1] What is ProteINSIDE:

Thank you to learn how to use ProteINSIDE. Let's begin with general informations.


ProteINSIDE is dedicated to a systematic and integrative analysis of protein's biological knowledge. Biological knowledge and functions for proteins is made possible by an overview of the biological meanings stored in public data base and of the annotations according to the gene ontology, the identification of secreted protein, and the identification and analysis of protein-protein interactions (PPi) networks.


There is three types of analysis with ProteINSIDE:

  • Basic Analysis:
  • Each settings are locked, the pipeline runs GO research, signal peptide prediction, and PPi research (on IntAct, UniprotKB and BioGrid).

  • Custom Analysis:
  • Allows the user to choose modules and settings that will be used by the pipeline.

  • Preset Analysis (registered users only):
  • Allows the user to use previous analysis settings to creat a new one.


2] Create an input file:

1) You can use 2003 to higher Excel's versions.

Excel files must contain at least: ranks / names of your samples / IDs, in this order.

You can have empty box and ohter comments after the thrid colum of your Excel file (second picture).




2) You can also made a .TXT or .TAB file, file format is the same as Excel file.

Structure of a TAB file or a TXT file must be like this : "RANK" tabulation "Other RANK or NAME" tabulation "IDENTIFIER".




3) If you don't want to create an input file, juste copy and paste your IDs on ProetINSIDE.



3] Create a Basic Analysis:

1) To realyze a job with basic settings analysis (locked settings), use the "Basic Analysis" button in the main menu [1].

Basic Analysis menu

2) There is 2 choices to create a job [2]. You can use an input file or directly add your ID. The input file must be inferior to 250kb / 8000 IDs and must specify the extension. There is also a "Sample" button that loads parameters for an example of analysis.

Basic Analysis settings

3) Once everything is completed, click on the button "Run the job" [3] to save the job.

Record the job

4) When the job is register, a special page appear and give the "Access code" (1) and a link (2) that you can put on your favorite to keep an eye on your job. Keep an eye on your job


4] Check your results:

1) Select the "Result Access" section of the webservice [1]

Result Access section menu !

2) Enter your code here and use the "submit" button to have access to your job status/results [2]

Code section

3) When a job is done, you will see a green circle next to it on the user view [1]

Job is done !
Results web-acces : you can also access to the online results view by clicking on this button.

5] Next step:

Now you can create Basic Analysis and get a lot of results, but you may wants to use just a part of ProteINSIDE or use specific module's options. That's why we have created Custom Analysis.


First steps are same as a Basic Analysis, when you have fill out each "general informations" and input you dataset, you will see a third part with "Settings". Here you can check you software of ProteINSIDE that you want to use and run the job. That's allow you to run an analysis with only "Gene Ontology" software activated, but with also the "Gene Ontology Tree network view" option activate (GOTree charts are directed tree layout network where GO are linked by terms association (only by GO ancestor find on the dataset)).


Don't forget to subscribe if you wants to get more functionalities and to save your jobs.