Mehmet U. Caglar, John R. Houser, Craig S. Barnhart, Daniel R. Boutz, Sean M. Carroll, Aurko Dasgupta, Walter F. Lenoir, Bartram L. Smith, Viswanadham Sridhara, Dariya K. Sydykova, Drew Vander Wood, Christopher J. Marx, Edward M. Marcotte, Jeffrey E. Barrick, Claus O. Wilke
The repository consists primarily of five different groups of folders, labeled with a_, b_, c_, d_, and e_, representing five different stages of the analysis. For each group, there is a code folder that holds all the code, a results folder that holds all generated output datafiles, and a figures folder that holds all generated figures.
As an example, the folder c_figures includes the figures generated by the code in the folder c_code_change_wrt_variables_RNA&Protein.
In addition to these five groups of folders, we have data folders named:
RNA_reads_06_13_2016: contains RNA abundancesProtein_reads_06_16_2016: contains protein abundancesDoublingTimeRawData: contains doubling timesFlux_reads_06_21_2016: contains flux data
We also have a folder text that contains the manuscript and a folder dictionary that includes files that map "YP" names for proteins to "ECB" names for RNAs.
Protein and RNA raw files are txt files that includes counts and gene / protein names.
The analysis pipeline follows alphabetical order in the code folders:
a) dataPreperation_RNA&Protein: The code in this folder combines distinct count files into single unique ones for mRNA and proteins; then it generates the meta data file associated with them.
`a_results` file contains:
- "rnaMatrix_mRNA.csv" contains raw mRNA data combined
- "resDf_protein_trT_set00_StcYtcNasAgrNgrMgh_SYAN_baseMgAllMg_baseNaAllNa_ExpAllPhase_noMatchFilter_p1Sf_noNorm.csv" contains mRNA data after DeSeq2 size factor normalization
- "resDf_protein_trT_set00_StcYtcNasAgrNgrMgh_SYAN_baseMgAllMg_baseNaAllNa_ExpAllPhase_noMatchFilter_p1Sf_vst.csv" contains mRNA data after DeSeq2 size factor normalization and vst trasformation (similar to log transformation)
- "rnaMatrix_meta.csv" is the meta mRNA file
- "proteinMatrix.csv" contains raw protein data combined
- "resDf_protein_trT_set00_StcYtcNasAgrNgrMgh_SYAN_baseMgAllMg_baseNaAllNa_ExpAllPhase_noMatchFilter_p1Sf_noNorm.csv" contains protein data after DeSeq2 size factor normalization
- "resDf_protein_trT_set00_StcYtcNasAgrNgrMgh_SYAN_baseMgAllMg_baseNaAllNa_ExpAllPhase_noMatchFilter_p1Sf_vst.csv" contains protein data after DeSeq2 size factor normalization and vst trasformation (similar to log transformation)
- "metaProtein.csv" is the meta protein file
b) histogram_RNA&Protein: This folder generates heat map figures for proteins and for RNA. Also calculates table 1.
c) change_wrt_variables_RNA&Protein: The code in this folder finds differentiall expressed genes using DeSeq2.
d) Mf_Pathway_Analyze: The code in this folder generates figures and edited tables from results of DAVID runs.
e) Flux_Analyze: The code in this folder performs flux data analysis. FluxSaltStressAnalyze.R generates concentration vs flux figures for RNA and proteins.
More details about the analysis pipeline can be found in the file instructions_for_pipeline.docx.