MAPKDB: A MAP kinase database for signal transduction element identification

The mitogen activated protein kinase (MAPK) cascade is a central signal transduction platform, ubiquitous within the eukaryotes. MAPKs function prominently in different essential cellular processes such as proliferation, differentiation, survival and defense to pathogen attack. The 32 MAPKs of Glycine max (soybean) have been examined functionally to determine if they have any defense role, focusing in on infection by the plant-parasitic nematode Heterodera glycines. Of these 32 MAPKs, 9 have been shown to have a defense function. Hence, the Mitogen Activated Protein Kinase database (MAPKDB) has been developed to assist in such research. The MAPKDB allows users to search the annotations with sequence data for G. max transgenic lines undergoing overexpression (OE) or RNA interference (RNAi) of its defense map kinases. These defense MAPKs include map kinase 2 (MPK2), MPK3, MPK4, MPK5, MPK6, MPK13, MPK16, and MPK20. The database also contains data analysis information for each sample that helps to detect the differential expression of the genes identified within these samples. The database also contains data for each sample that helps to detect the differential expression of the genes identified within these samples. The database has been developed to manage G. max MAPK sequences with sequence alignment for 18 different samples along with two additional OE and RNAi control experiments for a total of 20.

Availability: http://bioinformatics.towson.edu/MAPKDB/ Background: Living organisms are constantly inundated with stimuli of biotic or abiotic nature. These signals are transduced through transduction cascades, allowing them to survive. The mitogen activated protein kinase (MAPK) cascade is a central signal transduction platform that is ubiquitous in the eukaryotes. The cascade is three tiered, transducing input information through a stepwise series of phosphorylation events, leading to an appropriate output response having high fidelity [1]. Consequently, it has been stated that the MAPK platform functions as a cooperative enzyme, switching cells from one distinct state to another [2]. In less usual circumstances, MAPKs have been observed to function independently of both MEKKs (MAPK/ERK Kinase Kinase) and MEKs (MAPK/ERK Kinase) by auto phosphorylation of these proteins [3]. Therefore, there are many things that remain to become understood regarding the function of MAPK signalling, particularly in plants.  packages/release /bioc/html/ DEGseq.html) was then used for differential gene expression analysis of the samples. Experimental samples were compared to control samples in both the MAPK-OE and RNAi groups.

Figure 1: A snapshot of the MAPKDB main web page
The user interface (Figure 1) of MAPKDB provides users with the following functionalities:

Browse:
The user can browse any sample that has been stored in MAPKDB database. The Browse.aspx web page shows a table that can be exported to an Excel file that contains many sequence attributes such as geneID, transcript identification, description, KOG, gene ontology and PFAM. Also, users can see the details of each transcript that shows the transcript ID, description, and FASTA sequence when the plus image is clicked (at the beginning of the row).

Search:
The MAPKDB allows users to search the sequence information in two separate ways. Users can search sequence data through gene ID, or its accompanying description. When users search by gene ID, the exact gene ID has to be entered in the text box to get the matched result. Alternatively, partial characters or text can be entered into searches for genes if the user searches by description. All of the different searches return their query results in a nice table that also shows the sequence data.

Gene expression results:
Users can select a specific sample and retrieve a list of all the transcripts in that sample with their accompanying differential gene expression results (output from DEGSeq). The user can also narrow down the results by searching for specific gene(s) in the analysis. This is done by typing the exact gene ID(s) in the text box to get the gene information that matches those genes. In addition, the user can narrow down the results by searching for gene descriptions or parts of a description. This task is accomplished by typing the partial character(s) in the text box that exists beside the Search by Description identifier (Figure 2).

Figure 2:
A snapshot of the comparing samples page.

Comparing all samples:
The MAPKDB empowers users to compare any two samples. The search will compare the differential expression analysis results from each of the selected samples (MAPK-OE or RNAi experiments). In this web page, the web application enables users to retrieve the genes that are induced or suppressed in the first selected sample and induced or suppressed in the second sample. This search allows allow users to compare samples with their controls. All of these queries return their results in a user-friendly table and the user has the ability to download the data to an excel file.