TY - JOUR
T1 - Comparative transcriptome in large-scale human and cattle populations
AU - Yao, Yuelin
AU - Liu, Shuli
AU - Xia, Charley
AU - Gao, Yahui
AU - Pan, Zhangyuan
AU - Canela-Xandri, Oriol
AU - Khamseh, Ava
AU - Rawlik, Konrad
AU - Wang, Sheng
AU - Li, Bingjie
AU - Zhang, Yi
AU - Pairo-Castineira, Erola
AU - D’Mellow, Kenton
AU - Li, Xiujin
AU - Yan, Ze
AU - Li, Cong-jun
AU - Yu, Ying
AU - Zhang, Shengli
AU - Ma, Li
AU - Cole, John B.
AU - Ross, Pablo J.
AU - Zhou, Huaijun
AU - Haley, Chris
AU - Liu, George E.
AU - Fang, Lingzhao
AU - Tenesa, Albert
N1 - Publisher Copyright:
© 2022. The Author(s).
PY - 2022/8/22
Y1 - 2022/8/22
N2 - BACKGROUND: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes.RESULTS: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues.CONCLUSIONS: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.
AB - BACKGROUND: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes.RESULTS: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues.CONCLUSIONS: In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.
KW - Comparative transcriptome
KW - Gene co-expression
KW - Heritability enrichment
KW - Inter-individual variability
KW - RNA-seq
UR - http://www.scopus.com/inward/record.url?scp=85136200740&partnerID=8YFLogxK
U2 - 10.1186/s13059-022-02745-4
DO - 10.1186/s13059-022-02745-4
M3 - Article
C2 - 35996157
SN - 1474-7596
VL - 23
JO - Genome Biology
JF - Genome Biology
IS - 1
M1 - 176
ER -