Literature DB >> 33156327

TCRD and Pharos 2021: mining the human proteome for disease biology.

Timothy K Sheils1, Stephen L Mathias2, Keith J Kelleher1, Vishal B Siramshetty1, Dac-Trung Nguyen1, Cristian G Bologa2, Lars Juhl Jensen3, Dušica Vidović4,5, Amar Koleti4, Stephan C Schürer4,5,6, Anna Waller7, Jeremy J Yang2, Jayme Holmes2, Giovanni Bocci2, Noel Southall1, Poorva Dharkar1, Ewy Mathé1, Anton Simeonov1, Tudor I Oprea2,3,8,9.   

Abstract

In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that can potentially be modulated using small molecules or biologics. Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein-protein interactions, protein-disease and protein-phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33156327      PMCID: PMC7778974          DOI: 10.1093/nar/gkaa993

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  47 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Too many roads not taken.

Authors:  Aled M Edwards; Ruth Isserlin; Gary D Bader; Stephen V Frye; Timothy M Willson; Frank H Yu
Journal:  Nature       Date:  2011-02-10       Impact factor: 49.962

3.  A systematic approach for evaluating the quality of experimental toxicological and ecotoxicological data.

Authors:  H J Klimisch; M Andreae; U Tillmann
Journal:  Regul Toxicol Pharmacol       Date:  1997-02       Impact factor: 3.271

4.  DISEASES: text mining and data integration of disease-gene associations.

Authors:  Sune Pletscher-Frankild; Albert Pallejà; Kalliopi Tsafou; Janos X Binder; Lars Juhl Jensen
Journal:  Methods       Date:  2014-12-05       Impact factor: 3.608

5.  Novel drug targets in 2018.

Authors:  Oleg Ursu; Meir Glick; Tudor Oprea
Journal:  Nat Rev Drug Discov       Date:  2019-03-26       Impact factor: 84.694

6.  The ChEMBL database in 2017.

Authors:  Anna Gaulton; Anne Hersey; Michał Nowotka; A Patrícia Bento; Jon Chambers; David Mendez; Prudence Mutowo; Francis Atkinson; Louisa J Bellis; Elena Cibrián-Uhalte; Mark Davies; Nathan Dedman; Anneli Karlsson; María Paula Magariños; John P Overington; George Papadatos; Ines Smit; Andrew R Leach
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

7.  ProtVista: visualization of protein sequence annotations.

Authors:  Xavier Watkins; Leyla J Garcia; Sangya Pundir; Maria J Martin
Journal:  Bioinformatics       Date:  2017-07-01       Impact factor: 6.937

8.  UniProt: a worldwide hub of protein knowledge.

Authors: 
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

9.  A draft map of the human proteome.

Authors:  Min-Sik Kim; Sneha M Pinto; Derese Getnet; Raja Sekhar Nirujogi; Srikanth S Manda; Raghothama Chaerkady; Anil K Madugundu; Dhanashree S Kelkar; Ruth Isserlin; Shobhit Jain; Joji K Thomas; Babylakshmi Muthusamy; Pamela Leal-Rojas; Praveen Kumar; Nandini A Sahasrabuddhe; Lavanya Balakrishnan; Jayshree Advani; Bijesh George; Santosh Renuse; Lakshmi Dhevi N Selvan; Arun H Patil; Vishalakshi Nanjappa; Aneesha Radhakrishnan; Samarjeet Prasad; Tejaswini Subbannayya; Rajesh Raju; Manish Kumar; Sreelakshmi K Sreenivasamurthy; Arivusudar Marimuthu; Gajanan J Sathe; Sandip Chavan; Keshava K Datta; Yashwanth Subbannayya; Apeksha Sahu; Soujanya D Yelamanchi; Savita Jayaram; Pavithra Rajagopalan; Jyoti Sharma; Krishna R Murthy; Nazia Syed; Renu Goel; Aafaque A Khan; Sartaj Ahmad; Gourav Dey; Keshav Mudgal; Aditi Chatterjee; Tai-Chung Huang; Jun Zhong; Xinyan Wu; Patrick G Shaw; Donald Freed; Muhammad S Zahari; Kanchan K Mukherjee; Subramanian Shankar; Anita Mahadevan; Henry Lam; Christopher J Mitchell; Susarla Krishna Shankar; Parthasarathy Satishchandra; John T Schroeder; Ravi Sirdeshmukh; Anirban Maitra; Steven D Leach; Charles G Drake; Marc K Halushka; T S Keshava Prasad; Ralph H Hruban; Candace L Kerr; Gary D Bader; Christine A Iacobuzio-Donahue; Harsha Gowda; Akhilesh Pandey
Journal:  Nature       Date:  2014-05-29       Impact factor: 49.962

10.  The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

Authors:  G Thomas Hayman; Stanley J F Laulederkind; Jennifer R Smith; Shur-Jen Wang; Victoria Petri; Rajni Nigam; Marek Tutaj; Jeff De Pons; Melinda R Dwinell; Mary Shimoyama
Journal:  Database (Oxford)       Date:  2016-03-23       Impact factor: 3.451

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  18 in total

1.  NETISCE: a network-based tool for cell fate reprogramming.

Authors:  Lauren Marazzi; Milan Shah; Shreedula Balakrishnan; Ananya Patil; Paola Vera-Licona
Journal:  NPJ Syst Biol Appl       Date:  2022-06-20

