Biomaterial Database

An empirical Bayes method for robust variance estimation in detecting DEGs using microarray data. 2017

Na You, and Xueqin Wang

1 School of Mathematics, Southern China Center for Statistical Science, Sun Yat-sen University, Guangzhou 510275, P. R. China.

The microarray technology is widely used to identify the differentially expressed genes due to its high throughput capability. The number of replicated microarray chips in each group is usually not abundant. It is an efficient way to borrow information across different genes to improve the parameter estimation which suffers from the limited sample size. In this paper, we use a hierarchical model to describe the dispersion of gene expression profiles and model the variance through the gene expression level via a link function. A heuristic algorithm is proposed to estimate the hyper-parameters and link function. The differentially expressed genes are identified using a multiple testing procedure. Compared to SAM and LIMMA, our proposed method shows a significant superiority in term of detection power as the false discovery rate being controlled.

UI	MeSH Term	Description	Entries
D003198	Computer Simulation	Computer-based representation of physical systems and phenomena such as chemical processes.	Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000465	Algorithms	A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.	Algorithm
D001499	Bayes Theorem	A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.	Bayesian Analysis,Bayesian Estimation,Bayesian Forecast,Bayesian Method,Bayesian Prediction,Analysis, Bayesian,Bayesian Approach,Approach, Bayesian,Approachs, Bayesian,Bayesian Approachs,Estimation, Bayesian,Forecast, Bayesian,Method, Bayesian,Prediction, Bayesian,Theorem, Bayes
D015894	Genome, Human	The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.	Human Genome,Genomes, Human,Human Genomes
D059467	Transcriptome	The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.	Transcriptomes,Gene Expression Profiles,Gene Expression Signatures,Transcriptome Profiles,Expression Profile, Gene,Expression Profiles, Gene,Expression Signature, Gene,Expression Signatures, Gene,Gene Expression Profile,Gene Expression Signature,Profile, Gene Expression,Profile, Transcriptome,Profiles, Gene Expression,Profiles, Transcriptome,Signature, Gene Expression,Signatures, Gene Expression,Transcriptome Profile
D018401	Sample Size	The number of units (persons, animals, patients, specified circumstances, etc.) in a population to be studied. The sample size should be big enough to have a high likelihood of detecting a true difference between two groups. (From Wassertheil-Smoller, Biostatistics and Epidemiology, 1990, p95)	Sample Sizes,Size, Sample,Sizes, Sample
D020411	Oligonucleotide Array Sequence Analysis	Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.	DNA Microarrays,Gene Expression Microarray Analysis,Oligonucleotide Arrays,cDNA Microarrays,DNA Arrays,DNA Chips,DNA Microchips,Gene Chips,Oligodeoxyribonucleotide Array Sequence Analysis,Oligonucleotide Microarrays,Sequence Analysis, Oligonucleotide Array,cDNA Arrays,Array, DNA,Array, Oligonucleotide,Array, cDNA,Arrays, DNA,Arrays, Oligonucleotide,Arrays, cDNA,Chip, DNA,Chip, Gene,Chips, DNA,Chips, Gene,DNA Array,DNA Chip,DNA Microarray,DNA Microchip,Gene Chip,Microarray, DNA,Microarray, Oligonucleotide,Microarray, cDNA,Microarrays, DNA,Microarrays, Oligonucleotide,Microarrays, cDNA,Microchip, DNA,Microchips, DNA,Oligonucleotide Array,Oligonucleotide Microarray,cDNA Array,cDNA Microarray
D030541	Databases, Genetic	Databases devoted to knowledge about specific genes and gene products.	Genetic Databases,Genetic Sequence Databases,OMIM,Online Mendelian Inheritance In Man,Genetic Data Banks,Genetic Data Bases,Genetic Databanks,Genetic Information Databases,Bank, Genetic Data,Banks, Genetic Data,Data Bank, Genetic,Data Banks, Genetic,Data Base, Genetic,Data Bases, Genetic,Databank, Genetic,Databanks, Genetic,Database, Genetic,Database, Genetic Information,Database, Genetic Sequence,Databases, Genetic Information,Databases, Genetic Sequence,Genetic Data Bank,Genetic Data Base,Genetic Databank,Genetic Database,Genetic Information Database,Genetic Sequence Database,Information Database, Genetic,Information Databases, Genetic,Sequence Database, Genetic,Sequence Databases, Genetic