Wed. Feb 5, 2019, Oyster Seed Proteomics Uniprot and Network Mapping

remapping proteins sequences to 2019 Uniprot DB

reference this jupyter notebook: 20190130_Cg_Giga_cont_AA.fa_BLASTP_uniprot_swprot2019.ipynb

1. Rebuilt the BLAST index from 2019 Uniprot DB
   • it lives here http://gannet.fish.washington.edu/metacarcinus/Cgigas

2. remapped protein sequences from Steven’s file http://gannet.fish.washington.edu/halfshell/bu-git-repos/nb-2017/C_gigas/data/Cg_Giga_cont_AA.fa to updated Uniprot DB.

3. reformatted BLAST output to remove pipes in protein names and contain the following fields:
   • protein_ID
   • Entry
   • Entry_name
   • perc_ident_match
   • align_len
   • num_mismatch
   • num_gaps
   • querStart
   • querEnd
   • subjStart
   • subjEndevalue
   • bitscore
   • Entry.1
   • Entry_name.1
   • Protein_names
   • Gene_names
   • Organism
   • Protein_length Pathway
   • GO_bp
   • GO
   • GO_IDs
   • Protein_fams - first 10 lines of data file can be previewed here. Complete data file can be found here http://gannet.fish.washington.edu/metacarcinus/Cgigas/all_giga-uniprot-blastP-out.nopipe.annotations.tab

fold change analysis and p-value

• made all fold change comparisons for all time points and temperatures to time 0, and calculated p-values using chi square proportions test. Did not do anything with zero values.
  • analysis here and used this R project