hmeto

A dataset containing data regarding human MetO sites oxidized by H2O2.

datasets

Contains utilities for the analysis of post-translational modifications (PTMs) in proteins,
with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download,
filter and analyze data from the sulfoxidation database 'MetOSite', and integrate data from other main PTMs
(other databases). Utilities to search and characterize S-aromatic motifs in proteins are also provided.
In addition, functions to analyze sequence environments around modifiable residues in proteins can be found.
For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable
residues from the proteins of interest. Functions tailored to test statistical hypothesis related to
these differential sequence environments are also implemented. A number of utilities to assess the effect
of the modification/mutation of a given residue on the protein stability, have also been included in this package.
Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).

Juan Aledo

Analyses of Protein Post-Translational Modifications

Juan Carlos Aledo

hmeto function

A data frame with 4472 rows and 15 variables:<dl>
 <dt>prot_id</dt>
<dd>UniProt ID of the oxidized protein</dd> <dt>prot_name</dt>
<dd>the protein's name</dd> <dt>met_pos</dt>
<dd>the position of the MetO site in the primary structure</dd> <dt>met_vivo_vitro</dt>
<dd>conditions under which the oxidation experiment was carried out</dd> <dt>MetOsites</dt>
<dd>array with all the sites oxidized in that protein</dd> <dt>site_id</dt>
<dd>primary key identifying the site</dd> <dt>positive</dt>
<dd>sequence environment of the MetO site</dd> <dt>control</dt>
<dd>sequence environment of a non oxidized Met from the same protein</dd> <dt>IDP</dt>
<dd>Intrinsically Disordered Proteins, 0: the protein is not found in DisProt; 1: the protein contains disordered regions; 2: the protein may contain disordered regions but the experimental evidences are ambiguous</dd> <dt>IDR</dt>
<dd>Intrinsically Disordered Region, TRUE: the MetO site belong to the IDR, FALSE: the MetO site doesn't belong to the IDR</dd> <dt>abundance</dt>
<dd>protein abundance, in ppm</dd> <dt>N</dt>
<dd>protein length, in number of residues</dd> <dt>met</dt>
<dd>number of methionine residues</dd> <dt>fmet</dt>
<dd>relative frequency of Met in that protein</dd> <dt>prot_vivo_vitro</dt>
<dd>whether the protein has been described to be oxidized in vivo, in vitro or under both conditions</dd>
</dl>

Format

Human MetO sites oxidized by hydrogen peroxide treatment. — hmeto

A data frame with 4472 rows and 15 variables:<dl>
 <dt>prot_id</dt>
<dd>UniProt ID of the oxidized protein</dd>

 <dt>prot_name</dt>
<dd>the protein's name</dd>

 <dt>met_pos</dt>
<dd>the position of the MetO site in the primary structure</dd>

 <dt>met_vivo_vitro</dt>
<dd>conditions under which the oxidation experiment was carried out</dd>

 <dt>MetOsites</dt>
<dd>array with all the sites oxidized in that protein</dd>

 <dt>site_id</dt>
<dd>primary key identifying the site</dd>

 <dt>positive</dt>
<dd>sequence environment of the MetO site</dd>

 <dt>control</dt>
<dd>sequence environment of a non oxidized Met from the same protein</dd>

 <dt>IDP</dt>
<dd>Intrinsically Disordered Proteins, 0: the protein is not found in DisProt; 1: the protein contains disordered regions; 2: the protein may contain disordered regions but the experimental evidences are ambiguous</dd>

 <dt>IDR</dt>
<dd>Intrinsically Disordered Region, TRUE: the MetO site belong to the IDR, FALSE: the MetO site doesn't belong to the IDR</dd>

 <dt>abundance</dt>
<dd>protein abundance, in ppm</dd>

 <dt>N</dt>
<dd>protein length, in number of residues</dd>

 <dt>met</dt>
<dd>number of methionine residues</dd>

 <dt>fmet</dt>
<dd>relative frequency of Met in that protein</dd>

 <dt>prot_vivo_vitro</dt>
<dd>whether the protein has been described to be oxidized in vivo, in vitro or under both conditions</dd>


</dl>

hmeto: Human MetO sites oxidized by hydrogen peroxide treatment.

Description

Usage

Arguments

Format