Recon3D enables a three-dimensional view of gene variation in human metabolism

被引：456

作者：

Brunk, Elizabeth ^{[1
,2
]}

Sahoo, Swagatika ^{[3
,12
]}

Zielinski, Daniel C. ^{[1
]}

Altunkaya, Ali ^{[4
,5
]}

Drager, Andreas ^{[6
]}

Mih, Nathan ^{[1
]}

Gatto, Francesco ^{[1
,7
]}

Nilsson, Avlant ^{[7
]}

Gonzalez, German Andres Preciat ^{[3
]}

Aurich, Maike Kathrin ^{[3
]}

Prlic, Andreas ^{[4
]}

Sastry, Anand ^{[1
]}

Danielsdottir, Anna D. ^{[3
]}

Heinken, Almut ^{[3
]}

Noronha, Alberto ^{[3
]}

Rose, Peter W. ^{[4
]}

Burley, Stephen K. ^{[4
,8
,9
]}

Fleming, Ronan M. T. ^{[3
,10
]}

Nielsen, Jens ^{[2
,7
]}

Thiele, Ines ^{[3
]}

Palsson, Bernhard O. ^{[1
,2
,11
]}

机构：

[1] Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA

[2] Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, Lyngby, Denmark

[3] Univ Luxembourg, Luxembourg Ctr Syst Biomed, Campus Belval, Esch Sur Alzette, Luxembourg

[4] Univ Calif San Diego, San Diego Supercomp Ctr, RCSB Prot Data Bank, La Jolla, CA 92093 USA

[5] Arizona State Univ, Dept Comp Sci, Tempe, AZ 85281 USA

[6] Univ Tubingen, Ctr Bioinformat Tubingen ZBIT, Appl Bioinformat Grp, Tubingen, Germany

[7] Chalmers Univ Technol, Dept Biol & Biol Engn, Gothenburg, Sweden

[8] Rutgers State Univ, Dept Chem & Chem Biol, Ctr Integrat Proteom Res, Inst Quantitat Biomed, Piscataway, NJ USA

[9] Rutgers State Univ, Rutgers Canc Inst New Jersey, Piscataway, NJ USA

[10] Leiden Univ, Leiden Acad Ctr Drug Res, Fac Sci, Div Analyt Biosci, Leiden, Netherlands

[11] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

[12] Indian Inst Technol, Dept Chem Engn, Madras, Tamil Nadu, India

来源：

NATURE BIOTECHNOLOGY | 2018年 / 36卷 / 03期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

GLOBAL RECONSTRUCTION; PROTEIN-STRUCTURE; CANCER; PLATFORM; MODELS; GROWTH; DISCOVERY; RESPONSES; GENOMICS; DATABASE;

D O I：

10.1038/nbt.4072

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：

Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.

引用

页码：272 / +

页数：13

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