Pharos: Collating protein information to shed light on the druggable genome

被引：176

作者：

Dac-Trung Nguyen ^{[1
]}

Mathias, Stephen ^{[3
]}

Bologa, Cristian ^{[3
]}

Brunak, Soren ^{[8
]}

Fernandez, Nicolas ^{[2
]}

Gaulton, Anna ^{[9
]}

Hersey, Anne ^{[9
]}

Holmes, Jayme ^{[3
]}

Jensen, Lars Juhl ^{[8
]}

Karlsson, Anneli ^{[12
]}

Liu, Guixia ^{[3
,10
]}

Ma'ayan, Avi ^{[2
]}

Mandava, Geetha ^{[1
]}

Mani, Subramani ^{[3
]}

Mehta, Saurabh ^{[5
,6
]}

Overington, John ^{[12
]}

Patel, Juhee ^{[3
,11
]}

Rouillard, Andrew D. ^{[2
]}

Schurer, Stephan ^{[5
,7
]}

Sheils, Timothy ^{[1
]}

Simeonov, Anton ^{[1
]}

Sklar, Larry A. ^{[3
,4
]}

Southall, Noel ^{[1
]}

Ursu, Oleg ^{[3
]}

Vidovic, Dusica ^{[5
,7
]}

Waller, Anna ^{[3
,4
]}

Yang, Jeremy ^{[3
]}

Jadhav, Ajit ^{[1
]}

Oprea, Tudor I. ^{[3
]}

Guha, Rajarshi ^{[1
]}

机构：

[1] Natl Ctr Advancing Translat Sci, 9800 Med Ctr Dr, Rockville, MD 20850 USA

[2] Icahn Sch Med Mt Sinai, Dept Pharmacol Sci, Mt Sinai Ctr Bioinformat, One Gustave L Levy Pl,Box 1603, New York, NY 10029 USA

[3] Univ New Mexico, Sch Med, Translat Informat Div, Albuquerque, NM 87131 USA

[4] Univ New Mexico, Ctr Canc, Ctr Mol Discovery, Albuquerque, NM 87131 USA

[5] Univ Miami, Ctr Computat Sci, Coral Gables, FL 33146 USA

[6] Delhi Technol Univ, Dept Appl Chem, Delhi 110042, India

[7] Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA

[8] Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn, Ctr Prot Res, DK-2200 Copenhagen, Denmark

[9] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England

[10] East China Univ Sci & Technol, Dept Pharmaceut Sci, Shanghai, Peoples R China

[11] Univ New Mexico, Sch Med, BA MD Program, Albuquerque, NM 87131 USA

[12] BenevolentAI, 40 Churchway, London NW1 1LW, England

来源：

NUCLEIC ACIDS RESEARCH | 2017年 / 45卷 / D1期

基金：

美国国家卫生研究院;

关键词：

DATABASE; ONTOLOGY; TARGETS;

D O I：

10.1093/nar/gkw1072

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental techniques and a Knowledge Management Center (KMC) that would collect and organize information about protein targets from four families, representing the most common druggable targets with an emphasis on understudied proteins. Here, we describe two resources developed by the KMC: the Target Central Resource Database (TCRD) which collates many heterogeneous gene/protein datasets and Pharos (https://pharos.nih.gov), a multimodal web interface that presents the data from TCRD. We briefly describe the types and sources of data considered by the KMC and then highlight features of the Pharos interface designed to enable intuitive access to the IDG knowledgebase. The aim of Pharos is to encourage 'serendipitous browsing', whereby related, relevant information is made easily discoverable. We conclude by describing two use cases that highlight the utility of Pharos and TCRD.

引用

页码：D995 / D1002

页数：8

共 22 条

[1] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[2] UniProt: a hub for protein information [J].

Bateman, Alex ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Apweiler, Rolf ;

Alpi, Emanuele ;

Antunes, Ricardo ;

Arganiska, Joanna ;

Bely, Benoit ;

Bingley, Mark ;

Bonilla, Carlos ;

Britto, Ramona ;

Bursteinas, Borisas ;

Chavali, Gayatri ;

Cibrian-Uhalte, Elena ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Fazzini, Francesco ;

Gane, Paul ;

Cas-tro, Leyla Garcia ;

Garmiri, Penelope ;

Hatton-Ellis, Emma ;

Hieta, Reija ;

Huntley, Rachael ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

MacDougall, Alistair ;

Mutowo, Prudence ;

Nightin-gale, Andrew ;

Orchard, Sandra ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Turner, Edward ;

Volynkin, Vladimir ;

Wardell, Tony ;

Watkins, Xavier ;

Zellner, Hermann ;

Cowley, Andrew ;

Figueira, Luis ;

Li, Weizhong ;

McWilliam, Hamish .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D204-D212

[3] The ChEMBL bioactivity database: an update [J].

Bento, A. Patricia ;

Gaulton, Anna ;

Hersey, Anne ;

Bellis, Louisa J. ;

Chambers, Jon ;

Davies, Mark ;

Krueger, Felix A. ;

Light, Yvonne ;

Mak, Lora ;

McGlinchey, Shaun ;

Nowotka, Michal ;

Papadatos, George ;

Santos, Rita ;

Overington, John P. .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D1083-D1090

[4]

Chen YT, 2011, PLOS ONE, V6, DOI [10.1371/journal.pone.0023237, 10.1371/journal.pone.0017876]

[5] Too many roads not taken [J].

Edwards, Aled M. ;

Isserlin, Ruth ;

Bader, Gary D. ;

Frye, Stephen V. ;

Willson, Timothy M. ;

Yu, Frank H. .

NATURE, 2011, 470 (7333) :163-165

[6] The druggable genome [J].

Hopkins, AL ;

Groom, CR .

NATURE REVIEWS DRUG DISCOVERY, 2002, 1 (09) :727-730

[7] Network biology concepts in complex disease comorbidities [J].

Hu, Jessica Xin ;

Thomas, Cecilia Engel ;

Brunak, Soren .

NATURE REVIEWS GENETICS, 2016, 17 (10) :615-629

[8] DrugBank 4.0: shedding new light on drug metabolism [J].

Law, Vivian ;

Knox, Craig ;

Djoumbou, Yannick ;

Jewison, Tim ;

Guo, An Chi ;

Liu, Yifeng ;

Maciejewski, Adam ;

Arndt, David ;

Wilson, Michael ;

Neveu, Vanessa ;

Tang, Alexandra ;

Gabriel, Geraldine ;

Ly, Carol ;

Adamjee, Sakina ;

Dame, Zerihun T. ;

Han, Beomsoo ;

Zhou, You ;

Wishart, David S. .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D1091-D1097

[9] Expanding the Number of 'Druggable' Targets: Non-Enzymes and Protein-Protein Interactions [J].

Makley, Leah N. ;

Gestwicki, Jason E. .

CHEMICAL BIOLOGY & DRUG DESIGN, 2013, 81 (01) :22-32

[10] PANTHER version 10: expanded protein families and functions, and analysis tools [J].

Mi, Huaiyu ;

Poudel, Sagar ;

Muruganujan, Anushya ;

Casagrande, John T. ;

Thomas, Paul D. .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D336-D342

← 1 2 3 →