Literature DB >> 27896970

EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY.

Winston A Haynes1, Francesco Vallania, Charles Liu, Erika Bongen, Aurelie Tomczak, Marta Andres-Terrè, Shane Lofgren, Andrew Tam, Cole A Deisseroth, Matthew D Li, Timothy E Sweeney, Purvesh Khatri.   

Abstract

A major contributor to the scientific reproducibility crisis has been that the results from homogeneous, single-center studies do not generalize to heterogeneous, real world populations. Multi-cohort gene expression analysis has helped to increase reproducibility by aggregating data from diverse populations into a single analysis. To make the multi-cohort analysis process more feasible, we have assembled an analysis pipeline which implements rigorously studied meta-analysis best practices. We have compiled and made publicly available the results of our own multi-cohort gene expression analysis of 103 diseases, spanning 615 studies and 36,915 samples, through a novel and interactive web application. As a result, we have made both the process of and the results from multi-cohort gene expression analysis more approachable for non-technical users.

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Mesh：

Year:  2017        PMID： 27896970      PMCID： PMC5167529          DOI： 10.1142/9789813207813_0015

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN： 2335-6928


  24 in total

1.  A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma.

Authors:  Ron Chen; Purvesh Khatri; Pawel K Mazur; Melanie Polin; Yanyan Zheng; Dedeepya Vaka; Chuong D Hoang; Joseph Shrager; Yue Xu; Silvestre Vicent; Atul J Butte; E Alejandro Sweet-Cordero
Journal:  Cancer Res       Date:  2014-03-20       Impact factor: 12.701

2.  Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis.

Authors:  Timothy E Sweeney; Lindsay Braviak; Cristina M Tato; Purvesh Khatri
Journal:  Lancet Respir Med       Date:  2016-02-20       Impact factor: 30.700

Review 3.  The immunobiology of interferon-gamma inducible protein 10 kD (IP-10): a novel, pleiotropic member of the C-X-C chemokine superfamily.

Authors:  L F Neville; G Mathiak; O Bagasra
Journal:  Cytokine Growth Factor Rev       Date:  1997-09       Impact factor: 7.638

4.  Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma.

Authors:  Pawel K Mazur; Alexander Herner; Stephano S Mello; Matthias Wirth; Simone Hausmann; Francisco J Sánchez-Rivera; Shane M Lofgren; Timo Kuschma; Stephan A Hahn; Deepak Vangala; Marija Trajkovic-Arsic; Aayush Gupta; Irina Heid; Peter B Noël; Rickmer Braren; Mert Erkan; Jörg Kleeff; Bence Sipos; Leanne C Sayles; Mathias Heikenwalder; Elisabeth Heßmann; Volker Ellenrieder; Irene Esposito; Tyler Jacks; James E Bradner; Purvesh Khatri; E Alejandro Sweet-Cordero; Laura D Attardi; Roland M Schmid; Guenter Schneider; Julien Sage; Jens T Siveke
Journal:  Nat Med       Date:  2015-09-21       Impact factor: 53.440

5.  ExAtlas: An interactive online tool for meta-analysis of gene expression data.

Authors:  Alexei A Sharov; David Schlessinger; Minoru S H Ko
Journal:  J Bioinform Comput Biol       Date:  2015-06-09       Impact factor: 1.122

6.  Robust classification of bacterial and viral infections via integrated host gene expression diagnostics.

Authors:  Timothy E Sweeney; Hector R Wong; Purvesh Khatri
Journal:  Sci Transl Med       Date:  2016-07-06       Impact factor: 17.956

7.  Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline.

