Comprehensive literature review and statistical considerations for microarray meta-analysis

An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies

(2011) Jia Li et al.   Annals of Applied Statistics

Genomic biomarkers in predictive medicine. An interim analysis

(2011) Richard Simon   EMBO Molecular Medicine

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Bayesian meta-analysis for identifying periodically expressed genes in fission yeast cell cycle

(2010) Xiaodan Fan et al.   Annals of Applied Statistics

Module-based prediction approach for robust inter-study predictions in microarray data

(2010) Zhibao Mi et al.   BIOINFORMATICS

Meta-analysis for pathway enrichment analysis when combining multiple genomic studies

(2010) Kui Shen et al.   BIOINFORMATICS

Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database

(2010) Wei-Chung Cheng et al.   BMC BIOINFORMATICS

Comparison study of microarray meta-analysis methods

(2010) Anna Campain et al.   BMC BIOINFORMATICS

Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana

(2010) Gyan Srivastava et al.   BMC Systems Biology

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations

(2010) Neil A. Mabbott et al.   IMMUNOBIOLOGY

Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis

(2010) Gyan Prakash Srivastava et al.   International Journal of Data Mining and Bioinformatics

A Bayesian Model for Cross-Study Differential Gene Expression

(2010) Robert B. Scharpf et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Weighted Distance Weighted Discrimination and Its Asymptotic Properties

(2010) Xingye Qiao et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Gene Expression-Based Prognostic Signatures in Lung Cancer: Ready for Clinical Use?

(2010) J. Subramanian et al.   JNCI-Journal of the National Cancer Institute

Cancer Biomarkers: Can We Turn Recent Failures into Success?

(2010) E. P. Diamandis   JNCI-Journal of the National Cancer Institute

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

(2010) Ilya Kupershmidt et al.   PLoS One

Karl Pearson’s meta-analysis revisited

(2009) Art B. Owen   ANNALS OF STATISTICS

Biomarker detection in the integration of multiple multi-class genomic studies

(2009) Shuya Lu et al.   BIOINFORMATICS

Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction

(2009) Chunrong Cheng et al.   BIOINFORMATICS

A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide

(2009) Jonathan D. Wren   BIOINFORMATICS

Moderated effect size and P-value combinations for microarray meta-analyses

(2009) G. Marot et al.   BIOINFORMATICS

Integrative disease classification based on cross-platform microarray data

(2009) Chun-Chi Liu et al.   BMC BIOINFORMATICS

Human gene expression sensitivity according to large scale meta-analysis

(2009) Pei Hao et al.   BMC BIOINFORMATICS

A-MADMAN: Annotation-based microarray data meta-analysis tool

(2009) Andrea Bisognin et al.   BMC BIOINFORMATICS

RankAggreg, an R package for weighted rank aggregation

(2009) Vasyl Pihur et al.   BMC BIOINFORMATICS

Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast

(2009) Saumyadipta Pyne et al.   BMC GENOMICS

Measuring similarity between gene expression profiles: a Bayesian approach

(2009) Viet-Anh Nguyen et al.   BMC GENOMICS

Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family

(2009) Sandeep Sanga et al.   BMC Medical Genomics

PrognoScan: a new database for meta-analysis of the prognostic value of genes

(2009) Hideaki Mizuno et al.   BMC Medical Genomics

Unsupervised Analysis of Transcriptomic Profiles Reveals Six Glioma Subtypes

(2009) A. Li et al.   CANCER RESEARCH

Integrative Transcriptome Analysis Reveals Common Molecular Subclasses of Human Hepatocellular Carcinoma

(2009) Y. Hoshida et al.   CANCER RESEARCH

Housekeeping genes in prostate tumorigenesis

(2009) Jinyoung Byun et al.   INTERNATIONAL JOURNAL OF CANCER

An Integrative Network Approach to Map the Transcriptome to the Phenome

(2009) Michael R. Mehan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Improving the Biomarker Pipeline to Develop and Evaluate Cancer Screening Tests

(2009) Stuart G. Baker   JNCI-Journal of the National Cancer Institute

Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers

(2009) Jonathan M Dreyfuss et al.   Molecular Cancer

GeneSigDB—a curated database of gene expression signatures

(2009) Aedín C. Culhane et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Atlas at the European Bioinformatics Institute

(2009) Misha Kapushesky et al.   NUCLEIC ACIDS RESEARCH

Dynamism in gene expression across multiple studies

(2009) Alexander A. Morgan et al.   PHYSIOLOGICAL GENOMICS

Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases

(2009) Kai Wang et al.   PLoS Computational Biology

Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

(2009) Javier Carrera et al.   GENOME BIOLOGY

A toolbox of novel murine house-keeping genes identified by meta-analysis of large scale gene expression profiles

(2008) Markus Frericks et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments

(2008) Fangxin Hong et al.   BIOINFORMATICS

Merging two gene-expression studies via cross-platform normalization

(2008) Andrey A. Shabalin et al.   BIOINFORMATICS

Merging microarray data from separate breast cancer studies provides a robust prognostic test

(2008) Lei Xu et al.   BMC BIOINFORMATICS

MiMiR: an integrated platform for microarray data sharing, mining and analysis

(2008) Chris Tomlinson et al.   BMC BIOINFORMATICS

Pathway analysis reveals functional convergence of gene expression profiles in breast cancer

(2008) Ronglai Shen et al.   BMC Medical Genomics

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis

(2008) Andrew H Sims et al.   BMC Medical Genomics

Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age

(2008) Yohan Lee et al.   BMC Medical Genomics

Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasets

(2008) Emma Steele et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Genevestigator Transcriptome Meta-Analysis and Biomarker Search using Rice and Barley Gene Expression Databases

(2008) Philip Zimmermann et al.   Molecular Plant

Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data

(2008) A. E. Ivliev et al.   NUCLEIC ACIDS RESEARCH

A Visual Data Mining Tool that Facilitates Reconstruction of Transcription Regulatory Networks

(2008) Daniel C. Jupiter et al.   PLoS One

Identification of a Common Gene Expression Response in Different Lung Inflammatory Diseases in Rodents and Macaques

(2008) Jeroen L. A. Pennings et al.   PLoS One

TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database

(2008) Fabrice Lopez et al.   PLoS One

Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools

(2008) S L Rodriguez-Zas et al.   REPRODUCTION

Interlaboratory Evaluation of Genomic Signatures for Predicting Carcinogenicity in the Rat

(2008) Mark R. Fielden et al.   TOXICOLOGICAL SCIENCES

Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets

(2008) Adaikalavan Ramasamy et al.   PLOS MEDICINE

Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays

(2007) Elias Zintzaras et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY