Description
Post-Translational Modification Enrichment, Integration, and Matching Analysis.
Description
Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2022) <bioRxiv:10.1101/2022.11.09.515610>.
README.md
README
2022-10-27
PEIMAN2 
The PEIMAN2 package [@PEIMAN2] provides functions and mined database from UniProt for single enrichment analysis (SEA) and protein set enrichment analysis (PSEA) in a list of protein. The database is updated regularly with monthly changes in UniProt/SwissProt repository. To ensure you have the latest version of database, make sure to install the package from GitHub.
Installation
You can install the released version of PEIMAN from CRAN with:
install.packages("PEIMAN2")
And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("jafarilab/PEIMAN2")
Example
Singular Enrichment Analysis (SEA)
# Load PEIMAN2 package
library(PEIMAN2)
## Loading required package: tidyverse
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
## ✔ ggplot2 3.3.6 ✔ purrr 0.3.4
## ✔ tibble 3.1.7 ✔ dplyr 1.0.9
## ✔ tidyr 1.2.0 ✔ stringr 1.4.0
## ✔ readr 2.1.2 ✔ forcats 0.5.1
## Warning: package 'ggplot2' was built under R version 4.2.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
# First example dataset
pl1 <- exmplData1$pl1
# Run SEA on the list
enrich1 <- runEnrichment(protein = pl1, os.name = 'Homo sapiens (Human)')
head(enrich1, n = 6)
## PTM FreqinUniprot FreqinList Sample
## 1 N6-(pyridoxal phosphate)lysine 53 5 97
## 2 Pyridoxal phosphate 60 5 97
## 3 Isoglutamyl cysteine thioester (Cys-Gln) 7 2 97
## 4 Thioester bond 11 2 97
## 5 S-cysteinyl cysteine 3 1 97
## 6 Sulfation 57 3 97
## Population pvalue corrected pvalue AC
## 1 14256 2e-06 6e-05 Q96QU6; Q4AC99; Q8N5Z0; Q8NHS2; P17174
## 2 14256 3e-06 6e-05 Q96QU6; Q4AC99; Q8N5Z0; Q8NHS2; P17174
## 3 14256 1e-05 1e-04 P01023; A8K2U0
## 4 14256 5e-05 5e-04 P01023; A8K2U0
## 5 14256 1e-04 1e-03 P01009
## 6 14256 6e-04 4e-03 P05408; P08697; P05067
# Second example dataset
pl2 <- exmplData1$pl2
# Run SEA on the list
enrich2 <- runEnrichment(protein = pl2, os.name = 'Homo sapiens (Human)')
Plotting SEA for one list
plotEnrichment(x = enrich1, sig.level = 0.05)
Integration and matching analysis of two lists
plotEnrichment(x = enrich1, y = enrich2, sig.level = 0.05)
Protein Set Enrichment Analysis (PSEA)
psea_res <- runPSEA(protein = exmplData2, os.name = 'Rattus norvegicus (Rat)', nperm = 100)
head(psea_res[[1]], n = 6)
## PTM pval pvaladj FreqinUniProt FreqinList
## 1 Acetylation 0e+00 0e+00 1762 123
## 2 ADP-ribosylglycine 0e+00 0e+00 4 4
## 3 Cysteine sulfinic acid (-SO2H) 0e+00 0e+00 1 1
## 4 N-acetylaspartate 0e+00 0e+00 1 1
## 5 N-acetylglutamate 0e+00 0e+00 1 1
## 6 N6-acetyllysine 6e-15 7e-14 992 73
## ES NES nMoreExtreme size Enrichment
## 1 0.7521522 1.196043 1 123 Significant
## 2 0.7707317 1.864768 24 4 Significant
## 3 0.9423077 107.586957 6 1 Significant
## 4 -0.9615385 -16.694491 2 1 Not significant
## 5 -0.9663462 -8.258012 5 1 Not significant
## 6 0.7226249 1.130643 6 73 Significant
## AC
## 1 