Individual-level analysis of differential expression of genes and pathways for personalized medicine
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Qiang Sun | Mengmeng Zhang | Yunyan Gu | Lishuang Qi | Wenyuan Zhao | Zheng Guo | Yang Li | Hongwei Wang | Shu-Lin Liu | Pengfei Li | Yunyan Gu | Wenyuan Zhao | Zheng Guo | Qiang Sun | L. Qi | Hongwei Wang | Pengfei Li | Mengmeng Zhang | Shu-Lin Liu | Yang Li
[1] Alex E. Lash,et al. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..
[2] Yanchun Liang,et al. Weighted Change-Point Method for Detecting Differential Gene Expression in Breast Cancer Microarray Data , 2012, PloS one.
[3] Li-Jen Su,et al. Protein arginine methyltransferase 5 is a potential oncoprotein that upregulates G1 cyclins/cyclin‐dependent kinases and the phosphoinositide 3‐kinase/AKT signaling cascade , 2012, Cancer science.
[4] Bin Li,et al. Extensive increase of microarray signals in cancers calls for novel normalization assumptions , 2011, Comput. Biol. Chem..
[5] R. Gray. A Class of $K$-Sample Tests for Comparing the Cumulative Incidence of a Competing Risk , 1988 .
[6] Mitchell J. Mergenthaler. Nonparametrics: Statistical Methods Based on Ranks , 1979 .
[7] Mats Lambe,et al. Biomarker Discovery in Non–Small Cell Lung Cancer: Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation , 2012, Clinical Cancer Research.
[8] L. Hawthorn,et al. Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast , 2010, BMC Cancer.
[9] Rainer Breitling,et al. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments , 2004, FEBS letters.
[10] W. V. van IJcken,et al. Gene Expression-Based Classification of Non-Small Cell Lung Carcinomas and Survival Prediction , 2010, PloS one.
[11] Ilya Shmulevich,et al. Gene pair signatures in cell type transcriptomes reveal lineage control , 2013, Nature Methods.
[12] David M. Simcha,et al. Tackling the widespread and critical impact of batch effects in high-throughput data , 2010, Nature Reviews Genetics.
[13] Israel Steinfeld,et al. Novel Rank-Based Statistical Methods Reveal MicroRNAs with Differential Expression in Multiple Cancer Types , 2009, PloS one.
[14] Dimitris Kletsas,et al. Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints , 2006, Nature.
[15] Lang He,et al. Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis , 2012, Comput. Biol. Chem..
[16] F. Wilcoxon. Individual Comparisons by Ranking Methods , 1945 .
[17] R. Tibshirani,et al. Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[18] J. Tchinda,et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. , 2006, Science.
[19] E. Kaplan,et al. Nonparametric Estimation from Incomplete Observations , 1958 .
[20] Chuhsing Kate Hsiao,et al. Identification of a Novel Biomarker, SEMA5A, for Non–Small Cell Lung Carcinoma in Nonsmoking Women , 2010, Cancer Epidemiology, Biomarkers & Prevention.
[21] Doulaye Dembélé,et al. Fold change rank ordering statistics: a new method for detecting differentially expressed genes , 2014, BMC Bioinformatics.
[22] Baolin Wu,et al. Cancer outlier differential gene expression detection. , 2007, Biostatistics.
[23] Laura Lentini,et al. CENPA overexpression promotes genome instability in pRb-depleted human cells , 2009, Molecular Cancer.
[24] R. Tibshirani,et al. Outlier sums for differential gene expression analysis. , 2007, Biostatistics.
[25] D.,et al. Regression Models and Life-Tables , 2022 .
[26] K. Coombes,et al. Robust Gene Expression Signature from Formalin-Fixed Paraffin-Embedded Samples Predicts Prognosis of Non–Small-Cell Lung Cancer Patients , 2011, Clinical Cancer Research.