Authors:  Lun-Ching Chang; Hui-Min Lin; Etienne Sibille; George C Tseng
Journal:  BMC Bioinformatics       Date:  2013-12-21       Impact factor: 3.169

8.  A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation.

Authors:  Purvesh Khatri; Silke Roedder; Naoyuki Kimura; Katrien De Vusser; Alexander A Morgan; Yongquan Gong; Michael P Fischbein; Robert C Robbins; Maarten Naesens; Atul J Butte; Minnie M Sarwal
Journal:  J Exp Med       Date:  2013-10-14       Impact factor: 14.307

9.  Why most published research findings are false.

Authors:  John P A Ioannidis
Journal:  PLoS Med       Date:  2005-08-30       Impact factor: 11.613

10.  Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Authors:  Robert Petryszak; Tony Burdett; Benedetto Fiorelli; Nuno A Fonseca; Mar Gonzalez-Porta; Emma Hastings; Wolfgang Huber; Simon Jupp; Maria Keays; Nataliya Kryvych; Julie McMurry; John C Marioni; James Malone; Karine Megy; Gabriella Rustici; Amy Y Tang; Jan Taubert; Eleanor Williams; Oliver Mannion; Helen E Parkinson; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2013-12-04       Impact factor: 16.971
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  42 in total

1.  GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis.

Authors:  Adib Shafi; Tin Nguyen; Azam Peyvandipour; Sorin Draghici
Journal:  Bioinformatics       Date:  2020-01-15       Impact factor: 6.937

2.  METHODS TO ENSURE THE REPRODUCIBILITY OF BIOMEDICAL RESEARCH.

Authors:  Konrad J Karczewski; Nicholas P Tatonetti; Arjun K Manrai; Chirag J Patel; C Titus Brown; John P A Ioannidis
Journal:  Pac Symp Biocomput       Date:  2017

3.  Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival.

Authors:  Tej D Azad; Michele Donato; Line Heylen; Andrew B Liu; Shai S Shen-Orr; Timothy E Sweeney; Jonathan Scott Maltzman; Maarten Naesens; Purvesh Khatri
Journal:  JCI Insight       Date:  2018-01-25

4.  Hub genes associated with immune cell infiltration in breast cancer, identified through bioinformatic analyses of multiple datasets.

Authors:  Huanyu Zhao; Ruoyu Dang; Yipan Zhu; Baijian Qu; Yasra Sayyed; Ying Wen; Xicheng Liu; Jianping Lin; Luyuan Li
Journal:  Cancer Biol Med       Date:  2022-07-13       Impact factor: 5.347

5.  Identification of Key Biomarkers in Systemic Lupus Erythematosus by a Multi-Cohort Analysis.

Authors:  Meilin Wei; Qiguan Dong; Shaoqiu Chen; Junlong Wang; Hua Yang; Qin Xiong
Journal:  Front Immunol       Date:  2022-07-04       Impact factor: 8.786

6.  Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology.

Authors:  Laurynas Kalesinskas; Sanjana Gupta; Purvesh Khatri
Journal:  PLoS Comput Biol       Date:  2022-06-27       Impact factor: 4.779

7.  Comprehensive multi-cohort transcriptional meta-analysis of muscle diseases identifies a signature of disease severity.

Authors:  C J Walsh; J Batt; M S Herridge; S Mathur; G D Bader; P Hu; P Khatri; C C Dos Santos
Journal:  Sci Rep       Date:  2022-07-04       Impact factor: 4.996

8.  MAGE: An Open-Source Tool for Meta-Analysis of Gene Expression Studies.

Authors:  Ioannis A Tamposis; Georgios A Manios; Theodosia Charitou; Konstantina E Vennou; Panagiota I Kontou; Pantelis G Bagos
Journal:  Biology (Basel)       Date:  2022-06-10

9.  Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus.

Authors:  Winston A Haynes; D James Haddon; Vivian K Diep; Avani Khatri; Erika Bongen; Gloria Yiu; Imelda Balboni; Christopher R Bolen; Rong Mao; Paul J Utz; Purvesh Khatri
Journal:  JCI Insight       Date:  2020-02-27

10.  iPSC-endothelial cell phenotypic drug screening and in silico analyses identify tyrphostin-AG1296 for pulmonary arterial hypertension.

Authors:  Mingxia Gu; Michele Donato; Minzhe Guo; Neil Wary; Yifei Miao; Shuai Mao; Toshie Saito; Shoichiro Otsuki; Lingli Wang; Rebecca L Harper; Silin Sa; Purvesh Khatri; Marlene Rabinovitch
Journal:  Sci Transl Med       Date:  2021-05-05       Impact factor: 17.956
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