P0C1X8; P11030; P60711; P63259; Q63028; Q62847; Q62848; Q9WUC4; P31399; P29419; P21571; P15999; D3ZAF6; Q9JJW3; O08839; P0DP29; P0DP30; P0DP31; P18418; P26772; P63039; B0K020; P08081; P08082; P45592; Q91ZN1; P11240; Q63768; P10715; P62898; Q9JHL4; Q7M0E3; P62628; Q07266; P84060; P62870; P15429; P07323; P60841; P56571; B0BN94; P55053; P55051; P07483; Q62658; Q32PX7; Q99PF5; Q5XI73; Q63228; P62994; P01946; P02091; P11517; P62959; P82995; P34058; P27321; Q5XI72; P50411; Q6AXU6; Q5BK20; P11980; Q99MZ8; Q792I0; Q66HF9; P15205; Q5M7W5; P02688; B0BN72; P30904; O35763; P62775; Q71UE8; Q9JJ19; P13084; Q01205; P08461; Q920Q0; O88767; P04785; P31044; O55012; P10111; Q6J4I0; Q9R063; Q9EPC6; P02625; Q63475; P51583; Q68A21; P02401; P62982; P62859; Q6RJR6; Q9JK11; Q63945; B0BN85; P07632; Q66HL2; P28042; O35814; P13668; P37377; Q62880; P19332; P68370; Q6P9V9; Q6AYZ1; Q68FR8; Q5XIF6; Q6PEC1; P11232; P62076; P62078; Q9WV97; P48500; P04692; P58775; Q63610; P09495; Q7M767; Q9Z1A5; P63045
## 2 P62986; P62982; P0CG51; Q63429
## 3 O88767
## 4 P60711
## 5 P63259
## 6 P11030; Q62848; Q9WUC4; P31399; P29419; P21571; P15999; D3ZAF6; Q9JJW3; P0DP29; P0DP30; P0DP31; P18418; P26772; P63039; B0K020; P08081; P08082; P45592; P11240; P62898; Q9JHL4; Q7M0E3; P07323; P56571; Q62658; Q99PF5; Q5XI73; P62994; P01946; P62959; P82995; P34058; P27321; Q6AXU6; Q5BK20; P11980; Q99MZ8; P02688; B0BN72; P30904; O35763; P62775; Q71UE8; P13084; Q01205; P08461; O88767; P04785; P10111; Q9R063; Q63475; P51583; Q68A21; P02401; P62982; Q9JK11; Q63945; P07632; Q66HL2; P28042; O35814; P13668; P19332; P68370; Q6P9V9; Q6AYZ1; Q68FR8; Q5XIF6; P11232; P48500; P09495; Q9Z1A5
## leadingEdge
## 1 P62628; P31044; P37377; P45592; P11030; P02625; P29419; P62775; P21571; O88767; P31399; P02688; P08082; P62898; P63045; P62076; P11232; O35814; Q9WUC4; Q62658; Q63228; P07632; Q5XI73; B0K020; P08081; P62959
## 2 P62982; P0CG51; P62986; Q63429
## 3 O88767
## 4 P31044
## 5 P31044
## 6 P45592; P11030; P29419; P62775; P21571; O88767; P31399; P02688; P08082; P62898; P11232; O35814; Q9WUC4; Q62658; P07632; Q5XI73; B0K020; P08081; P62959
Plotting PSEA
plotPSEA(x = psea_res)
plotRunningScore(x = psea_res, nplot = 8)
Translate PEIMAN results for Mass spectrometry searching tools
psea2mass(x = psea_res, sig.level = 0.05)
## MOD_ID name
## 1 MOD:00085 N6-methyl-L-lysine
## 2 MOD:00127 N6-lipoyl-L-lysine
## 3 MOD:00322 1'-methyl-L-histidine
## 4 MOD:00051 N-acetyl-L-aspartic acid
## 5 MOD:00053 N-acetyl-L-glutamic acid
## 6 MOD:00685 deamidated L-glutamine
## def
## 1 "converts an L-lysine residue to N6-methyl-L-lysine." [ChEBI:17604, DeltaMass:165, PubMed:11875433, PubMed:3926756, RESID:AA0076, Unimod:34#K]
## 2 "converts an L-lysine residue to N6-lipoyl-L-lysine." [DeltaMass:0, OMSSA:67, PubMed:3421911, PubMed:3522581, PubMed:7719855, RESID:AA0118, Unimod:42#K]
## 3 "converts an L-histidine residue to tele-methyl-L-histidine." [PubMed:10601317, PubMed:11474090, PubMed:11875433, PubMed:6692818, PubMed:8076, PubMed:8645219, RESID:AA0317]
## 4 "converts an L-aspartic acid residue to N-acetyl-L-aspartic acid." [ChEBI:21547, PubMed:1560020, PubMed:2395459, RESID:AA0042]
## 5 "converts an L-glutamic acid residue to N-acetyl-L-glutamic acid." [ChEBI:17533, PubMed:6725286, RESID:AA0044]
## 6 "converts an L-glutamine residue to L-glutamic acid." [PubMed:1881881, PubMed:4565668, PubMed:4922541, PubMed:6692818, PubMed:9192900, PubMed:957425, RESID:AA0006#GLN, Unimod:7#Q]
## FreqinList
## 1 9
## 2 2
## 3 2
## 4 1
## 5 1
## 6 1