2026-16-06
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")
# or
devtools::install_github("pnickchi/PEIMAN2")# Load PEIMAN2 package
library(PEIMAN2)
# First example dataset
pl1 <- exmplData1$pl1
# Run SEA on the list
enrich1 <- runEnrichment(protein = pl1, os.name = 'Homo sapiens (Human)')
head(enrich1, n = 6)## PTM FreqinPopulation FreqinSample Sample
## 1 N6-(pyridoxal phosphate)lysine 53 5 97
## 2 Isoglutamyl cysteine thioester (Cys-Gln) 7 2 97
## 3 Glycoprotein 4726 41 97
## 4 Thioester bond 11 2 97
## 5 S-cysteinyl cysteine 3 1 97
## 6 Disulfide bond 3885 33 97
## Population pvalue corrected pvalue
## 1 20431 2e-07 7e-06
## 2 20431 4e-06 7e-05
## 3 20431 8e-06 1e-04
## 4 20431 2e-05 2e-04
## 5 20431 7e-05 5e-04
## 6 20431 1e-04 9e-04
## AC
## 1 Q96QU6; Q4AC99; Q8N5Z0; Q8NHS2; P17174
## 2 P01023; A8K2U0
## 3 P08195; P08908; P28222; P28221; P28566; P30939; P28223; P41595; P28335; P46098; O95264; Q70Z44; A5X5Y0; Q13639; P47898; P34969; P21589; P02763; P19652; P20848; P01009; P04217; P08697; P02750; P01023; A8K2U0; U3KPV4; Q9NPC4; Q9UNA3; P05067; P30542; P29274; P29275; P0DMS8; P22760; Q15758; P01011; P54619; Q9UGJ0; Q9UGI9; Q13131
## 4 P01023; A8K2U0
## 5 P01009
## 6 P08195; P08908; P28222; P28221; P28566; P30939; P28223; P41595; P28335; P46098; O95264; Q8WXA8; A5X5Y0; Q13639; P47898; P50406; P34969; P21589; P05408; P02763; P19652; P04217; P08697; P02750; P01023; A8K2U0; P05067; P30542; P29274; P29275; P0DMS8; Q9NS82; P22760# Second example dataset
pl2 <- exmplData1$pl2
# Run SEA on the list
enrich2 <- runEnrichment(protein = pl2, os.name = 'Homo sapiens (Human)')plotEnrichment(x = enrich1, sig.level = 0.05)## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## ℹ The deprecated feature was likely used in the PEIMAN2 package.
## Please report the issue to the authors.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
plotEnrichment(x = enrich1, y = enrich2, sig.level = 0.05)
psea_res <- runPSEA(protein = exmplData2, os.name = 'Rattus norvegicus (Rat)', nperm = 100)## Warning: `rerun()` was deprecated in purrr 1.0.0.
## ℹ Please use `map()` instead.
## # Previously
## rerun(100, psea(x = protein, y = pro.pathway, p = pexponent, perm = TRUE))
##
## # Now
## map(1:100, ~ psea(x = protein, y = pro.pathway, p = pexponent, perm = TRUE))
## ℹ The deprecated feature was likely used in the PEIMAN2 package.
## Please report the issue to the authors.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.head(psea_res[[1]], n = 6)## PTM pval pvaladj FreqinPopulation FreqinSample
## 1 Acetylation 0 0 1787 125
## 2 ADP-ribosylglycine 0 0 4 4
## 3 Cysteine sulfinic acid (-SO2H) 0 0 1 1
## 4 L-cysteine coenzyme A disulfide 0 0 1 1
## 5 N-acetylaspartate 0 0 1 1
## 6 N-acetylglutamate 0 0 1 1
## ES NES nMoreExtreme size Enrichment
## 1 0.7455919 1.177273 3 125 Over presented
## 2 0.7707317 1.470956 29 4 Over presented
## 3 0.9423077 -27.960452 5 1 Under presented
## 4 -0.5817308 34.084507 43 1 Over presented
## 5 -0.9615385 -187.037037 6 1 Under presented
## 6 -0.9663462 25.632576 1 1 Over presented
## 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; P30009; P02688; B0BN72; P30904; O35763; P62775; Q05982; 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 Q05982
## 5 P60711
## 6 P63259
## 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 P31044plotPSEA(x = psea_res)
plotRunningScore(x = psea_res, nplot = 8) 
psea2mass(x = psea_res, sig.level = 0.05)## MOD_ID name
## 1 MOD:00064 N6-acetyl-L-lysine
## 2 MOD:01819 N6-succinyl-L-lysine
## 3 MOD:00085 N6-methyl-L-lysine
## 4 MOD:00322 1'-methyl-L-histidine
## 5 MOD:00720 L-methionine (R)-sulfoxide
## 6 MOD:00053 N-acetyl-L-glutamic acid
## 7 MOD:00267 L-cysteine sulfinic acid
## def
## 1 "converts an L-lysine residue to N6-acetyl-L-lysine." [ChEBI:17752, DeltaMass:214, OMSSA:24, PubMed:11369851, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:1680872, PubMed:670159, RESID:AA0055, Unimod:1#K]
## 2 "converts an L-lysine residue to N6-succinyl-L-lysine." [PubMed:16582421, PubMed:21151122, RESID:AA0545]
## 3 "converts an L-lysine residue to N6-methyl-L-lysine." [ChEBI:17604, DeltaMass:165, PubMed:11875433, PubMed:3926756, RESID:AA0076, Unimod:34#K]
## 4 "converts an L-histidine residue to tele-methyl-L-histidine." [PubMed:10601317, PubMed:11474090, PubMed:11875433, PubMed:6692818, PubMed:8076, PubMed:8645219, RESID:AA0317]
## 5 "oxygenates an L-methionine residue to L-methionine sulfoxide R-diastereomer." [ChEBI:45764, PubMed:21406390, PubMed:22116028, PubMed:23911929, RESID:AA0581]
## 6 "converts an L-glutamic acid residue to N-acetyl-L-glutamic acid." [ChEBI:17533, PubMed:6725286, RESID:AA0044]
## 7 "dioxygenates an L-cysteine residue to L-cysteine sulfinic acid." [ChEBI:16345, OMSSA:162, PubMed:12686488, PubMed:9252331, PubMed:9586994, RESID:AA0262, Unimod:425#C]
## FreqinSample
## 1 75
## 2 31
## 3 9
## 4 2
## 5 2
## 6 1
## 7 1