BIOINFORMATICS PLATFORM


	SAMI User's Guide A guide for SAMI users with a brief description of the main functions of SAMI and comments of displayed results. Real-time RT-PCR Kenneth J. livak and Thomas D. Schmittgen Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2-ΔΔC_T Methids 25, 402-408 (2001) Michael W. Pfaffl A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Research, 29 (2001) Jo Vandesompele et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Genome biology (2003) Michael W. Pfaffl, Graham W. Horgan and Leo Dempfle Relative expression software tool (REST) for group-wise comparison and statisitical analysis of relative expression results in real-time PCR Nucleic Acids Research (2002). Jan H. Schefe, Kerstin E. Lehmann, Ivo R. Buschmann, Thomas Unger, Heiko Funke-kaiser Quantitative real-time RT-PCR data analysis: current concepts and the novel "gene expression's C_T" formula J Mol Med (2006) Yann Karlen, Alan McNair, Sébastien Perseguers, Chrisitian Mazza and Nicolas Mermod Statistical significance of quantitative PCR BMC Bioinformatics (2007) Christian Ramakers, Jan M. Ruijter, Ronald H. Lekanne Deprez, Antoon F. M. Moorman Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data Neuroscience Letters, 339 (2003) Stuart N. Peirson, Jason N. Butler and Russell G. Foster Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis Nucleic Acids Research, 31 (2003) J Huggett, K Dheda, S Bustin and A Zumla Real-time RT-PCR normalisation; strategies and considerations Genes and Immunity, 6 (2005) Statistical Analysis of Microarrays and Real-time RT-PCR The R Project for Statistical Computing Official web site for the R Foundation. R is available for downloading. Bioconductor Official web site for the Bioconductor Project Bioconductor, with instructions to install Bioconductor properly. The "Bioconductor Project" site also provides multiple packages that may be downloaded and installed to use additionally in R and Bioconductor. LIMMA: Linear Models for Microarray Data Official web site for downloading and installing the Limma package, although already installed with the basic microarray analysis packages of Bioconductor. SAM: Significance Analysis of Microarrays Official web site for the SAM package for R and Bioconductor, and also available as an add in for Microsoft Excel. Tools TM4 MeV: TIGR MultiExperiment Viewer Provides a complete set of tools that generates informative and interrelated displays of expression and annotation data from single or multiple experiments (clustering, trees, networks, normalization, statistica analysis of microarrays...). BRB ArrayTools Official web site of the Biometric Research Branch, in the National Cancer Institute. BRB ArrayTools is available for installing as an add in for Microsoft Excel. Free Statistics And Forecasting Software Provides a complete set of free tools for the mathematical and statistical analysis of data. R Graph Gallery A site with an extensive list of packages for the implentation of a large source of graphics in R. Web Servers for Microarray Analysis GEPAS: Gene Expression Pattern Analysis Suite Web site that provides a set of tools for a multiple variety of microarray analysis (diferential expression, CGH, CHIP on chip...), from background correction to complete statistical analysis. T-REX Web server in GEPAS that provides for statistical analysis of normalized data from differential expression tests. DNMAD Web server that provides help in the normalization of microarray data at the CNIO. This application is part of the Asterias Suite for the analysis of genomic and proteomic data. Softwares for Real-time RT-PCR CAmpER: Calculation of Amplification Efficiencies for RT-PCR Web tool for the automatic analysis of Real-time RT-PCR qBase: Management and automated analysis of real-time quantitative PCR data qBase is a collection of macros for Microsoft Excel (currently only Windows version) for the management and automated analysis of real-time quantitative PCR data. geNorm geNorm is a popular algorithm to determine the most stable reference (housekeeping) genes from a set of tested candidate reference genes in a given sample panel. Apart from a stand alone program available below, the geNorm algorithm is also integrated in the qBasePlus software for real-time PCR data analysis (available from Biogazelle.). DART-PCR: Data Analysis for Real-Time PCR provides a simple means of analysing real-time PCR data from raw flurescence data. GENEX: Gene Expression Macro Simple tool for calculating relative expression values from real-time PCR data generated by the iCycler iQ or MyiQ systems. Microarray Analysis Databases GEO: Gene Expression Omnibus Database of experimental results on gene expression at the NCBI. ArrayExpress A public repository of microarray data at the EBI. SMD - Stanford Microarray Database A private repository of experimental results on microarrays Microarray Designs Affymetrix - Netaffx Analysis Center Server to correlate results of microarray analysis with the design and annotation information of Affymetrix chips. Agilent: eArray An application to design and print custom arrays from Agilent. University of Michigan: Microarray Lab Site for Affymetrix custom designs. Real-time RT-PCR Designs Applied Biosystems: Gene Expression Assays and Arrays Site for Micro Fluidic Card (384 Well Arrays) custom designs. Web Browsers NCBI: National Center for Biotechnology Information A public database with almost everything can be needed for biological and computational biology research (sequences, motifs, domains, expression, profiles, structures, tools...) PubMed The public database of scientific publications. UCSC Genome Bioinformatics A site with the reference sequence and working draft assemblies of genomes. Provides a set of tools to analyze expression, homology, genome mapping... Ensembl Genome Browser Server with annotation on a variety of eucaryotic genomes. The Gene Ontology A source of vocabulary to describe genes and their products attributes. And for almost anything you need to know... Wikipedia English version of the Wikipedia. Viquipèdia Catalan version of the Wikipedia. Wikipedia Spanish version of the Wikipedia. This site was last updated on 16th July 2007.