Contents:

1. Query: Search for Genes or Proteins
   • Input Gene or Protein List
     • Gene and Protein Names, Identifiers and Sources
     • Format of the Input List: Name Separators
     • Use Wild Cards
   • Choose Organism and Search Options
2. Your Query:
   • Re-select Genes for your Query
   • Choose your Query Type
     • Network of Operons and Regulons
     • Metabolic Pathways and KEGG Maps
     • Gene Expression Profiles
3. Results: Network of Operons and Regulons

1. Query: Search for Genes or Proteins

• Input Gene or Protein List

A query to ProdoNet requires a set of input names and the selection of the corresponding species. The input name might be either a gene or a protein name or database identifier.

• Gene and Protein Names, Identifiers and Sources

ProdoNet accepts a broad range of different gene or protein names or database IDs as query input. The following list shows the ProdoNet data sources and an example name or ID.

• Format of the Input List: Name Separators

A list of gene names can be separated by different symbols. The ProdoNet Query accepts the following name separators:

• Use Wild Cards

The ProdoNet Query accepts the following wild cards in your input(sql standard wild cards):

• Choose Organism and Search Options

The selection of the species corresponding to your query genes is mandatory. The current dataset comprises the model organisms Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Rhodobacter sphaeroides and Staphylococcus aureus as well as 38 further organisms from the families Bacillaceae, Enterobacteriaceae and Pseudomonadaceae (dataset table).

You can specify the type of your input gene / protein names. For locus tags, short names and UniProtKB IDs, you can speed up your query by selecting the corresponding Search Option. For other input types, e.g., EcoGene accession numbers, larger queries will take some time.

2. Your Query:

• Re-Select Genes for your Query

In the first step of the query, your input gene or protein names are compared with the ProdoNet gene dataset. In the second step, the query page shows the matches found for your input query term(s). Query terms that resulted in more than one match are indicated in red. You can now select the genes of your interest and request either the corresponding gene regulatory network or the metabolic pathways or gene expression profiles involving your genes.

• Choose Your Query Type

You can choose between 3 alternative query types:

• Network of Operons and Regulons

This query will request the Network of Operons and Regulons. Several options can expand the defaut query. The selection of one or more options may due to an extended loading time for the applet.

• "include predicted regulons" will additionally show interactions that were predicited with the Virtual Footprint algorithm.
• "include gene expression profiles" will connect genes that were found co-regulated in a gene expression profile and link to the experiment in PRODORIC.
• "show data tables" will depict the data presented in the network in a tabular form.

• Metabolic Pathways and KEGG Maps

This query returns a table that lists all enzymes from your query together with the corresponding metabolic pathways. The table include links to the corresponding KEGG maps and can be downloaded as tab delimited file.
Please be aware that only enzymes are treated in this analysis, other gene products give no results. If you requested several enzymes from the same pathway, the enzyme names will be listed together. The KEGG map depicts the EC numbers of all enzymes from your query in red.

• Gene Expression Profiles

This query returns a table that lists all genes from your query that were found co-regulated under defined conditions in a gene expression profile. The table include links to the PRODORIC entry of the referring expression profile condition and can be downloaded as tab delimited file.

3. Results: Network of Operons and Regulons

The result of the "operons and regulons" query shows all selected genes in the context of their operons and, if any known, regulators of these operons. Depending on your query, this network may be quite large. The result is temporarily stored and can be downloaded as GraphML file. A detailed figure legend is given at the bottom of the network page.

By default, the network presents only the part of the complete gene regulatory network that was queried by the selected input genes (Level 1). For deeper insights into the network, the view can be interactively expanded by choosing a higher expansion level. In this case, all transcription factor nodes are extended both by upstream regulators and further downstream target operons.

The network layout is dynamic. That means, when choosing another expansion level, the network will be completely rearranged. Alternatively, the layout can be set to "static". In this case, the network will keep the positions of items as arranged by the user.

If the "expression profiles" option was choosen in the query, the profile information can be interactively removed from the network by unselecting "show expression profiles". The option "expression profile weighting" re-arranges the network by including the expression profile information in the calculation of the network layout.

The network is depicted by a Java applet created with the prefuse vizualisation toolkit. The applet requires Java version 1.6. In case of trouble with loading the applet, please make sure that your browser has Java and JavaScript enabled. You can find detailed information and help about how to fix troubles with applets at the Java homepage.