You can enter single or multiple proteins. Multiple entries should be separated by a delimiter, either a space, carriage return, comma or tab. Proteins entered should all use the same naming convention. Example: "P04150 Q16633 P51948", which are all SwissProt ID's. Other naming conventions can be selected using the 'Protein Format' drop-down box.
By default, interactions are stored and predicted with the most up-to-date information available to I2D. Interactions predicted using older data (older versions of SwissProt, Entrez Gene etc.) are available to search using the I2D version drop-down box.
You can select between several different target organisms using the 'Target Organism' drop-down box.
I2D can output data in several formats, an HTML page, a Navigator compatible text file, an applet graph viewer and a pipe-delimited text file. Once you have selected your output format, you can click on the 'Search' button to submit your search to OPHID.
On multi-protein searches exceeding 300 proteins, you will be asked for your e-mail address, and you will recieve an e-mail notifying you of your searches completion and where you can find your search results. Large queries may take anywhere from minutes to hours, depending on the protein convention used and the size of the search.
Search ResultsI2D can output data in several formats: an HTML page, a Navigator compatible text file, an applet graph viewer and a pipe-delimited text file.
HTML output contains information regarding an interaction and both proteins involved, including information regarding the source of the orginal interaction. Information about different fields in the result is available in a legend located at the bottom of the result page. If available proteins and interaction sources are hotlinked to additional information.
Pipe Delimeted Text contains information in columns separated by a pipe character '|'. Rows are in the format: (Interaction Source)|(Protein 1 SwissProt ID)|(Protein 1 Annotation)|(Protein 1 LocusLink IDs)|(Protein 2 SwissProt ID)|(Protein 2 Annotation)|(Protein 2 LocusLink IDs)
Navigator format is a plaintext file format that is readable by the Navigator Viewer.
The Graph viewer displays the output as a graph in an applet. On multi-protein searches exceeding 50 proteins, you will be asked for your e-mail address. The graph is exported as text file which is emailed to you. The file can be opened for visualization and analysis in NAViGaTOR.
The applet key and mouse buttom reference is as follows:
The entirety of I2D can be downloaded in plain-text format. Downloads have been separated by target organism.