Database

We have integrated genomic information from public database resources and generated the Arabidopsis MAPK Cascade and Signal Transduction Database - MAPKDB. The database provides detailed descriptions of Arabidopsis genes important for the regulation of plant signaling networks. For example, the Arabidopsis genes covered in our database perform essential functions in MAPK cascade signaling, two-component signaling, calcium sensing and signaling, G-protein signaling, and transcription.

Protocols/FAQ

Protocols useful for working with Arabidopsis and maize protoplasts may be requested. We have also compiled a list of frequently asked questions, and provided answers based on our knowledge and experience with Arabidopsis and maize protoplast experiments.

Education

To better share the information we have learned from our research, we have provided three PowerPoint presentations covering 1) an overview of plant signal transduction, 2) sugar signaling, and 3) MAPK signaling in innate immunity.

Nomenclature

A simplified nomenclature for Arabidopsis MAPKs and MAPKKs is being proposed in a soon-to-be published article in Trends in Plant Science. A portion of that paper may be viewed here.

T-DNA lines

Signal transduction research will likely benefit from the increasing availability of T-DNA insertion lines. We provide a regularly-updated list of putative T-DNA mutants in MAPK cascade genes that are available from the SALK Institute or the Torrey Mesa Research Institute (TMRI)/Syngenta.

Mapk Cascade Gene Expression

This web page displays 87 sets of gene expression data for each putative MAPK cascade gene on the Affymetrix ATH1 chip from NASCArrays and AtGenExpress. The data have been collected from AMPL and PlantsP. The nomenclature is based on the TIPS review (7: 301-308, 2002) by the international MAPK group and the Gene Family files submitted to TAIR.

Affymetrix

Affymetrix Genechip (8K): Based on the currently available resources, we have found incorrect or ambiguous annotation for a large number of Arabidopsis genes on the 8K Affymetrix Genechip. Although many papers on global gene expression profiling have been published based on the existing annotation of Arabidopsis Affymetrix Genechip, the problems of incorrect or ambiguous annotation have never been brought up until NetAffx provided the actual 8K GeneChip sequences. Three types of annotation problems are described in problems in Affymetrix GeneChip annotation. To eliminate the problems, we have written a Perl program to systematically gather the correct information. A new list (generated through a multi-step strategy as described in the strategy for determining Affymetrix annotation) with matching AGI names and GeneChip IDs and relevant information can now be searched or downloaded through our database. An updated GeneChip annotation generated independently using a different approach can also be searched or downloaded from the Schroeder lab web site.

GeneChip ATH1 Genome Array (25K): In collaboration with TIGR, Affymetrix has provided better and informative annotation for its 25K GeneChip. As the annotaiton was done before TIGR's third major release (3.0) of the Arabidopsis genome annotation. The Affymetrix annotation has missed new genes added since version 2.0 and other important updates. In the mean time, to facilitate global gene expression analysis and extract useful information from massive amount of data (e.g., generated by Affymetrix GeneChips and microarrays) to reveal biological insights, we have initiated an effort to classify Arabidopsis genes based on related functions. Therefore, we updated and enriched the annotation for the 25K GeneChip based on TIGR's updated data and the additional gene functional information collected both systematically and manually from literature, websites and blast searches.

Plant MAPK scientists

The plant MAPK research community is constantly growing. While not exhaustive, this list includes contacts for many of the plant MAPK scientists around the world.

Functional Genomics of Plant Phosphorylation

PlantsP is an excellent information source for plant protein phospatases and kinases. Among other things, it features plant protein phosphatase and complete kinase classifications, name and keyword search and PlantsP Knockout Resources.

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