Add Proteomics
Proteomics processed datasets are usually provided in supplementary information of scientific papers. For that reason, no automatic downloading system is provided by Bacnet. The user has to download and format each proteomic expression dataset as tab-delimited expression tables. All datasets will be then integrated into the proteomic expression atlas tables, one for each genome.
Upon arriving at this panel you should have created the Proteomes.txt proteomics table in the BioConditions panel.
The table lists all proteomes present in this file.
Click on Validate Proteomics database. If some proteomes are still unvalidated (Validated box unchecked) click on Add unvalidated Proteomes to the database. This step will take few minutes as it convert all proteomic files to appropriate binary files. It creates the files in the Proteomes folder of your database (Eclipse console is giving you detailed pathway and files).
When all proteomes are added click on Create Proteome atlas. The following process might take few minutes. Look at Eclipse console for checking the progress. The proteome atlas is saved in a table format in Database/Proteomes/Table_Expr_Listeria monocytogenes EGD-e
When everything is finished, you should be able to visualize every proteomics datasets on the genome viewer. Run bacnet.e4.rap, go in Proteomics panel, select all datasets, and click on Visualize their proteomics dataset on the Genome Viewer.
Now, if you want to use proteome atlas and visualize all proteomics datasets on a heatmap go back to Proteomics panel. Click on the HeatMap Viewer button.
You can also go on the home page, click on Genes information. Select your gene of interest, and click on the Expression atlas panel. You will see in which proteome dataset the corresponding protein was observed.
Now pursue on the Co Expression Network panel.