Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues

被引:5
|
作者
Tan, Tao [1 ,11 ]
Xia, Lin [2 ,3 ]
Tu, Kailing [2 ,3 ]
Tang, Jie [2 ,3 ]
Yin, Senlin [2 ,3 ]
Dai, Lunzhi [2 ,3 ,5 ,6 ]
Lei, Peng [2 ,3 ,7 ]
Dong, Biao [2 ,3 ,8 ]
Hu, Hongbo [2 ,3 ,9 ]
Fan, Yong [10 ]
Yu, Yang [1 ]
Xie, Dan [2 ,3 ,4 ]
机构
[1] Peking Univ, Dept Obstet & Gynecol, Hosp 3, Beijing, Peoples R China
[2] Sichuan Univ, West China Hosp, State Key Lab Biotherapy, Chengdu, Sichuan, Peoples R China
[3] Sichuan Univ, West China Hosp, Collaborat Innovat Ctr Biotherapy, Chengdu, Sichuan, Peoples R China
[4] Sichuan Univ, W China Hosp, Ctr Precis Med, Chengdu, Sichuan, Peoples R China
[5] Sichuan Univ, West China Hosp, Lab PTM, Chengdu, Sichuan, Peoples R China
[6] Sichuan Univ, West China Hosp, Dept Gen Practice, Chengdu, Sichuan, Peoples R China
[7] Sichuan Univ, West China Sch Basic Med Sci & Forens Med, Chengdu, Sichuan, Peoples R China
[8] Sichuan Univ, West China Hosp, Natl Clin Res Ctr Geriatr, Chengdu, Sichuan, Peoples R China
[9] Sichuan Univ, West China Hosp, Dept Rheumatol & Immunol, Chengdu, Sichuan, Peoples R China
[10] Guangzhou Med Univ, Key Lab Major Obstet Dis Guangdong Prov, Affiliated Hosp 3, Guangzhou, Guangdong, Peoples R China
[11] Kunming Univ Sci & Technol, Inst Primate Translat Med, Yunnan Key Lab Primate Biomed Res, Kunming 650500, Yunnan, Peoples R China
来源
BMC GENOMICS | 2018年 / 19卷
基金
中国国家自然科学基金;
关键词
Crab-eating macaque; Evolution; Gene regulation; EMBRYONIC STEM-CELLS; GENOME ANNOTATION; CYNOMOLGUS; TRANSCRIPTOME; GENERATION; MACAQUES; MONKEY; RECONSTRUCTION; TRANSMISSION; EUKARYOTES;
D O I
10.1186/s12864-018-5183-y
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
BackgroundsMacaca fascicularis (M. fascicularis) is a primate model organism that played important role in studying human health. It is vital to better understand the similarity and differences of gene regulation between M. fascicularis and human. Current comparative study of gene regulation between the two species are limited by low quality of gene annotation and lack of regulatory element data on M. fascicularis genome.ResultsIn this study, we improved the M. fascicularis gene annotation with 57 gene expression data from multiple tissues and, more importantly, a manual curation procedure. The new annotation enabled us to map gene expression and identify gene location more accurately.ConclusionsComparing with human gene expression data from the same cell types, we characterized the evolution of expression patterns of homologous genes.
引用
收藏
页数:12
相关论文
共 50 条
  • [31] Bioinformatics Analysis for Multiple Gene Expression Profiles in Sepsis
    Zhai, Jianhua
    Qi, Anlong
    Zhang, Yan
    Jiao, Lina
    Liu, Yancun
    Shou, Songtao
    MEDICAL SCIENCE MONITOR, 2020, 26
  • [32] Gene expression profiles in Finnish twins with multiple sclerosis
    Särkijärvi, S
    Kuusisto, H
    Paalavuo, R
    Levula, M
    Airla, N
    Lehtimäki, T
    Kaprio, J
    Koskenvuo, M
    Elovaara, I
    BMC MEDICAL GENETICS, 2006, 7
  • [33] A memetic co-clustering algorithm for gene expression profiles and biological annotation
    Speer, N
    Spieth, C
    Zell, A
    CEC2004: PROCEEDINGS OF THE 2004 CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1 AND 2, 2004, : 1631 - 1638
  • [34] Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis
    Karimizadeh, Elham
    Sharifi-Zarchi, Ali
    Nikaein, Hassan
    Salehi, Seyedehsaba
    Salamatian, Bahar
    Elmi, Naser
    Gharibdoost, Farhad
    Mahmoudi, Mahdi
    BMC MEDICAL GENOMICS, 2019, 12 (01)
  • [35] Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis
    Elham Karimizadeh
    Ali Sharifi-Zarchi
    Hassan Nikaein
    Seyedehsaba Salehi
    Bahar Salamatian
    Naser Elmi
    Farhad Gharibdoost
    Mahdi Mahmoudi
    BMC Medical Genomics, 12
  • [36] Biochemical networks: The evolution of gene annotation
    Simon Kasif
    Martin Steffen
    Nature Chemical Biology, 2010, 6 : 4 - 5
  • [37] BIOCHEMICAL NETWORKS The evolution of gene annotation
    Kasif, Simon
    Steffen, Martin
    NATURE CHEMICAL BIOLOGY, 2010, 6 (01) : 4 - 5
  • [38] Interactome analysis of gene expression profiles of cervical cancer reveals dysregulated mitotic gene clusters
    Cheng, Jing
    Lu, Xiaosheng
    Wang, Jianguang
    Zhang, Huina
    Duan, Ping
    Li, Chunyang
    AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH, 2017, 9 (06): : 3048 - 3059
  • [39] Formal Meta-Analysis of Hypoxic Gene Expression Profiles Reveals a Universal Gene Signature
    Puente-Santamaria, Laura
    Sanchez-Gonzalez, Lucia
    Pescador, Nuria
    Martinez-Costa, Oscar
    Ramos-Ruiz, Ricardo
    del Peso, Luis
    BIOMEDICINES, 2022, 10 (09)
  • [40] Analysis of gene expression profiles of gastric normal and cancer tissues by SAGE
    Lee, JY
    Eom, EM
    Kim, DS
    Ha-Lee, YM
    Lee, DH
    GENOMICS, 2003, 82 (01) : 78 - 85