WebArrayDB: cross-platform microarray data analysis and public data repository
نویسندگان
چکیده
MOTIVATION Cross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating and analyzing large amounts of microarray data obtained from different array platforms. RESULTS An open source integrated microarray database and analysis suite, WebArrayDB (http://www.webarraydb.org), has been developed that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion, and allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters. AVAILABILITY The software package is available for the use on a public web server (http://www.webarraydb.org) or can be downloaded. are available at Bioinformatics online.
منابع مشابه
ArrayExpress—a public repository for microarray gene expression data at the EBI
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 approximately 12,000 hybridizations covering 35 species. Data can be submitted online or directly from local databases or LIMS in a standard format,...
متن کاملArrayExpress—a public database of microarray experiments and gene expression profiles
UNLABELLED ArrayExpress is a public database for high throughput functional genomics data. ArrayExpress consists of two parts--the ArrayExpress Repository, which is a MIAME supportive public archive of microarray data, and the ArrayExpress Data Warehouse, which is a database of gene expression profiles selected from the repository and consistently re-annotated. Archived experiments can be queri...
متن کاملMediante: a web-based microarray data manager
UNLABELLED Mediante is a MIAME-compliant microarray data manager that links together annotations and experimental data. Developed as a J2EE three-tier application, Mediante integrates a management system for production of long oligonucleotide microarrays, an experimental data repository suitable for home made or commercial microarrays, and a user interface dedicated to the management of microar...
متن کاملMapping Microarray Chip Feature Ids to Gene Ids for Microarray Platforms in Ncbi Geo
The Gene Expression Omnibus or NCBI GEO (http://www.ncbi.nlm.nih.gov/projects/geo/) is one of the most comprehensive public repositories of microarray data. The data in NCBI GEO is organized into samples, series, datasets and platforms. Platform files specify the characteristics of a particular type of microarray chip, including a mapping of chip features to genetic features. These mappings are...
متن کاملComparing alternative pipelines for cross-platform microarray gene expression data integration with RNA-seq data in breast cancer
Background: According to major public repositories statistics an overwhelming majority of the existing and newly uploaded data originates from microarray experiments. Unfortunately, the potential of this data to bring new insights is limited by the effects of individual study-specific biases due to small number of biological samples. Increasing sample size by direct microarray data integration ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Bioinformatics
دوره 25 18 شماره
صفحات -
تاریخ انتشار 2009