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PLEXdb Tools

BLAST | Microarray Analysis | Genomics Exploration | Visualization | Download Sequences

Quick Links
Gene List Suite Create, analyze and annotate gene lists.
Gene OscilloScope Search for experiments where the expressions of queried genes fluctuate (oscillate) the most.
Fluctuation Filter Data mining via fluctuation in expression: Get the probe sets /genes whose fluctuation in expression (Coeff. of Variation or CV) matches your specifications.
Get Sequences Get consensus sequence for probesets.
Download Annotation for Probesets View or download a table showing all annotation for a list of probesets.
Model Genome Interrogator For a selected list of genes from any GeneChip, derives the physical position on the model genomes(rice or Arabidopsis) with supporting information from predicted ORF and full-length cDNA; can view gene structures and retrieve corresponding sequences.
Microarray Platform Translator Translate probe sets from one microarray platform to another.
GO Annotator Get GO annotation for a list of probe set ids.
VMatch Search for PLEXdb probes that match your sequence.
Plant Ontology Browser Search for latest PO terms.
Plant Development Ontology Browser Search for latest growth and development PO terms.
BLAST Tools
PLEXdb BLAST Search the PLEXdb database for matching exemplars from microarray platforms.
PlantGDB BLAST Search the PlantGDB databases.
Dedicated BLAST Search PlantGDB
Dedicated VMATCH Search for PLEXdb probes that match your sequence.
 
Microarray Data Analysis Tools
Data normalization was carried out by a script using Bioconductor and R.
  • Bioconductor/R : Bioconductor is an open source project for microarray data analysis, visualization and annotation. It started in fall of 2001 and quickly evolved into a high-profile project. It provides packages for analyzing both Affymetrix GeneChip data (affy, affydata and affycomp packages) and cDNA spotted microarrays. PLEXdb uses 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.
  • R is a GNU project. It is an open source language and environment for statistical computing. R is a functional programming language and has powerful graphical and visualization capabilities. Bioconductor is developed with R.
  • 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, the presence/absence call and the p-values of calls.
  • dChip: This is one of the most common normalization methods 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 PLEXdb.
  • The Power Atlas is a web-based resource to assist investigators in the planning and design of microarray and expression based experiments. This software is currently aimed at estimating the power and sample size for a two-group comparison based upon pilot data.

Genomics Data Exploration Tools
  • Model Genome Interrogator This tool allows the user to input a selected list of genes from a microarray to derive the physical position on the rice and Arabidopsis thaliana genomes with hyperlinks to the alignments on the GRAMENE rice and the TAIR Arabidopsis thaliana browsers.

  • MapViewer and SeqViewer are 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 permits searching for names or short sequences and viewing hits against the whole genome. MapViewer works from the other direction, letting users select chromosomes or segments, locating relevant makers, clones and gene sequence information.

General Purpose Data Visualization Tools
  • GGobi:The GGobi software is a system for the visualization of high-dimensional data. It can be directly accessed from R, Perl or Python. It supports databases 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 the user.

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

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

 
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