[27] Hugues Bersini,et al. Batch effect removal methods for microarray gene expression data integration: a survey , 2013, Briefings Bioinform..
[28] Jing Zhu,et al. Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories , 2008, Bioinform..
[29] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[30] Zheng Guo,et al. Separate enrichment analysis of pathways for up- and downregulated genes , 2014, Journal of The Royal Society Interface.
[31] Xavier Estivill,et al. Gene expression signatures in breast cancer distinguish phenotype characteristics, histologic subtypes, and tumor invasiveness , 2010, Cancer.
[32] Greg Tucker-Kellogg,et al. A Comparison of Methods for Data-Driven Cancer Outlier Discovery, and An Application Scheme to Semisupervised Predictive Biomarker Discovery , 2011, Cancer informatics.
[33] H. Toutenburg,et al. Lehmann, E. L., Nonparametrics: Statistical Methods Based on Ranks, San Francisco. Holden‐Day, Inc., 1975. 480 S., $ 22.95 . , 1977 .
[34] Elisabeth Brambilla,et al. Ectopic Activation of Germline and Placental Genes Identifies Aggressive Metastasis-Prone Lung Cancers , 2013, Science Translational Medicine.
[35] Gordon K Smyth,et al. Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .
[36] E. Lehmann,et al. Nonparametrics: Statistical Methods Based on Ranks , 1976 .
[37] L. O’Driscoll,et al. Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis. , 2013, Carcinogenesis.
[38] Daniel Q. Naiman,et al. Simple decision rules for classifying human cancers from gene expression profiles , 2005, Bioinform..
[39] Guillem Rigaill,et al. Identifying subgroup markers in heterogeneous populations , 2013, Nucleic acids research.
[40] Rafael A Irizarry,et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.
[41] H. Lian. MOST: detecting cancer differential gene expression. , 2007, Biostatistics.
[42] Pier Paolo Pandolfi,et al. Subtle variations in Pten dose determine cancer susceptibility , 2010, Nature Genetics.
[43] Rafael Rosell,et al. Gene expression profiling reveals novel biomarkers in nonsmall cell lung cancer , 2011, International journal of cancer.
[44] J. Mazières,et al. DNA replication stress response involving PLK1, CDC6, POLQ, RAD51 and CLASPIN upregulation prognoses the outcome of early/mid-stage non-small cell lung cancer patients , 2012, Oncogenesis.
[45] Paolo Toniolo,et al. Pregnancy‐induced chromatin remodeling in the breast of postmenopausal women , 2012, International journal of cancer.
[46] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[47] F. Harrell,et al. Prognostic/Clinical Prediction Models: Multivariable Prognostic Models: Issues in Developing Models, Evaluating Assumptions and Adequacy, and Measuring and Reducing Errors , 2005 .
[48] Daniel Q. Naiman,et al. Classifying Gene Expression Profiles from Pairwise mRNA Comparisons , 2004, Statistical applications in genetics and molecular biology.
[49] Renee Rubio,et al. Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue , 2009, Breast Cancer Research and Treatment.
[50] Peter M Schlag,et al. Identification of early molecular markers for breast cancer , 2011, Molecular Cancer.
[51] Shridar Ganesan,et al. X chromosomal abnormalities in basal-like human breast cancer. , 2006, Cancer cell.
[52] Jianhua Hu,et al. Cancer outlier detection based on likelihood ratio test , 2008, Bioinform..
[53] D. Wolfe,et al. Nonparametric Statistical Methods. , 1974 .
[54] Hiroaki Kitano,et al. Large-Scale Analysis of Network Bistability for Human Cancers , 2010, PLoS Comput. Biol..
[55] D. Cox. Regression Models and Life-Tables , 1972 .
[56] Satoru Miyano,et al. Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. , 2012, Cancer research.
[57] Benjamin Haibe-Kains,et al. DNA methylation profiling reveals a predominant immune component in breast cancers , 2011, EMBO molecular medicine.