ptm map

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: MotrpacRatTraining6moData
 Title: Data for analysis of the MoTrPAC endurance exercise training study
     in 6-month-old rats
-Version: 1.4.0
+Version: 1.5.0
 Authors@R: c(
     person("Nicole", "Gay", , "nicole.r.gay@gmail.com", role = c("cre", "aut")),
     person("Pierre", "Jean Beltran", , "pjeanbeltran@gmail.com", role = "aut"),

NEWS.md

@@ -1,3 +1,7 @@
+# MotrpacRatTraining6moData 1.5.0 (2022-10-14)
+
+* Add `RAT_TO_HUMAN_PHOSPHO` 
+
 # MotrpacRatTraining6moData 1.4.0 (2022-10-10)
 
 * Add `FEATURE_TO_GENE_FILT` for faster indexing 

R/data.R

@@ -103,7 +103,7 @@
 #'     For fast(er) indexing, convert this object to a [data.table::data.table()] and use 
 #'     [data.table::setkey()] to set the key to the column you are matching. 
 #'     This dramatically improves performance. 
-#'     
+#' @source \code{gs://motrpac-data-freeze-pass/pass1b-06/v1.1/analysis/resources/master_feature_to_gene_20211116.RData}
 "FEATURE_TO_GENE"
 
 
@@ -209,6 +209,28 @@
 "REPEATED_FEATURES"
 
 
+#' @name RAT_TO_HUMAN_PHOSPHO
+#' @title Rat-to-human phosphosite map 
+#' @description Sequence-identity-based mapping between rat and human protein phosphorylation sites 
+#' @format A data frame with 202610 rows and 2 variables:
+#' \describe{
+#'   \item{\code{ptm_id_rat_refseq}}{character, RefSeq ID for rat phosphosite}
+#'   \item{\code{ptm_id_human_uniprot}}{character, Uniprot ID for human phosphosite} 
+#'}
+#' @details We used the NCBI Reference Protein Sequence database (RefSeq) to annotate protein IDs. 
+#' Most of the Post-Translational Modification (PTM) resources and tools available are for humans; 
+#' rat annotation is lacking. To leverage information from humans, we mapped PTM sites from rats to 
+#' humans following a bioinformatics approach. Briefly, we used BLASTp to align all rat sequences 
+#' to the human review UniProt fasta sequence database (download date: 02/03/2021). The median 
+#' protein sequence identity between rats and humans is 85%. Only alignments with a sequence identity 
+#' greater than 60% were included for mapping. For most proteins, BLASTp outputs multiple pairwise 
+#' alignments (one-to-many). In those cases, we selected the alignment with the larger "positives" 
+#' and "identities" values and required an exact match for the S/T/Y residues identified in this study. 
+#' As a result, we could map with confidence 73.5% of all the phosphorylation sites we identified.
+#' @source \code{gs://motrpac-data-hub/pass1b-06/analysis/resources/motrpac_pass1b-06_proteomics-ph-rat2human-20211016.csv}
+"RAT_TO_HUMAN_PHOSPHO"
+
+
 #' @title Metabolite feature IDs and metadata
 #' @description Mapping between various metabolite feature identifiers used
 #'   at different stages of data processing. Also includes some feature metadata

_pkgdown.yml

@@ -64,6 +64,7 @@ reference:
     - FEATURE_TO_GENE_FILT
     - REPEATED_FEATURES
     - RAT_TO_HUMAN_GENE
+    - RAT_TO_HUMAN_PHOSPHO
     - METAB_FEATURE_ID_MAP
     - ATAC_FEATURE_ANNOT
     - METHYL_FEATURE_ANNOT