Machine Learning of all public Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

Data repository for applying independent component analysis decomposition on P. aeruginosa transcriptomic data as described in biorxiv

Repository Structure

• Data: Files created throughout the ICA decomposition and analysis process

  • External

    • Contains files extracted from external repositories e.g. KEGG and GO enrichments

  • iModulondb

    • Includes files to build iModulondb website

  • Interim

    • Contains data processed by pipeline and which is also required for further analysis

  • Processed Data

    • Includes the final data used for ICA analysis such as X, M, and A matrices as well as metadata and the Transcriptional Regulatory Netwrok (TRN) files

  • Raw Data

    • Contains the transcripts count and multiqc files of the data form SRA

  • Sequence Files

    • Includes sequence files for P. aeruginosa PAO1

• Notebooks

  • 01_expression_QC_SOP : Notebook to take raw reads and multiqc stats files. filtering thes samples, and produce log_tpm file
  • 02_expression_visualization : Visualization of logTPM files by cluster map and PCA plots, and normalize the data (log_TPM_norm)
  • 03_ica_dimensionality : After running the ICA decomposition using nextflow, this notebook used to check the dimensionality to determine optimal M and A matrices
  • 04_ica_data_compile : Compile various files and save it as single .json file
  • 05_ica_summary : Summarize various iModulons in form of scatter plot on the basis of their functions
  • 06_simulation_CF : Creates the heatmap, scatter plot, and barplots for the iModulons might have some role in Cystic Fibrosis
  • 07_Carbon_AA_metabolism : Notebook to various plots for Carbon and Amino Acid metabolism
  • 08_Clustermap : Clustering all the iModulons based on similar functionality on the basis of Pearson correlation coefficient (PCC)
  • 09_Tradeoff : Notebooks to create scatter plot between the RpoS and Translational iModulon
  • 10_DIMAPlot : Differential iModulon activity (DIMA) plot between the M9glucAA+Paraquat and M9glucAA

• Figures

  • Complete Figures: 05 Figures which are used in main manuscript
  • Supplementary Figures: 06 Figures which are used as Supplemenatry figures

• paeru_104_imodulon_ica.json : .json files with all the information of 104 iModulons

• README.md