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

被引:172
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
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
收藏
页码:D995 / D1002
页数:8
相关论文
共 22 条
  • [1] Gene Ontology: tool for the unification of biology
    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
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [2] UniProt: a hub for protein information
    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
    [J]. NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) : D204 - D212
  • [3] The ChEMBL bioactivity database: an update
    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.
    [J]. 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
    Edwards, Aled M.
    Isserlin, Ruth
    Bader, Gary D.
    Frye, Stephen V.
    Willson, Timothy M.
    Yu, Frank H.
    [J]. NATURE, 2011, 470 (7333) : 163 - 165
  • [6] The druggable genome
    Hopkins, AL
    Groom, CR
    [J]. NATURE REVIEWS DRUG DISCOVERY, 2002, 1 (09) : 727 - 730
  • [7] Network biology concepts in complex disease comorbidities
    Hu, Jessica Xin
    Thomas, Cecilia Engel
    Brunak, Soren
    [J]. NATURE REVIEWS GENETICS, 2016, 17 (10) : 615 - 629
  • [8] DrugBank 4.0: shedding new light on drug metabolism
    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.
    [J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D1091 - D1097
  • [9] Expanding the Number of 'Druggable' Targets: Non-Enzymes and Protein-Protein Interactions
    Makley, Leah N.
    Gestwicki, Jason E.
    [J]. CHEMICAL BIOLOGY & DRUG DESIGN, 2013, 81 (01) : 22 - 32
  • [10] PANTHER version 10: expanded protein families and functions, and analysis tools
    Mi, Huaiyu
    Poudel, Sagar
    Muruganujan, Anushya
    Casagrande, John T.
    Thomas, Paul D.
    [J]. NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) : D336 - D342