Literature DB >> 27482531

Statistical Methods in Integrative Genomics.

Sylvia Richardson1, George C Tseng2, Wei Sun3.   

Abstract

Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions.

Entities:  

Keywords:  genomics; horizontal data integration; integrative genomics; vertical data integration

Year:  2016        PMID: 27482531      PMCID: PMC4963036          DOI: 10.1146/annurev-statistics-041715-033506

Source DB:  PubMed          Journal:  Annu Rev Stat Appl        ISSN: 2326-8298            Impact factor:   5.810


  99 in total

1.  Joint analysis of miRNA and mRNA expression data.

Authors:  Ander Muniategui; Jon Pey; Francisco J Planes; Angel Rubio
Journal:  Brief Bioinform       Date:  2012-06-12       Impact factor: 11.622

2.  A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits.

Authors:  Samsiddhi Bhattacharjee; Preetha Rajaraman; Kevin B Jacobs; William A Wheeler; Beatrice S Melin; Patricia Hartge; Meredith Yeager; Charles C Chung; Stephen J Chanock; Nilanjan Chatterjee
Journal:  Am J Hum Genet       Date:  2012-05-04       Impact factor: 11.025

3.  Regularized Multivariate Regression for Identifying Master Predictors with Application to Integrative Genomics Study of Breast Cancer.

Authors:  Jie Peng; Ji Zhu; Anna Bergamaschi; Wonshik Han; Dong-Young Noh; Jonathan R Pollack; Pei Wang
Journal:  Ann Appl Stat       Date:  2010-03       Impact factor: 2.083

4.  Multiset Statistics for Gene Set Analysis.

Authors:  Michael A Newton; Zhishi Wang
Journal:  Annu Rev Stat Appl       Date:  2015-04       Impact factor: 5.810

5.  Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis.

Authors:  James C Lee; Paul A Lyons; Eoin F McKinney; John M Sowerby; Edward J Carr; Francesca Bredin; Hannah M Rickman; Huzefa Ratlamwala; Alexander Hatton; Tim F Rayner; Miles Parkes; Kenneth G C Smith
Journal:  J Clin Invest       Date:  2011-09-26       Impact factor: 14.808

Review 6.  Comprehensive literature review and statistical considerations for GWAS meta-analysis.

Authors:  Ferdouse Begum; Debashis Ghosh; George C Tseng; Eleanor Feingold
Journal:  Nucleic Acids Res       Date:  2012-01-12       Impact factor: 16.971

7.  Integrating diverse genomic data using gene sets.

Authors:  Svitlana Tyekucheva; Luigi Marchionni; Rachel Karchin; Giovanni Parmigiani
Journal:  Genome Biol       Date:  2011-10-21       Impact factor: 13.583

8.  A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules.

Authors:  Wei Zhang; Jun Zhu; Eric E Schadt; Jun S Liu
Journal:  PLoS Comput Biol       Date:  2010-01-15       Impact factor: 4.475

9.  Harnessing naturally randomized transcription to infer regulatory relationships among genes.

Authors:  Lin S Chen; Frank Emmert-Streib; John D Storey
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

10.  Mendelian randomisation and causal inference in observational epidemiology.

Authors:  Nuala A Sheehan; Vanessa Didelez; Paul R Burton; Martin D Tobin
Journal:  PLoS Med       Date:  2008-08-26       Impact factor: 11.069

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  33 in total

1.  Integrative linear discriminant analysis with guaranteed error rate improvement.

Authors:  Quefeng Li; Lexin Li
Journal:  Biometrika       Date:  2018-10-22       Impact factor: 2.445

2.  Integrative Sparse K-Means With Overlapping Group Lasso in Genomic Applications for Disease Subtype Discovery.

Authors:  Zhiguang Huo; George Tseng
Journal:  Ann Appl Stat       Date:  2017-07-20       Impact factor: 2.083

3.  IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration.

Authors:  Ziqiao Wang; Peng Wei
Journal:  Bioinformatics       Date:  2021-04-01       Impact factor: 6.937

4.  Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks.

Authors:  Hans-Ulrich Klein; Martin Schäfer; David A Bennett; Holger Schwender; Philip L De Jager
Journal:  PLoS Comput Biol       Date:  2020-04-07       Impact factor: 4.475

5.  Meta-analytic principal component analysis in integrative omics application.

Authors:  SungHwan Kim; Dongwan Kang; Zhiguang Huo; Yongseok Park; George C Tseng
Journal:  Bioinformatics       Date:  2018-04-15       Impact factor: 6.937

6.  The association between copy number aberration, DNA methylation and gene expression in tumor samples.

Authors:  Wei Sun; Paul Bunn; Chong Jin; Paul Little; Vasyl Zhabotynsky; Charles M Perou; David Neil Hayes; Mengjie Chen; Dan-Yu Lin
Journal:  Nucleic Acids Res       Date:  2018-04-06       Impact factor: 16.971

Review 7.  Value of Collaboration among Multi-Domain Experts in Analysis of High-Throughput Genomics Data.

Authors:  Daoud Meerzaman; Barbara K Dunn
Journal:  Cancer Res       Date:  2019-07-23       Impact factor: 12.701

8.  Simultaneous Covariance Inference for Multimodal Integrative Analysis.

Authors:  Yin Xia; Lexin Li; Samuel N Lockhart; William J Jagust
Journal:  J Am Stat Assoc       Date:  2019-06-28       Impact factor: 5.033

Review 9.  Statistical genomics in rare cancer.

Authors:  Farnoosh Abbas-Aghababazadeh; Qianxing Mo; Brooke L Fridley
Journal:  Semin Cancer Biol       Date:  2019-08-19       Impact factor: 15.707

10.  Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer.

Authors:  Naim U Rashid; Xianlu L Peng; Chong Jin; Richard A Moffitt; Keith E Volmar; Brian A Belt; Roheena Z Panni; Timothy M Nywening; Silvia G Herrera; Kristin J Moore; Sarah G Hennessey; Ashley B Morrison; Ryan Kawalerski; Apoorve Nayyar; Audrey E Chang; Benjamin Schmidt; Hong Jin Kim; David C Linehan; Jen Jen Yeh
Journal:  Clin Cancer Res       Date:  2019-11-21       Impact factor: 12.531

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