Add Transcriptomics
Bacnet allows to integrate microarray, tiling and RNA-Seq datasets. Once the correct ArrayExpress ftp link is provided in Bioconditions.txt, it will download all files part of the MAGE-TAB format (IDF, SDRF, ADF files) describing each differential expression experiment. At this point a human curation is usually needed to correctly name dataset and correct if necessary the different metadata information provided in the IDF.
All differential expression (log(Fold Change)) tables will be imported, and, if available, all absolute expression (log(Expression)) datasets. For RNASeq datasets, the user should also provide coverage file in WIG format.
Then, every dataset will be serialized in binary format to ease loading. Differential expression tables for all type of transcriptomic datasets will be normalized by centering and variance normalization as described in the Listeriomics paper. For each genome an expression table will be saved. These tables are the one then used by the expression atlas tool.
Upon arriving at this panel you should have created the Transcriptomes.txt transcriptomics table in the BioConditions panel.
The table lists all unique transcriptome present in this file. On the right side of the screen you can see the actual number of transcriptomes in the file as well as the different type of data present.
Click on Validate Transcriptomics database. If some transcriptomes are still unvalidated (Validated box unchecked) click on Add unvalidated Transcriptomes to the database. This step will take few minutes as it convert all transcriptomic files to appropriate binary files. It put the files in the StreamingData folder.
When all transcriptomes are added click on Create Transcriptome atlas. This creates the expression atlas by processing all differential expression tables containing log(Fold Change) values. It normalize all log(FC) columns by reducing the variance to 1 (see Listeriomics. The following process might take few minutes. Look at Eclipse console for checking the progress. The expression atlas is saved in a table format in Database/Transcriptomes/Table_LOGFC_Listeria monocytogenes EGD-e
When everything is finished, you should be able to visualize every transcriptomic datasets on the genome viewer. Run bacnet.e4.rap, go in Transcriptomic panel, select all datasets, and click on Visualize their transcriptomics dataset on the Genome Viewer. you can see that we have tiling arrays, expression arrays, transcription start sites (TSS), transcription termination sites (TTS), RNA-Seq, Ribosome profiling (Ribo-Seq).
Now, if you want to use expression atlas and visualize all transcriptomics datasets on a heatmap go back to Transcriptomics panel. Click on the HeatMap Viewer_ viewer.
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 transcriptome dataset your gene is differently expressed.
Now pursue on the Proteomics panel.