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")
# or
devtools::install_github("pnickchi/PEIMAN2")Example
Singular Enrichment Analysis (SEA)
# Load PEIMAN2 package
library(PEIMAN2)
# First example dataset
pl1 <- exmplData1$pl1
# Run SEA on the list
enrich1 <- runEnrichment(protein = pl1, os.name = 'Homo sapiens (Human)')
head(enrich1, n = 6)## PTM FreqinPopulation FreqinSample Sample
## 1 N6-(pyridoxal phosphate)lysine 53 5 97
## 2 Isoglutamyl cysteine thioester (Cys-Gln) 7 2 97
## 3 Glycoprotein 4721 41 97
## 4 Thioester bond 11 2 97
## 5 S-cysteinyl cysteine 3 1 97
## 6 Disulfide bond 3844 33 97
## Population pvalue corrected pvalue
## 1 20417 2e-07 7e-06
## 2 20417 4e-06 7e-05
## 3 20417 8e-06 1e-04
## 4 20417 2e-05 2e-04
## 5 20417 7e-05 5e-04
## 6 20417 1e-04 7e-04
## AC
## 1 Q96QU6; Q4AC99; Q8N5Z0; Q8NHS2; P17174
## 2 P01023; A8K2U0
## 3 P08195; P08908; P28222; P28221; P28566; P30939; P28223; P41595; P28335; P46098; O95264; Q70Z44; A5X5Y0; Q13639; P47898; P34969; P21589; P02763; P19652; P20848; P01009; P04217; P08697; P02750; P01023; A8K2U0; U3KPV4; Q9NPC4; Q9UNA3; P05067; P30542; P29274; P29275; P0DMS8; P22760; Q15758; P01011; P54619; Q9UGJ0; Q9UGI9; Q13131
## 4 P01023; A8K2U0
## 5 P01009
## 6 P08195; P08908; P28222; P28221; P28566; P30939; P28223; P41595; P28335; P46098; O95264; Q8WXA8; A5X5Y0; Q13639; P47898; P50406; P34969; P21589; P05408; P02763; P19652; P04217; P08697; P02750; P01023; A8K2U0; P05067; P30542; P29274; P29275; P0DMS8; Q9NS82; P22760# Second example dataset
pl2 <- exmplData1$pl2
# Run SEA on the list
enrich2 <- runEnrichment(protein = pl2, os.name = 'Homo sapiens (Human)')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 FreqinPopulation FreqinSample
## 1 Acetylation 0 0 1774 124
## 2 ADP-ribosylglycine 0 0 4 4
## 3 Cysteine sulfinic acid (-SO2H) 0 0 1 1
## 4 N-acetylaspartate 0 0 1 1
## 5 N-acetylglutamate 0 0 1 1
## 6 N6-acetyllysine 0 0 997 74
## ES NES nMoreExtreme size Enrichment
## 1 0.7472783 1.179016 0 124 Over presented
## 2 0.7707317 1.436098 33 4 Over presented
## 3 0.9423077 -12.750000 11 1 Under presented
## 4 -0.9615385 -7.968442 2 1 Under presented
## 5 -0.9663462 40.119760 5 1 Over presented
## 6 0.7149518 1.129027 6 74 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; 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; P30009; 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; P62959Plotting 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:00060 N-acetyl-L-serine
## 2 MOD:00085 N6-methyl-L-lysine
## 3 MOD:00322 1'-methyl-L-histidine
## 4 MOD:00720 L-methionine (R)-sulfoxide
## 5 MOD:00051 N-acetyl-L-aspartic acid
## 6 MOD:00052 N-acetyl-L-cysteine
## 7 MOD:00053 N-acetyl-L-glutamic acid
## def
## 1 "converts an L-serine residue to N-acetyl-L-serine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:1880797, PubMed:2106685, PubMed:6997045, RESID:AA0051]
## 2 "converts an L-lysine residue to N6-methyl-L-lysine." [ChEBI:17604, DeltaMass:165, PubMed:11875433, PubMed:3926756, RESID:AA0076, Unimod:34#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 "oxygenates an L-methionine residue to L-methionine sulfoxide R-diastereomer." [ChEBI:45764, PubMed:21406390, PubMed:22116028, PubMed:23911929, RESID:AA0581]
## 5 "converts an L-aspartic acid residue to N-acetyl-L-aspartic acid." [ChEBI:21547, PubMed:1560020, PubMed:2395459, RESID:AA0042]
## 6 "converts an L-cysteine residue to N-acetyl-L-cysteine." [ChEBI:28939, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:1500421, PubMed:15350136, PubMed:6725286, RESID:AA0043]
## 7 "converts an L-glutamic acid residue to N-acetyl-L-glutamic acid." [ChEBI:17533, PubMed:6725286, RESID:AA0044]
## FreqinSample
## 1 11
## 2 9
## 3 2
## 4 2
## 5 1
## 6 1
## 7 1