PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses

Nucleic Acids Res. 2007 Jan;35(Database issue):D841-5. doi: 10.1093/nar/gkl835. Epub 2006 Nov 11.

Abstract

Plants react to pathogen attack by expressing specific proteins directed toward the infecting pathogens. This involves the transcriptional activation of specific gene sets. PathoPlant, a database on plant-pathogen interactions and signal transduction reactions, has now been complemented by microarray gene expression data from Arabidopsis thaliana subjected to pathogen infection and elicitor treatment. New web tools enable identification of plant genes regulated by specific stimuli. Sets of genes co-regulated by multiple stimuli can be displayed as well. A user-friendly web interface was created for the submission of gene sets to be analyzed. This results in a table, listing the stimuli that act either inducing or repressing on the respective genes. The search can be restricted to certain induction factors to identify, e.g. strongly up- or down-regulated genes. Up to three stimuli can be combined with the option of induction factor restriction to determine similarly regulated genes. To identify common cis-regulatory elements in co-regulated genes, a resulting gene list can directly be exported to the AthaMap database for analysis. PathoPlant is freely accessible at http://www.pathoplant.de.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis / microbiology*
  • Binding Sites
  • Databases, Genetic*
  • Gene Expression Profiling*
  • Gene Expression Regulation, Plant*
  • Internet
  • Oligonucleotide Array Sequence Analysis
  • Regulatory Elements, Transcriptional
  • Transcription Factors / metabolism
  • User-Computer Interface

Substances

  • Transcription Factors