Results 1 - 10 of 722

Genes, Themes and Microarrays - Using Information Retrieval for Large-Scale Gene Analysis

by Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski, W. John, Wilbur Mark Boguski , 2000
"... The immense volume of data resulting from DNA microarray experiments, accompanied byanincrease in the number of publications discussing gene-related discoveries, presents a major data analysis challenge. Current methods for genome-wide analysis of expression data typically rely on cluster analy ..."
Abstract - Cited by 98 (8 self) - Add to MetaCart
The immense volume of data resulting from DNA microarray experiments, accompanied byanincrease in the number of publications discussing gene-related discoveries, presents a major data analysis challenge. Current methods for genome-wide analysis of expression data typically rely on cluster

An Empirical Bayes Approach to Inferring Large-Scale Gene Association Networks

by Juliane Schäfer, Korbinian Strimmer - BIOINFORMATICS , 2004
"... Motivation: Genetic networks are often described statistically by graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis where the sample size is small compared to the number of considered genes. This renders many standar ..."
Abstract - Cited by 237 (6 self) - Add to MetaCart
Motivation: Genetic networks are often described statistically by graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis where the sample size is small compared to the number of considered genes. This renders many

On testing the significance of sets of genes

by Bradley Efron, Robert Tibshirani - Annals of Applied Statistics
"... This paper discusses the problem of identifying differentially expressed groups of genes from a microarray experiment. The groups of genes are externally defined, for example, sets of gene pathways derived from biological databases. Our starting point is the interesting Gene Set Enrichment Analysis ..."
Abstract - Cited by 166 (3 self) - Add to MetaCart
This paper discusses the problem of identifying differentially expressed groups of genes from a microarray experiment. The groups of genes are externally defined, for example, sets of gene pathways derived from biological databases. Our starting point is the interesting Gene Set Enrichment Analysis

Transitive functional annotation by shortestpath analysis of gene expression data

by Xianghong Zhou , Ming-Chih J Kao , Wing Hung Wong - PNAS
"... Current methods for the functional analysis of microarray gene expression data make the implicit assumption that genes with similar expression profiles have similar functions in cells. However, among genes involved in the same biological pathway, not all gene pairs show high expression similarity. ..."
Abstract - Cited by 108 (9 self) - Add to MetaCart
. Here, we propose that transitive expression similarity among genes can be used as an important attribute to link genes of the same biological pathway. Based on large-scale yeast microarray expression data, we use the shortestpath analysis to identify transitive genes between two given genes from

Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes

by Harald H H Göring , Joanne E Curran , Matthew P Johnson , Thomas D Dyer , Jac Charlesworth , Shelley A Cole , Jeremy B M Jowett , Lawrence J Abraham , David L Rainwater , Anthony G Comuzzie , Michael C Mahaney , Laura Almasy , Jean W Maccluer , Ahmed H Kissebah , Gregory R Collier , Eric K Moses , John Blangero - Nat. Genet , 2007
"... Quantitative differences in gene expression are thought to contribute to phenotypic differences between individuals. We generated genome-wide transcriptional profiles of lymphocyte samples from 1,240 participants in the San Antonio Family Heart Study. The expression levels of 85% of the 19,648 dete ..."
Abstract - Cited by 45 (2 self) - Add to MetaCart
,648 detected autosomal transcripts were significantly heritable. Linkage analysis uncovered 41,000 cis-regulated transcripts at a false discovery rate of 5% and showed that the expression quantitative trait loci with the most significant linkage evidence are often located at the structural locus of a given

KEGG/EXPRESSION: A Database for Browsing and Analysing Microarray Expression Data

by Susumu Goto, Shuichi Kawashima, Yoshinori Okuji, Tomomi Kamiya, Satoshi, Minoru Kanehisa , 2000
"... Introduction The recent progress of DNA chip and microarray technologies produces a large amount of expression data with various experiments. A new database management system that integrates large-scale study of gene expression with other molecular biology databases and various analysis tools is re ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
Introduction The recent progress of DNA chip and microarray technologies produces a large amount of expression data with various experiments. A new database management system that integrates large-scale study of gene expression with other molecular biology databases and various analysis tools

ONCOMINE: a cancer microarray database and integrated data-mining platform

by Daniel R. Rhodes, Jianjun Yu, K. Shanker Z, An Deshp, Radhika Varambally, Debashis Ghosh, Terrence Barrette, Akhilesh P, Ey B, Arul M. Chinnaiyan - Neoplasia , 2004
"... DNA microarray technology has led to an explosion of oncogenomic analyses, generating a wealth of data and uncovering the complex gene expression patterns of cancer. Unfortunately, due to the lack of a unifying bioinformatic resource, the majority of these data sit stagnant and disjointed following ..."
Abstract - Cited by 83 (8 self) - Add to MetaCart
publication, massively underutilized by the cancer research community. Here, we present ONCOMINE, a cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses. To date, ONCOMINE contains 65 gene expression datasets comprising nearly 48

ArrayExpress—a public repository for microarray gene expression data at the EBI

by H. Parkinson, U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. Garcia Lara, E. Holloway, M. Kapushesky, P. Lilja, G. Mukherjee, A. Oezcimen, T. Rayner, P. Rocca-serra, A. Sharma, S. Sansone, A. Brazma - Nucleic Acids Res , 2005
"... ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from 12 000 hybridizations covering 35 species. Data can ..."
Abstract - Cited by 77 (11 self) - Add to MetaCart
. A facility to query experiments by gene and sample properties is provided for a growing subset of curated data that is loaded in to the ArrayExpress data warehouse. Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at

Optimal gene expression analysis by microarrays

by Lance D. Miller, Philip M. Long, Limsoon Wong, Sayan Mukherjee, Lisa M. Mcshane, Edison T. Liu - Cancer Cell , 2002
"... DNA microarrays make possible the rapid and comprehensive assessment of the transcriptional activity of a cell, and as such have proven valuable in assessing the molecular contributors to biological processes and in the classification of human cancers. The major challenge in using this technology is ..."
Abstract - Cited by 21 (2 self) - Add to MetaCart
, and the ability to make sense of the results through intelligent database interrogation. Expression array technology Expression genomics is an approach that examines gene expression in a comprehensive and massively parallel fashion. The core technology in expression genomics is microarrays, whereby thousands

Disease Gene Characterization through Large-Scale Co-Expression Analysis

by Allen Day, Jun Dong, Vincent A. Funari, Bret Harry, Samuel P. Strom, Dan H. Cohn, Stanley F
"... Background: In the post genome era, a major goal of biology is the identification of specific roles for individual genes. We report a new genomic tool for gene characterization, the UCLA Gene Expression Tool (UGET). Results: Celsius, the largest co-normalized microarray dataset of Affymetrix based g ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
Background: In the post genome era, a major goal of biology is the identification of specific roles for individual genes. We report a new genomic tool for gene characterization, the UCLA Gene Expression Tool (UGET). Results: Celsius, the largest co-normalized microarray dataset of Affymetrix based
Results 1 - 10 of 722