Add Biological conditions

Prior to any transcriptomic or proteomic integration, one has to create BioConditions.txt tab-delimited text file. This file referenced all biological conditions which will be integrated in the multiomic website. It can be either metadata information on transcriptomic datasets from ArrayExpress or proteomic datasets found on specific publication.

If the file BioConditions.txt is found with the path indicated on the right of the screen, the list of all the bioconditions is presented in a table. The indicated number of bioconditions in the database and the number of bioconditions in the table can differ if some conditions are present more than once.

Click on Validate BioConditions database.

The validated box should be checked for every condition in the table. If it is not the case you need to click on Add unvalidated Biological conditions to the database.

When all conditions are validated click on Create Transcriptomics table then on Create Proteomics table. The created tables can be found, as stated in the console, in respectively the Transcriptomes and Proteomes folders of your database. Chck their creation by running bacnet.e4.rap and click in the Banner in Transcriptomics or Proteomics button.

You will now be able to integrate all transcriptomics and proteomics datasets. Once all omics datasets are integrated in the multi-omics database it will be possible for you, just by running bacnet.e4.rap, to either visualize every dataset on the genome viewer, or to visualize their differential expression and absolute expression in heatmap tables. For every corresponding genes and proteins, the expression and proteome atlas will be enable. Giving you the opportunity to directly see which genomic element is highlighted in one of the omic dataset integrated in the database.

But first pursue database creation by running Comparisons panel in bacnet.e4.rap.setup.