Scans the indicated protein in search of disease-related PTM sites




up_id a character string corresponding to the UniProt ID.


Returns a dataframe where each row corresponds to a residue, and the colums inform about the disease-related modifications.


Hornbeck et al. Nucleic Acids Res. 2019 47:D433-D441.

See Also

ac.scan(), meto.scan(), p.scan(), me.scan(),ub.scan(), su.scan(), gl.scan(), sni.scan(), ni.scan(), ptm.scan(), reg.scan()


The different posttranslational modifications participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases.

The package ptm has a function, dis.scan(), which allows to scan a protein, let’s say Catenin beta-1 (P35222), for known PTM sites related with diseases. The straightforward use would be:

catenin <- dis.scan('P35222')

19P35222Homo sapiensT41-pPSPcolorectal cancer
20P35222Homo sapiensS37-pPSPcolorectal cancer
21P35222Homo sapiensS45-pPSPcolorectal cancer
22P35222Homo sapiensS33-pPSPcolorectal cancer
98P35222Homo sapiensS45-pPSPWilm’s tumor
451P35222Homo sapiensS33-pPSPovarian cancer
465P35222Homo sapiensS33-pPSPmelanoma skin cancer
585P35222Homo sapiensS552-pPSPcolonic inflamation
597P35222Homo sapiensY333-pPSPglioblastoma
599P35222Homo sapiensT120-pPSPprostate cancer
631P35222Homo sapiensY654-pPSPIPF

This function can also be used in more elaborated ways. Suppose, for whatever reasons, we are interested in knowing those sites related to diseases found in proteins contained in the database MetOSite. To achieve this goal, we start making a list with UniProt ID for all the proteins from MetOSite:

meto <- unique(meto.search()$prot_id)

Now, we can procedure to a recursive scan for all the MetOSite’s proteins:

meto_disease <- catenin[0,] # To inherit the headers of the 'catenin' dataframe
for (i in 1:length(meto)){
  t <- dis.scan(meto[i])
  if (is.data.frame(t)){
    meto_disease <- rbind(meto_disease, t)
125P04637Homo sapiensS15-pPSPataxia-telangiectasia
275P04637Homo sapiensS37-pPSPT cell leukemia
528P04637Homo sapiensS20-pPSPovarian cancer
529P04637Homo sapiensS392-pPSPovarian cancer
603P04637Homo sapiensS46-pPSPHuntington’s disease
793P04637Homo sapiensS392-pPSPhepatocellular carcinoma

The object meto_disease is a dataframe containing hundreds of entries (rows), although only the first ones have been shown herein.