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| Description of PathoPlant® |
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Pathogen recognition and signal transduction is essential for plants to induce a
variety of defense responses like hypersensitive reaction, oxidative burst or systemic
acquired resistance. The amount of information on signal transduction mechanisms during
plant-pathogen interactions has accumulated tremendously. To facilitate easy access to
published data and to permit comparative studies of different pathogen response pathways,
a database is indispensable to give a broad overview of the components and interactions
so far known. PathoPlant® has been developed as a relational database for annotation of all identified signal transduction mechanisms during plant-pathogen interactions. PathoPlant®'s source of information are publications from which data is not only extracted but also validated by a scoring system based on the experimental procedure employed. PathoPlant® contains main tables for plants, pathogens, and molecules. These tables are linked with each other and with additional tables defining the type of interaction or reaction. All relevant components in signal transduction like elicitors, proteins, peptides or second messengers are organized in the table for molecules where they are functionally classified. The reactions and interactions that molecules are involved in are annotated and validated in the table for reactions and linked to the respective molecules. Additional information about the subcellular compartment, organ or developmental stage is given in a location table. Furthermore, the involved plants and pathogens and the resulting diseases are listed and linked to the corresponding reactions. Gene expression data from Arabidopsis thaliana microarray experiments have been incorporated into PathoPlant®. This enables to search for specific genes regulated upon pathogen infection or elicitor treatment. All tables are linked to references and to external databases for additional information to provide a comprehensive tool for the research community. The partial E/R-Diagram gives an overview about the main tables and their relations. |
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Search for records in the database
Plant, pathogen, molecule and interaction database records can be searched through their
individual search pages accessible through the respective left-hand Search submenu. This
can be done either by a quick search by name which considers the name, common name and
synonym fields of the records, or by an advanced search with free choice of 3 search
fields and selection of the Boolean operator.By leaving the search fields blank, all database records are displayed. |
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Results list
Search results are displayed in a results list. Detailed information on a record is
displayed by clicking on the Accession No. of the record. A subsequent return to the
results list is possible by pressing the Browser's Back button.Depending on the number of search results, this list may be split into several pages that can be displayed by clicking on the arrows indicating next or previous. The number of results displayed per page can be adjusted. By default, only main attributes of the records are displayed. This can be changed by clicking the button to show all attributes. A search within the listed records enables easy combination of the previous search with a new search term. This feature can also be used to extend the advanced search when more than 3 search fields are needed. The order of the records displayed in the results list can be changed by clicking on the headers of the table. |
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Detailed record information
The detailed information pages contain all information stored in the database for a specific
record. The information is displayed in various sections. The first section contains general
information on the record. The following sections contain additional information that generally
refers to other record in PathoPlant® or in external data resources.
Records listed in Lower or Higher Hierarchy display entries related to the actual one that are
more specific or more general, respectively.The detailed information pages can be reached by clicking on the Acc. No. in a results list or by a direct link from another detailed information page. Alternatively, if the Acc. No. of the record is known, the respective page is retrievable directly by record of the complete Acc. No. in the Search by Accession Number field accessible through the left-hand Search main menu. |
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Microarray expression data
Gene expression data from Arabidopsis thaliana microarray experiments are incorporated
in PathoPlant®. Normalized (print-tip-group lowess method) expression data from experiments
with Arabidopsis thaliana upon pathogen infection or elicitor treatment are searchable.
Two modes of search are available. A list of genes can be submitted to obtain expression data
on these genes for all stimuli annotated in PathoPlant®. This search can be restricted to
certain induction factors. Alternatively, up to 3 different stimuli can be submitted for a
search for genes regulated by these stimuli. Stimuli can be combined to find only genes that
match all stimuli (AND operator) or for displaying all genes that match at least one of the
stimuli (OR operator). This search can also be restricted to certain induction factors. Besides
the induction factors given for a single experiment, mean induction factors were determined
that cover results from replicate experiments. In order to validate mean and single induction
factors, the number of replicates (n) and base-10 logarithm of standard deviation are given.
The result list can be resorted by Locus, Description, Stimulus, Factor, and Mean factor by
clicking on the respective column header. A list of genes obtained by a expression search can
directly be submitted to the Search by locus/gene ID form in PathoPlant®. Additionally, the
gene list can be transferred to AthaMap for a transcription factor binding site analysis.
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In silico expression analysis
An in silico expression analysis can be performed in order to validate short DNA sequences
as cis-elements responsive to different biotic and abiotic stimuli. The potential
cis-sequence is used to perform a genome-wide Arabidopsis thaliana promoter screening.
Either 500 nt or 1000 nt long promoter lengths can be selected for analysis. Genes potentially
regulated by small RNAs can be excluded from the analysis.As search result, the total number of genes as well as the number of genes potentially regulated by small RNAs is displayed. By selecting the respective links, the genes are listed in tables. Gene descriptions are displayed when selecting the arrow. The gene sets are used to calculate mean induction factors for every Arabidopsis thaliana microarray experiment stored within the PathoPlant® database. These mean values are normalized according to overall expression values of each stimulus. This results in a ranked list of microarray experiments according to their mean induction factors. The most probable stimuli the potential cis-element is responsible for can be identified by looking at the highest-ranked stimuli. For each stimulus, the number of expression values used for mean induction factor calculation is given. The corresponding p-value is also calculated for each mean factor to assess its significance. By default, the table is ranked by mean induction factors and can be resorted in descending or ascending order by selecting the headers Stimulus, Mean induction factor, or p-value. The list of genes obtained by the in silico expression analysis can direcly be submitted to the Microarray expression function of PathoPlant® to obtain expression data of these genes for all stimuli. Additionally, this list can also be transferred to AthaMap's Gene Analysis function for a transcription factor binding sites analysis. The number of expression values can be selected to show detailed information about the genes and their individual expression values for a given stimulus. By doing so, a new window or tab will open showing the number of genes present on the microarray chip and a table with the genes, positional information from the promoter screening and gene expression details. The orientation and relative distance refers to the distance of the first match position to the point of reference that can either be the transcription start site (TSS), if known, or otherwise the translation start site (ATG). The individual and mean induction factors of each gene are given as well as the number of replicates (n) and the base-10 logarithm of the standard deviation for mean induction factor calculation of each gene. |
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Printing
Each page contains a link to display the page in a printer-friendly version without the left
and upper frames. The normal display is restored by using the Back button of the Browser or
by clicking on any link on the page. A long results list may be adapted by reducing the number
of results displayed per page.
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Saving a query result
A search result can easily be saved by creation of a bookmark with the Browser's Bookmark
function. Alternatively, the URL displayed by the Browser can be copied and saved separately.
To resume a query result, the saved URL has to be pasted into the Browser's URL field.
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