Analysis of human upstream open reading frames and impact on
gene expression
Yuhua Yea, Yidan Lianga, Qiuxia Yua, Lingling Hua, Haoli Lia, Zhenhai
Zhangb,c,d* & Xiangmin Xua*
a
Department of Medical Genetics, School of Basic Medical Sciences, Southern
Medical University, Guangzhou, China.
b
State Key Laboratory of Organ Failure Research and, cNational Clinical Research
Center for Kidney Disease, dDivision of Nephrology, Nanfang Hospital, Southern
Medical University, Guangzhou, Guangdong, 510515, China
Corresponding authors:
Xiangmin Xu, Department of
Medical Genetics, School of Basic Medical Sciences, Southern Medical University, G
uangzhou 510515, Guangdong, P.R. China. Tel: +86-020-61648293. Fax: +86-020-87
278766. E-mail: gzxuxm@pub.guangzhou.gd.cn
Zhenhai Zhang, Division of Nephrology, Nanfang Hospital, Southern Medical
University, Guangzhou 510515, Guangdong, P.R. China. E-mail:
zhenhaismu@163.com
Table S1. The correspondence between the substitute numbers and the tissues for Fig.
2a.
Substitute Number
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Tissue
Adult Adrenal
Adult Colon
Adult Esophagus
Adult Frontal Cortex
Adult Gallbladder
Adult Heart
Adult Kidney
Adult Liver
Adult Lung
Adult Ovary
Adult Pancreas
Adult Prostate
Adult Rectum
Adult Retina
Adult Spinal Cord
Adult Testis
Adult Urinary Bladder
B Cells
CD4 Cells
CD8 Cells
Fetal Brain
Fetal Gut
Fetal Heart
Fetal Liver
Fetal Ovary
Fetal Testis
Monocytes
NK Cells
Placenta
Platelets
100%
Minus_identical
90%
Minus_complement
80%
Plus_identical
70%
60%
50%
40%
30%
20%
10%
0%
ClinVar
COSMIC
TCGA_37
TCGA_36
Figure S1. The consistency between the reference nucleotide of each presented
variation and its corresponding position in human genome hg19. Blue bars indicate
the reference nucleotide and its hg19 corresponding position are identical given the
strand is a plus strand. Red bars indicate the reference nucleotide and its hg19
corresponding position are base-complementary given the strand is a minus strand. As
the variant records in COSMIC has divided the plus and minus strand according to
RefGene, 97.21% of the entries whose reference nucleotide and its hg19
corresponding position are always identical.
Table S2. The GO terms that uORF genes are enriched in.
GO term ID
GO term
p value
0005882
intermediate filament
3.75128E-11
0045095
keratin filament
5.9813E-11
0044822
poly(A) RNA binding
8.09032E-09
0005198
structural molecule activity
9.73258E-09
0050789
regulation of biological process
1.58522E-08
0003700
sequence-specific DNA binding transcription factor activity
2.80049E-08
0006355
regulation of transcription, DNA-templated
3.21538E-08
0001071
nucleic acid binding transcription factor activity
3.5957E-08
0065007
biological regulation
3.97601E-08
0005576
extracellular region
5.22067E-08
0003723
RNA binding
1.26541E-07
0035556
intracellular signal transduction
1.53163E-07
0030529
ribonucleoprotein complex
1.88428E-07
0046872
metal ion binding
2.1263E-06
0070062
extracellular vesicular exosome
2.45475E-06
0065010
extracellular membrane-bounded organelle
2.45475E-06
0043169
cation binding
2.5239E-06
0005634
nucleus
1.13403E-05
0050794
regulation of cellular process
1.41408E-05
0007165
signal transduction
2.09173E-05
0003677
DNA binding
2.50662E-05
0006351
transcription, DNA-templated
8.60893E-05
0043167
ion binding
0.000123429
0032991
macromolecular complex
0.000165091
0042995
cell projection
0.000183242
0009966
regulation of signal transduction
0.00021263
0045893
positive regulation of transcription, DNA-templated
0.000264491
0010646
regulation of cell communication
0.000276592
0044267
cellular protein metabolic process
0.000299065
0003735
structural constituent of ribosome
0.000342283
0006412
translation
0.000376857
0010468
regulation of gene expression
0.000503052
0044421
extracellular region part
0.000591215
0000981
sequence-specific DNA binding RNA polymerase II transcription factor activity
0.000722597
0045047
protein targeting to ER
0.000888552
0006613
cotranslational protein targeting to membrane
0.000888552
031982
vesicle
0.001120198
0031988
membrane-bounded vesicle
0.001424449
0006414
translational elongation
0.001690669
2001141
regulation of RNA biosynthetic process
0.001745987
0044391
ribosomal subunit
0.001797848
0006614
SRP-dependent cotranslational protein targeting to membrane
0.001988005
0060255
regulation of macromolecule metabolic process
0.002039866
0006357
regulation of transcription from RNA polymerase II promoter
0.002351032
0019222
regulation of metabolic process
0.002506615
0005840
ribosome
0.002679485
0006413
translational initiation
0.003232669
0000139
Golgi membrane
0.003820427
0036211
protein modification process
0.00432175
0006464
cellular protein modification process
0.00432175
0005615
extracellular space
0.004529194
0005886
plasma membrane
0.008799083
2000112
regulation of cellular macromolecule biosynthetic process
0.016180632
0016020
membrane
0.01884283
0060089
molecular transducer activity
0.02178162
0004871
signal transducer activity
0.02178162
0032774
RNA biosynthetic process
0.02195449
0019083
viral transcription
0.03128947
0044767
single-organism developmental process
0.04771212
0016021
integral component of membrane
0.04909508