hindbrain9.06e-2212
gyrus1.30e-216
segmental subdivision of nervous system5.87e-2013
anatomical cluster2.58e-19373
brainstem2.65e-196
occipital lobe6.11e-185
temporal lobe8.11e-186
parietal lobe9.24e-185
limbic system3.04e-175
epithelium1.84e-16306
cell layer3.44e-16309
organ part1.57e-15218
corpus striatum4.13e-144
striatum4.13e-144
ventral part of telencephalon4.13e-144
future corpus striatum4.13e-144
regional part of metencephalon9.20e-149
metencephalon9.20e-149
future metencephalon9.20e-149
multi-tissue structure1.13e-12342
frontal cortex9.10e-123
diencephalon3.59e-117
future diencephalon3.59e-117
caudate-putamen6.51e-113
dorsal striatum6.51e-113
pons1.11e-103
medulla oblongata2.39e-103
myelencephalon2.39e-103
future myelencephalon2.39e-103
spinal cord3.31e-103
dorsal region element3.31e-103
dorsum3.31e-103
organ4.95e-09503
middle temporal gyrus1.69e-082
middle frontal gyrus2.33e-082
embryo3.68e-08592
germ layer4.64e-08560
germ layer / neural crest4.64e-08560
embryonic tissue4.64e-08560
presumptive structure4.64e-08560
germ layer / neural crest derived structure4.64e-08560
epiblast (generic)4.64e-08560
amygdala5.59e-082
developing anatomical structure6.45e-08581
embryonic structure6.50e-08564
caudate nucleus7.88e-082
future caudate nucleus7.88e-082
Ammon's horn9.34e-082
lobe parts of cerebral cortex9.34e-082
hippocampal formation9.34e-082
limbic lobe9.34e-082
regional part of diencephalon1.11e-074


Overrepresented TFBS (DNA) motifs on this co-expression cluster
Summary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs

data

Novel motifs


JASPAR motifs
Motifs-log10(p-value)
MA0003.113.2451
MA0004.10.00496355
MA0006.13.53795
MA0007.10.587552
MA0009.10.0388877
MA0014.111.0588
MA0017.10.401652
MA0019.10.0980324
MA0024.10.209026
MA0025.10.581023
MA0027.11.26202
MA0028.10.0141074
MA0029.10.093339
MA0030.10.418709
MA0031.10.147879
MA0038.10.0623951
MA0040.10.239834
MA0041.10.282244
MA0042.10.124598
MA0043.10.632701
MA0046.10.03626
MA0048.14.73454
MA0050.10.207691
MA0051.10.530364
MA0052.10.0992373
MA0055.19.81063
MA0056.10
MA0057.14.17896
MA0058.10.00711556
MA0059.10.00691374
MA0060.10.115344
MA0061.10.216394
MA0063.10
MA0066.10.023972
MA0067.10.500379
MA0068.10.798421
MA0069.10.141138
MA0070.10.132824
MA0071.10.413501
MA0072.10.306304
MA0073.121.7327
MA0074.10.0590845
MA0076.10.000877415
MA0077.10.0301867
MA0078.10.0208972
MA0081.10.18597
MA0083.10.0407684
MA0084.10.77642
MA0087.10.302806
MA0088.10.915528
MA0089.10
MA0090.11.58588
MA0091.10.0835774
MA0092.10.0500079
MA0093.10.00040018
MA0095.10
MA0098.10
MA0100.10.259171
MA0101.10.187191
MA0103.10.146766
MA0105.11.16156
MA0106.10.0945562
MA0107.10.0458457
MA0108.20.144905
MA0109.10
MA0111.11.20354
MA0113.10.109763
MA0114.10.148757
MA0115.10.400693
MA0116.10.535387
MA0117.10.411069
MA0119.10.0529522
MA0122.10.454558
MA0124.10.108113
MA0125.10.0740881
MA0130.10
MA0131.10.313346
MA0132.10
MA0133.10
MA0135.10.0468355
MA0136.10.00704588
MA0139.12.59291
MA0140.10.265642
MA0141.10.181407
MA0142.10.43205
MA0143.10.357511
MA0144.10.0152101
MA0145.10.570727
MA0146.11.74456
MA0147.10.560948
MA0148.10.189327
MA0149.10.539444
MA0062.20.00270268
MA0035.20.0843735
MA0039.21.32519
MA0138.21.25155
MA0002.20.170947
MA0137.20.00252811
MA0104.20.690544
MA0047.20.084197
MA0112.21.15151
MA0065.20.110249
MA0150.10.101973
MA0151.10
MA0152.10.0913819
MA0153.10.240551
MA0154.11.10394
MA0155.13.42796
MA0156.10.00739187
MA0157.10.36998
MA0158.10
MA0159.10.131321
MA0160.10.128718
MA0161.10
MA0162.113.2821
MA0163.113.1343
MA0164.10.586218
MA0080.20.0014469
MA0018.20.0392078
MA0099.20.0150312
MA0079.237.8476
MA0102.20.31059
MA0258.10.0582441
MA0259.10.293789
MA0442.10


ENCODE TF ChIP-seq peak enrichment analysis
Summary: 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.
Analyst: Erik Arner



link to source dataset


data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488124.918980418770837.36337494877413e-060.000211386343121226
CTCF#10664451.576545992080890.0008376231428620510.00631902076115066
RAD21#5885332.233438683333728.74177219459004e-060.00023597362270116
SUZ12#23512103.275541236017180.001075595966564580.00759579195023588
ZNF263#10127321.719600865257140.001484676973091750.00949529567622349



Relative expression of the co-expression cluster
Summary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data