Question: How do I link to InterologFinder?
Answer: The URL is http://www.interologfinder.org/simpleIfWS?taxid=9606&genes;=124,125,165 where taxid= is one of the five species’ taxonomy identifier included in InterologFinder and genes= is followed by NCBI Entrez Gene identifiers separated with commas. The possible tax IDs are <9606, 10090, 4932, 6239, 7227>
Question: When I have my initial list of interologs for my input list how can I expand my interolog network?
Answer: The checkboxes next to each gene allow you to select one gene, the checkbox at the top of a column allows you to select all of the genes in that column. Click Expand Network to see the genes you have selected and all of their interologs.
Question: How does the Visualize Network work?
Answer: Like Expand Network, Visualize Network takes the genes you have selected with the checkboxes and finds their connections. The Flash movie that is started allows you to interact and explore the resulting interolog network. The genes you selected are identified with larger circles and the edges are color coded to match experimental and predicted interactions.
Question: Can I use InterologFinder if I don’t know the NCBI Entrez Gene IDs?
Answer: Yes. To start an analysis without a list of gene identifiers type www.interologfinder.org This will allow you to paste in your identifiers and InterologFinder will attempt to find matching NCBI identifiers to use for the analysis. You will be able to select the conversions you think are correct.
Question: What data sources do you use for InterologFinder?
Answer: NCBI provides the thesaurus when converting between identifiers and we use NCBI Entrez Gene IDs and gene names in the output pages. Ensembl’s and NCIBI’s MiMI are used for orthology and interaction information respectively.
Question: How often is your data updated?
Answer: Our policy is to update the data at least twice a year. The current data from NCBI and NCIBI’s MiMI was downloaded December 2010. For Ensembl it is version 60.
Question: What does Expand Network do?
Answer: The Expand Network button takes the selected nodes and includes them and their interactants in the Results Page. Therefore, if you expand a given row of data, you will find a path from the original search node to the subsequent interactant by way of the original search node’s interactant.
Question: What do the file extensions mean in the downloaded file?
Answer: The zipped collection of files provided by Download Network of Selected Rows for Cytoscape are a combination of .sif, .eda, and .noa files. Each can be imported into Cytoscape Cytoscape to recreate the simple visualization InterologFinder provides. The interaction file (.sif) contains the interactions identified with NCBI Entrez Gene IDs.
The edge attribute files (.eda) contain the edge annotations including experiment support, species support and scores for each interaction. The node attribute file (.noa) contains the translation between Ensembl and NCBI Entrez Gene IDs. The .csv file provided by Download Network of Selected Rows as CSV contains all of the network details, one row per interaction.