Hello! Guest! Please Login or Register! Log Out



A. Use microarray element sequences to search other databases:

  • NCBI BLAST - Search the NCBI databases using the Barley1 exemplar sequences
  • PlantGDB BLAST - Search the PlantGDB databases using the Barley1 exemplar sequences

B. Use your own sequence to search Barley1 and other Microarray Elements:

  • BarleyBase BLAST - Search the BarleyBase databases for matching exemplars from Barley1 or ATH1.
  • Dedicated BLAST - Search the Barley1 exemplars stored in PlantGDB
  • Dedicated VMATCH - Search for Barley1 probes that match the sequence you provide.

C. Microarray platform translator (MPT): Mapping microarray elements between platforms. Or mapping from GenBank AC/GI numbers to microarray platforms.

Microarray Data Analysis Tools

Microarray raw data acquisition are conducted with Affymetrix Microarray Suite 5.0 (MAS5.0). Data normalization was carried out with affy package of Bioconductor and MAS5.0 Suite.  R and  Bioconductor are used for expression data analysis and some visualizations:

  • Bioconductor/R : Bioconductor is an open source project aimed at providing comprehensive capability for microarray data analysis, visualization and annotation. It started in fall of 2001, and quickly evolved into a high-profile projects. It provides packages for analyzing both Affymetrix oligo GeneChip data (Affy, affydata and affycomp packages) and cDNA spotted microarray. BarleyBase used its affy package for estimation of expression values by Robust Multi-chip Average (RMA) and MAS5.0 methods. A note from Dr. Dan Nettleton demonstrates how RMA estimation is carried out.

Bioconductor is developed with R, R is a GNU project, an open language and environment for statistical computing. It is a functional programming language and has powerful graphical and visualization capabilities.

  • MAS5.0: Affymetrix provides with its Microarray Analysis Suite 5.0 the function to do absolute and comparative expression estimation. MAS5.0 uses statistical algorithm for normalization and calculate the expression values, he presence/absence call and the p-values of calls.
  • dChip: This is one of the several mostly used normalization method for estimating expression signals. It is free for academic use, though it is not open source. dChip used model-based estimate for gene expression indeces (MBEI), which was proposed by Li and Wong (2001). Bioconductor has a very rough approximation of dChip's  method. dChip is not used in BarleyBase.

Microarray Data Interpretation Tools

  • Functionalize Expression (FuncExpression) supports two way-integration of plant gene functional annotation and the gene expression data. Multiple gene lists can be classified, compared and visualized. The gene function information includes the gene ontology classification, InterPro protein functional domain prediction, metabolic pathway and gene family information. It also support functional classification of  Plant GenBank sequences and TIGR Gene Indices.

Genomics Data Exploration Tools

  • MapViewer and SeqViewer are the two complementary visualization tools developed by TAIR for integrative exploration of the genetic and physical maps, markers, sequences and other annotation information concerning Arabidopsis.

SeqViewer let user to search for names or short sequences and view search hits against the whole genome. MapViewer started from the other way, letting user to select chromosome or segments, locating relevant makers, clones and gene sequence information.

General Purpose Data Visualization Tools

  • GGobi:The GGobi software is a system for visualization of high-dimensional data in interactive and dynamic way. It can be directly access from R, Perl or Python. It supports database like Postgres and MySQL and can support XML formatted data.

  • MATLAB: MATLAB is a commercial high-level language that integrates mathematical computing and visualization. Similar to R, it is easily extensible by user.

  • S-PLUS: This is the commercial counterpart of R, which are both implementation of S programming language.

  • Manet : MANET is a Macintosh-based software for interactive visualization for studying multivariate features of data sets with missing values.


Copyright@2001-2005 The BarleyBase Group
All rights reserved.

For problems with the webpages, contact barleybasewebmaster