2.  Metabolic modeling-based drug repurposing in Glioblastoma.

Authors:  Claudio Tomi-Andrino; Alina Pandele; Klaus Winzer; John King; Ruman Rahman; Dong-Hyun Kim
Journal:  Sci Rep       Date:  2022-07-01       Impact factor: 4.996

3.  Combining mass spectrometry and machine learning to discover bioactive peptides.

Authors:  Mads Grønborg; Ulrik de Lichtenberg; Christian T Madsen; Jan C Refsgaard; Felix G Teufel; Sonny K Kjærulff; Zhe Wang; Guangjun Meng; Carsten Jessen; Petteri Heljo; Qunfeng Jiang; Xin Zhao; Bo Wu; Xueping Zhou; Yang Tang; Jacob F Jeppesen; Christian D Kelstrup; Stephen T Buckley; Søren Tullin; Jan Nygaard-Jensen; Xiaoli Chen; Fang Zhang; Jesper V Olsen; Dan Han
Journal:  Nat Commun       Date:  2022-10-20       Impact factor: 17.694

4.  Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform.

Authors:  Kei G I Webber; Thy Truong; S Madisyn Johnston; Sebastian E Zapata; Yiran Liang; Jacob M Davis; Alexander D Buttars; Fletcher B Smith; Hailey E Jones; Arianna C Mahoney; Richard H Carson; Andikan J Nwosu; Jacob L Heninger; Andrey V Liyu; Gregory P Nordin; Ying Zhu; Ryan T Kelly
Journal:  Anal Chem       Date:  2022-04-06       Impact factor: 8.008

5.  Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration.

Authors:  Dhouha Grissa; Alexander Junge; Tudor I Oprea; Lars Juhl Jensen
Journal:  Database (Oxford)       Date:  2022-03-28       Impact factor: 4.462

6.  Spatial transcriptomics of dorsal root ganglia identifies molecular signatures of human nociceptors.

Authors:  Diana Tavares-Ferreira; Stephanie Shiers; Pradipta R Ray; Andi Wangzhou; Vivekanand Jeevakumar; Ishwarya Sankaranarayanan; Anna M Cervantes; Jeffrey C Reese; Alexander Chamessian; Bryan A Copits; Patrick M Dougherty; Robert W Gereau; Michael D Burton; Gregory Dussor; Theodore J Price
Journal:  Sci Transl Med       Date:  2022-02-16       Impact factor: 19.319

7.  Identifying nootropic drug targets via large-scale cognitive GWAS and transcriptomics.

Authors:  Max Lam; Chia-Yen Chen; Tian Ge; Yan Xia; David W Hill; Joey W Trampush; Jin Yu; Emma Knowles; Gail Davies; Eli A Stahl; Laura Huckins; David C Liewald; Srdjan Djurovic; Ingrid Melle; Andrea Christoforou; Ivar Reinvang; Pamela DeRosse; Astri J Lundervold; Vidar M Steen; Thomas Espeseth; Katri Räikkönen; Elisabeth Widen; Aarno Palotie; Johan G Eriksson; Ina Giegling; Bettina Konte; Annette M Hartmann; Panos Roussos; Stella Giakoumaki; Katherine E Burdick; Antony Payton; William Ollier; Ornit Chiba-Falek; Deborah C Koltai; Anna C Need; Elizabeth T Cirulli; Aristotle N Voineskos; Nikos C Stefanis; Dimitrios Avramopoulos; Alex Hatzimanolis; Nikolaos Smyrnis; Robert M Bilder; Nelson B Freimer; Tyrone D Cannon; Edythe London; Russell A Poldrack; Fred W Sabb; Eliza Congdon; Emily Drabant Conley; Matthew A Scult; Dwight Dickinson; Richard E Straub; Gary Donohoe; Derek Morris; Aiden Corvin; Michael Gill; Ahmad R Hariri; Daniel R Weinberger; Neil Pendleton; Panos Bitsios; Dan Rujescu; Jari Lahti; Stephanie Le Hellard; Matthew C Keller; Ole A Andreassen; Ian J Deary; David C Glahn; Hailiang Huang; Chunyu Liu; Anil K Malhotra; Todd Lencz
Journal:  Neuropsychopharmacology       Date:  2021-05-25       Impact factor: 8.294

8.  Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity.

Authors:  Jessica Binder; Oleg Ursu; Cristian Bologa; Shanya Jiang; Nicole Maphis; Somayeh Dadras; Devon Chisholm; Jason Weick; Orrin Myers; Praveen Kumar; Jeremy J Yang; Kiran Bhaskar; Tudor I Oprea
Journal:  Commun Biol       Date:  2022-02-11

Review 9.  Trends in kinase drug discovery: targets, indications and inhibitor design.

Authors:  Misty M Attwood; Doriano Fabbro; Aleksandr V Sokolov; Stefan Knapp; Helgi B Schiöth
Journal:  Nat Rev Drug Discov       Date:  2021-08-05       Impact factor: 84.694

10.  Combining Human Genetics of Multiple Sclerosis with Oxidative Stress Phenotype for Drug Repositioning.

Authors:  Stefania Olla; Maristella Steri; Alessia Formato; Michael B Whalen; Silvia Corbisiero; Cristina Agresti
Journal:  Pharmaceutics       Date:  2021-12-02       Impact factor: 6.321

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