E. coli genes

Data Type

relational

Abstract

Data giving characteristics of each ORF (potential gene) in the E. coli genome. Sequence, homology (similarity to other genes) and structural information, and function (if known) are provided.

Sources

Original Owner and Donor

  Ross D. King
  Department of Computer Science, 
  University of Wales Aberystwyth, 
  SY23 3DB, Wales
  rdk@aber.ac.uk
Date Donated: July 14, 2001

Data Characteristics

The data was collected from several sources, including GenProtEC and SWISSPROT. Structure prediction was made by PROF. Homology search was provided by PSI-BLAST.

The data is in Datalog format. Missing values are not explicit, but some genes have more relationships than others.

Dependencies

E. coli genes (ORFs) are related to each other by the predicate ecoli_to_ecoli(EcoliNumber,E-value,Psi-blast_iteration). They are related to other (SWISSPROT) proteins by the predicate e_val(AccNo,E-value). All the data for a single gene (ORF) is enclosed between delimiters of the form:

   begin(model(EcoliNumber)).
   end(model(EcoliNumber)). 

Other Relevant Information

The gene functional classes are in a hierarchy. See http://genprotec.mbl.edu/start (note: the classes may have changed since original data collection).

Data Format

There are two datalog files: ecoli_data.pl and ecoli_functions.pl

ecoli_functions.pl

Lists classes and ORF functions. Lines are of the following form:

   class(5,1,1,'Colicin-related functions').
   class(5,1,'Laterally acquirred elements').
   class(5,'Extrachromosomal'). 

Arguments are up to 3 numbers (describing class at up to 3 different levels), followed by a string class description. For example:

   function(ecoli210,7,0,0,'b0217','putative aminopeptidase').

Arguments are ORF number, exactly 3 class numbers, gene name (or blattner number if no gene name), ORF description.

ecoli_data.pl

Data for each ORF (gene) is delimited by

   begin(model(ecoliX)).
   end(model(ecoliX)).
where X is the ORF number. Other predicates are as follows (examples):
   ecoli_orf(ecoliX).    % X is ORF number
   ecoli_mol_wt(176624.1).  % float
   ecoli_theo_pI(5.81).     %float
   ecoli_atomic_comp(c,7940).   % {c,h,n,o,s} , int
   ecoli_aliphatic_index(69.57). % float
   ecoli_hydro(-0.549).          % float
   sec_struc(1,c,2).           % int (start), {a,b,c}, int (length)
   sec_struc_coil(1,2).        % int (start), int (length)
   sec_struc_beta(1,5).        % int (start), int (length)
   sec_struc_alpha(1,7).       % int (start), int (length)
   sequence_length(255).       % int
   amino_acid_ratio(a,8.9).    % amino_acid_char, float
   amino_acids(ecoli3013,a,70). % ORF_num, amino_acid_char, int
   amino_acid_pair_ratio(a,a,9.0). % amino_acid_char, amino_acid_char, float
   amino_acid_pairs(a,a,7).    % amino_acid_char, amino_acid_char, int
   ecoli_to_ecoli(1170,1.0e-105,5).  % ORF_num, double (e-value), int (iteration) 
   e_val(o42893,2.0e-99).  % accession_number, double (e-value)
   psi_iter(o42893,5).     % accession_number, int (iteration)
   species(p52494,'candida_albicans__yeast_').  % accession_number, string
   mol_wt(p52494,104022). % accession_number, int 
   classification(p52494,candida).  % accession_number, name
   keyword(p25195,'plasmid').   % accession_number, string

Past Usage

King, R. D., Karwath, A., Clare, A. and Dehaspe, L. (2000) Accurate prediction of protein functional class in the M. tuberculosis and E. coli genomes using data mining. Journal of Comparative and Functional Genomics, 17, p283-293.

Acknowledgements, Copyright Information, and Availability

Usage Restrictions

Copyright 2000 by R. D. King, A. Karwath, A. Clare, L. Dehaspe

There are no restrictions data usage. This data is provided "as is" and without any express or implied warranties, including, without limitation, the implied warranties of merchantibility and fitness for a particular purpose.

Citation Requests

Please cite King et al. (2000).

Acknowledgements

This work was supported by the following grants: G78/6609, BIF08765, GR/L62849 and by PharmaDM, Ambachtenlaan, 54/D, B-3001 Leuven, Belgium

References and Further Information

King, R. and Karwath, A. and Clare, A. and Dehaspe, L. (2001). The Utility of Different Representations of Protein Sequence for Predicting Functional Class, Bioinformatics, 17(5), pages 445--454.


The UCI KDD Archive
Information and Computer Science
University of California, Irvine
Irvine, CA 92697-3425
Last modified: August 7, 2001