Search - iRefWeb - Wodak Lab

Example Queries

In the following set of queries we build a yeast interactome in several steps; before starting take a moment to observer the general distribution of interactions across all filters.

1. We select saccharomyces cerevisiae from the Organism filter. We would like to avoid complexes to the extent possible, so under the Number of Interacting Proteins filter we also check off 2 exactly.
   Run Search For Step 1

Downloading Your Interactome

• The file format is MITAB. The first line of the file provides the column headers.
• The idea of building and downloading an interactome is to create a query that is sufficiently refined as to represent a data set that has been filtered of noise. See below for details on obtaining the complete data set. Therefore the limit on the number of interactions that can be downloaded is 50,000. This number should sufficient to capture a reasonable interactome for any organism. For example, while yeast may have over 100,000 interactions, many are of questionable reliability and quality—certainly no one expects that yeast does, in reality, actually have this many true interactions.
• Interactions that are supported by evidence only from CORUM, DIP, HPRD and MPACT, will be excluded from your download. There should be sufficient overlap with public databases in most cases to still provide you with a reasonable set of records.
• Should your results contain complexes, they will be expanded into binary records.
• Because in some cases records maybe excluded (private databases), and in other cases expanded (complexes), the number of lines in the file will not necessarily be exactly the same as the number interactions that matched your search.

Obtaining the Complete Data Set

• If you wish to have the entire data set, please visit iRefIndex.