Data Set Information:

The data was collected from several sources, including the Sanger Centre ([Web link]) and SWISSPROT ([Web link]). Structure prediction was made by PROF ([Web link]). Homology search was made by PSI-BLAST ([Web link]).

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

Dependencies:

M. tuberculosis genes (ORFs) are related to each other by the predicate tb_to_tb_evalue(TBNumber,E-value). 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(TBNumber)).
  end(model(TBNumber)).

Other Relevant Information:

The gene functional classes are in a hierarchy. See [Web link].


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

1. tb_functions.pl

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

  class([1,0,0,0],"Small-molecule metabolism ").
  class([1,1,0,0],"Degradation ").
  class([1,1,1,0],"Carbon compounds ").  

Arguments are a list of 4 numbers (describing class at the 4 different levels), followed by a string class description. For example,

  function(tb186,[1,1,1,0],'bglS',"beta-glucosidase").

Arguments are ORF number, list of 4 class numbers, gene name (or null if no gene name) in single quotes, ORF description in double quotes.

2. tb_data.pl

Data for each ORF (gene) is delimited by

  begin(model(X)).
  end(model(X)).

where X is the ORF number. Other predicates are as follows (examples):

  tb_protein(X).    % X is gene number
  function(2,1,5,0,'gyrA','DNA gyrase subunit A').  % 4 levels of functional hierarchy, gene name, description
  coding_region(7302,9815). % start,end. integers
  tb_mol_wt(19934).  % integer
  access(1,e,20). % int (position), {e,i,b}, int (length)
  access_exposed(1,20). % int (position), int (length)
  access_intermediate(26,1). % int (position), int (length)
  access_burried(1,2). % int (position), int (length)
  access_dist(b,42.8). % {e,i,b}, float (percentage)
  sec_struc(1,c,23). % int (position), {a,b,c}, int (length)
  sec_struc_coil(1,23). % int (position), int (length)
  sec_struc_alpha(1,15). % int (position), int (length)
  sec_struc_beta(1,6). % int (position), int (length)
  struc_dist(a,32.1). % {a,b,c}, float (percentage)
  sec_struc_conf(78.8). % float (confidence)
  sec_struc_conf_alpha(88.9). % float (confidence)
  sec_struc_conf_beta(58.0). % float (confidence)
  sec_struc_conf_coil(77.7). % float (confidence)
  psi_sequences_found(1,7). % how many found, which iteration
  psi_sequences_found_again(2,7).  % how many found, which iteration
  psi_sequences_found_new(2,0). % how many found, which iteration
  amino_acid_ratio(a,11.2). % amino acid letter, float
  amino_acid_pair_ratio(a,c,0.0). % amino acid letter, amino acid letter, float (out of 1000, ie 2.8 = 0.28%)
  sequence_length(187).  % integer
  tb_to_tb_evalue(tb3671,1.100000e-01). % ORF number, e-value (double)  
  e_val(p35925,7.0e-59). % SWISSPROT accession no, e-value (double)
  species(p35925,'streptomyces_coelicolor'). % SWISSPROT acc no, string
  classification(p35925,bacteria). % SWISSPROT acc no, name
  mol_wt(p35925,19772). % SWISSPROT acc no, integer
  keyword(p35925,'hypothetical_protein'). % SWISSPROT acc no, string
  db_ref(p35925,embl,l27063,g436026,null). % SWISSPROT acc no, db id, primary id, secondary id, status id
  signalip(c,35,no). % {c,y,s}, int (signal peptide c/y/s score), yes/no
  signalip(ss,1,34,no). % ss, int, int, yes/no
  signalip(cleavage,59,60). % cleavage, int/null, int/null
  hydro_cons(-0.498,-0.474,0.624,3.248,0.278). % double, double, double, double, double
  gene_name(p41514,'gyrb'). % SWISSPROT acc no, string

Attribute Information:

N/A

Relevant Papers:

King, R. and Karwath, A. and Clare, A. and Dehaspe, L. (2000). Genome Scale Prediction of Protein Functional Class from Sequence Using Data Mining, In Proceedings of the Seventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.
[Web link]

King, R. and Karwath, A. and Clare, A. and Dehaspe, L. (2000). Accurate prediction of protein functional class in the M. tuberculosis and E. coli genomes using data mining, Comparative and Functional Genomics, 17, pp 283--293.
[Web link]

Citation Request:

Usage Restrictions:

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

There are no restrictions. 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.

Ross D. King
 Department of Computer Science,
 University of Wales Aberystwyth,
 SY23 3DB, Wales
 rdk '@' aber.ac.uk
http://users.aber.ac.uk/rdk