Properties of Yeast proteins

Description

A data frame which details 33 properties of proteins in the Yeast Genome

Usage

data(proteinProperties)

Format

A data frame with 6718 observations on the following 33 variables.

yORF

a factor representing yeast ORF names, with levels Q0010, Q0017, etc.

SGDID

a factor representing SGD IDs

molwt

a numeric vector giving Molecular Weight in Daltons

pi

a numeric vector denoting the theoretical isoelectric point(pI), the pH at which the protein carries no net charge

cai

a numeric vector denoting Codon Adaptation Index

length

a numeric vector denoting length of the protein (number of amino acids)

nterm

a factor representing N Term Sequence with levels MAAACIC MAAAPWY, etc.

cterm

a factor representing N Term Sequence with levels AAAAMLL AAADKKT, etc.

codonBias

a numeric vector denoting Codon Bias

The next set of columns, designated by amino acids, is the number of times that particular residue appears in the protein sequence. For example, if the ALA column is 2, then the protein contains 2 alanines. These columns (should) add up to the length column.

ALA

a numeric vector

ARG

a numeric vector

ASN

a numeric vector

ASP

a numeric vector

CYS

a numeric vector

GLN

a numeric vector

GLU

a numeric vector

GLY

a numeric vector

HIS

a numeric vector

ILE

a numeric vector

LEU

a numeric vector

LYS

a numeric vector

MET

a numeric vector

PHE

a numeric vector

PRO

a numeric vector

SER

a numeric vector

THR

a numeric vector

TRP

a numeric vector

TYR

a numeric vector

VAL

a numeric vector

The remaining columns are:

fop

FOP score, a numeric vector, denoting Frequency of Optimal Codons

gravy

Gravy score, a numeric vector denoting Hydropathicity of Protein

aromaticity

Aromaticity score, a numeric vector denoting Frequency of aromatic amino acids: Phe, Tyr, Trp

type

Feature type, a factor with levels ORF|Dubious ORF|Uncharacterized ORF|Verified ORF|Verified|silenced_gene pseudogene transposable_element_gene

Details

This data frame is downloaded directly from SGD. It contains 33 characteristics for 6714 open reading frames (ORFS). From the SGD README:

“Contains basic protein information about each ORF in SGD. This file does not include information on deleted or merged ORFs. Note, however, that it includes ORFs of all other classifications (Verified, Uncharacterized, and Dubious).”

For more details see http://www.yeastgenome.org/help/protein_page.html.

Source

ftp://genome-ftp.stanford.edu/pub/yeast/protein_info/protein_properties.tab. This file is updated weekly (Saturday). The version used here was downloaded on 2006-11-03.

Examples

data(proteinProperties)
pairs(proteinProperties[, c("molwt", "pi", "cai", "gravy", "aromaticity")],
      pch = ".", col = as.numeric(proteinProperties$type))