2022-10-27
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.
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")# 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)')plotEnrichment(x = enrich1, sig.level = 0.05)
plotEnrichment(x = enrich1, y = enrich2, sig.level = 0.05)
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; P62959plotPSEA(x = psea_res)
plotRunningScore(x = psea_res, nplot = 8) 
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