Literature DB >> 21415015

Integrative analysis and variable selection with multiple high-dimensional data sets.

Shuangge Ma1, Jian Huang, Xiao Song.   

Abstract

In high-throughput -omics studies, markers identified from analysis of single data sets often suffer from a lack of reproducibility because of sample limitation. A cost-effective remedy is to pool data from multiple comparable studies and conduct integrative analysis. Integrative analysis of multiple -omics data sets is challenging because of the high dimensionality of data and heterogeneity among studies. In this article, for marker selection in integrative analysis of data from multiple heterogeneous studies, we propose a 2-norm group bridge penalization approach. This approach can effectively identify markers with consistent effects across multiple studies and accommodate the heterogeneity among studies. We propose an efficient computational algorithm and establish the asymptotic consistency property. Simulations and applications in cancer profiling studies show satisfactory performance of the proposed approach.

Entities:  

Mesh:

Substances:

Year:  2011        PMID: 21415015      PMCID: PMC3169668          DOI: 10.1093/biostatistics/kxr004

Source DB:  PubMed          Journal:  Biostatistics        ISSN: 1465-4644            Impact factor:   5.899


  12 in total

1.  Merging two gene-expression studies via cross-platform normalization.

Authors:  Andrey A Shabalin; Håkon Tjelmeland; Cheng Fan; Charles M Perou; Andrew B Nobel
Journal:  Bioinformatics       Date:  2008-03-05       Impact factor: 6.937

2.  Microarray-based identification of differentially expressed growth- and metastasis-associated genes in pancreatic cancer.

Authors:  H Friess; J Ding; J Kleeff; L Fenkell; J A Rosinski; A Guweidhi; J F Reidhaar-Olson; M Korc; J Hammer; M W Büchler
Journal:  Cell Mol Life Sci       Date:  2003-06       Impact factor: 9.261

3.  Integrative analysis of multiple gene expression profiles applied to liver cancer study.

Authors:  Jung Kyoon Choi; Jong Young Choi; Dae Ghon Kim; Dong Wook Choi; Bu Yeo Kim; Kee Ho Lee; Young Il Yeom; Hyang Sook Yoo; Ook Joon Yoo; Sangsoo Kim
Journal:  FEBS Lett       Date:  2004-05-07       Impact factor: 4.124

4.  Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer.

Authors:  Craig D Logsdon; Diane M Simeone; Charles Binkley; Thiruvengadam Arumugam; Joel K Greenson; Thomas J Giordano; David E Misek; Rork Kuick; Samir Hanash
Journal:  Cancer Res       Date:  2003-05-15       Impact factor: 12.701

5.  Molecular alterations in pancreatic carcinoma: expression profiling shows that dysregulated expression of S100 genes is highly prevalent.

Authors:  Tatjana Crnogorac-Jurcevic; Edoardo Missiaglia; Ekaterina Blaveri; Rathi Gangeswaran; Melanie Jones; Benoit Terris; Eithne Costello; John P Neoptolemos; Nicholas R Lemoine
Journal:  J Pathol       Date:  2003-09       Impact factor: 7.996

6.  A group bridge approach for variable selection.

Authors:  Jian Huang; Shuange Ma; Huiliang Xie; Cun-Hui Zhang
Journal:  Biometrika       Date:  2009-06       Impact factor: 2.445

7.  Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data.

Authors:  Ronglai Shen; Debashis Ghosh; Arul M Chinnaiyan
Journal:  BMC Genomics       Date:  2004-12-14       Impact factor: 3.969

8.  Meta-analysis combines affymetrix microarray results across laboratories.

Authors:  John R Stevens; R W Doerge
Journal:  Comp Funct Genomics       Date:  2005

9.  Regularized gene selection in cancer microarray meta-analysis.

Authors:  Shuangge Ma; Jian Huang
Journal:  BMC Bioinformatics       Date:  2009-01-01       Impact factor: 3.169

10.  A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments.

Authors:  Hyungwon Choi; Ronglai Shen; Arul M Chinnaiyan; Debashis Ghosh
Journal:  BMC Bioinformatics       Date:  2007-09-27       Impact factor: 3.169

View more
  23 in total

1.  Identification of Breast Cancer Prognosis Markers via Integrative Analysis.

Authors:  Shuangge Ma; Ying Dai; Jian Huang; Yang Xie
Journal:  Comput Stat Data Anal       Date:  2012-09-01       Impact factor: 1.681

2.  Sparse meta-analysis with high-dimensional data.

Authors:  Qianchuan He; Hao Helen Zhang; Christy L Avery; D Y Lin
Journal:  Biostatistics       Date:  2015-09-21       Impact factor: 5.899

3.  A Selective Review of Group Selection in High-Dimensional Models.

Authors:  Jian Huang; Patrick Breheny; Shuangge Ma
Journal:  Stat Sci       Date:  2012       Impact factor: 2.901

4.  Analyzing Association Mapping in Pedigree-Based GWAS Using a Penalized Multitrait Mixed Model.

Authors:  Jin Liu; Can Yang; Xingjie Shi; Cong Li; Jian Huang; Hongyu Zhao; Shuangge Ma
Journal:  Genet Epidemiol       Date:  2016-06-01       Impact factor: 2.135

5.  Identification of breast cancer prognosis markers using integrative sparse boosting.

Authors:  S Ma; J Huang; Y Xie; N Yi
Journal:  Methods Inf Med       Date:  2012-02-20       Impact factor: 2.176

6.  GRIA: Graphical Regularization for Integrative Analysis.

Authors:  Changgee Chang; Jihwan Oh; Qi Long
Journal:  Proc SIAM Int Conf Data Min       Date:  2020

7.  Integrating approximate single factor graphical models.

Authors:  Xinyan Fan; Kuangnan Fang; Shuangge Ma; Qingzhao Zhang
Journal:  Stat Med       Date:  2019-11-20       Impact factor: 2.373

8.  Integrative analysis of multiple cancer prognosis studies with gene expression measurements.

Authors:  Shuangge Ma; Jian Huang; Fengrong Wei; Yang Xie; Kuangnan Fang
Journal:  Stat Med       Date:  2011-08-25       Impact factor: 2.373

9.  Integrative sparse principal component analysis of gene expression data.

Authors:  Mengque Liu; Xinyan Fan; Kuangnan Fang; Qingzhao Zhang; Shuangge Ma
Journal:  Genet Epidemiol       Date:  2017-11-08       Impact factor: 2.135

10.  Integrative Analysis of Cancer Diagnosis Studies with Composite Penalization.

Authors:  Jin Liu; Jian Huang; Shuangge Ma
Journal:  Scand Stat Theory Appl       Date:  2014-03-01       Impact factor: 1.396

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.