% 1. Title of Database: E. coli promoter gene sequences (DNA) % with associated imperfect domain theory % % 2. Sources: % (a) Creators: % - promoter instances: C. Harley (CHARLEY@McMaster.CA) and R. Reynolds % - non-promoter instances and domain theory: M. Noordewier % -- (non-promoters derived from work of lab of Prof. Tom Record, % University of Wisconsin Biochemistry Department) % (b) Donor: M. Noordewier and J. Shavlik, {noordewi,shavlik}@cs.wisc.edu % (c) Date received: 6/30/90 % % 3. Past Usage: % (a) biological: % -- Harley, C. and Reynolds, R. 1987. % "Analysis of E. Coli Promoter Sequences." % Nucleic Acids Research, 15:2343-2361. % machine learning: % -- Towell, G., Shavlik, J. and Noordewier, M. 1990. % "Refinement of Approximate Domain Theories by Knowledge-Based % Artificial Neural Networks." In Proceedings of the Eighth National % Conference on Artificial Intelligence (AAAI-90). % (b) attributes predicted: member/non-member of class of sequences with % biological promoter activity (promoters initiate the process of gene % expression). % (c) Results of study indicated that machine learning techniques (neural % networks, nearest neighbor, contributors' KBANN system) performed as % well/better than classification based on canonical pattern matching % (method used in biological literature). % % 4. Relevant Information Paragraph: % This dataset has been developed to help evaluate a "hybrid" learning % algorithm ("KBANN") that uses examples to inductively refine preexisting % knowledge. Using a "leave-one-out" methodology, the following errors % were produced by various ML algorithms. (See Towell, Shavlik, & % Noordewier, 1990, for details.) % % System Errors Comments % ------ ------ -------- % KBANN 4/106 a hybrid ML system % BP 8/106 std backprop with one hidden layer % O'Neill 12/106 ad hoc technique from the bio. lit. % Near-Neigh 13/106 a nearest-neighbor algo (k=3) % ID3 19/106 Quinlan's decision-tree builder % % Type of domain: non-numeric, nominal (one of A, G, T, C) % -- Note: DNA nucleotides can be grouped into a hierarchy, as shown below: % % X (any) % / \ % (purine) R Y (pyrimidine) % / \ / \ % A G T C % % % 5. Number of Instances: 106 % % 6. Number of Attributes: 59 % -- class (positive or negative) % -- instance name % -- 57 sequential nucleotide ("base-pair") positions % % 7. Attribute information: % -- Statistics for numeric domains: No numeric features used. % -- Statistics for non-numeric domains % -- Frequencies: Promoters Non-Promoters % --------- ------------- % A 27.7% 24.4% % G 20.0% 25.4% % T 30.2% 26.5% % C 22.1% 23.7% % % Attribute #: Description: % ============ ============ % 1 One of {+/-}, indicating the class ("+" = promoter). % 2 The instance name (non-promoters named by position in the % 1500-long nucleotide sequence provided by T. Record). % 3-59 The remaining 57 fields are the sequence, starting at % position -50 (p-50) and ending at position +7 (p7). Each of % these fields is filled by one of {a, g, t, c}. % % 8. Missing Attribute Values: none % % 9. Class Distribution: 50% (53 positive instances, 53 negative instances) % % The Domain Theory (for recognizing promoters): % % % Promoters have a region where a protein (RNA polymerase) must make contact % % and the helical DNA sequence must have a valid conformation so that % % the two pieces of the contact region spatially align. % % Prolog notation is used. % promoter :- contact, conformation. % % % There are two regions "upstream" from the beginning of the gene % % at which the RNA polymerase makes contact. % contact :- minus_35, minus_10. % % % The following rules describe the compositions of possible contact regions. % minus_35 :- p-37=c, p-36=t, p-35=t, p-34=g, p-33=a, p-32=c. % minus_35 :- p-36=t, p-35=t, p-34=g, p-32=c, p-31=a. % minus_35 :- p-36=t, p-35=t, p-34=g, p-33=a, p-32=c, p-31=a. % minus_35 :- p-36=t, p-35=t, p-34=g, p-33=a, p-32=c. % % minus_10 :- p-14 t, p-13 a, p-12=t, p-11=a, p-10=a, p-9=t. % minus_10 :- p-13 t, p-12=a, p-10=a, p-8=t. % minus_10 :- p-13 t, p-12=a, p-11=t, p-10=a, p-9=a, p-8=t. % minus_10 :- p-12=t, p-11=a, p-7=t. % % % The following rules describe sequence characteristics that produce % % acceptable conformations. % conformation :- p-47=c, p-46=a, p-45=a, p-43=t, p-42=t, p-40=a, p-39=c, % p-22=g, p-18=t, p-16=c, p-8=g, p-7=c, p-6=g, p-5=c, % p-4=c, p-2=c, p-1=c. % conformation :- p-45=a, p-44=a, p-41=a. % conformation :- p-49=a, p-44=t, p-27=t, p-22=a, p-18=t, p-16=t, p-15=g, % p-1=a. % conformation :- p-45=a, p-41=a, p-28=t, p-27=t, p-23=t, p-21=a, p-20=a, % p-17=t, p-15=t, p-4=t. % % % If exact matches are required, this domain theory matches NONE % % of the examples below. Also note that some of the MINUS_35 rules % % are subsumed by another MINUS_35 rule. This occurs because the % % biological evidence is inconclusive wrt the correct specificity. % % % % Information about the dataset % CLASSTYPE: nominal % CLASSINDEX: first % @relation molecular-biology-promoters @attribute 'class' {+,-} @attribute 'instance' {1019,1024,1108,1149,1163,1169,1171,1203,1216,1218,1226,1320,1321,1355,1384,1442,1481,19,217,230,244,260,296,313,35,39,413,464,507,521,557,630,648,660,663,668,751,753,780,794,799,802,835,850,867,91,915,918,93,957,987,988,991,ALAS,AMPC,ARABAD,ARAC,AROH,BIOA,BIOB,DEOP1,DEOP2,FOL,GALP2,GLNS,HIS,HISJ,ILVGEDA,LACI,LACP1,LEU1_TRNA,LEXA,LPP,M1RNA,MALEFG,MALK,MALT,PORI-L,PORI-R,RECA,RPLJ,RPOA,RPOB,RRNAB_P1,RRNAB_P2,RRNDEX_P2,RRND_P1,RRNE_P1,RRNG_P1,RRNG_P2,RRNX_P1,S10,SPC,SPOT42,STR,SUBB-E,THR,TNAA,TRP,TRPP2,TRPR,TUFB,TYRT,UVRBP1,UVRBP3,UVRB_P2} @attribute 'p-50' {a,c,g,t} @attribute 'p-49' {a,c,g,t} @attribute 'p-48' {a,c,g,t} @attribute 'p-47' {a,c,g,t} @attribute 'p-46' {a,c,g,t} @attribute 'p-45' {a,c,g,t} @attribute 'p-44' {a,c,g,t} @attribute 'p-43' {a,c,g,t} @attribute 'p-42' {a,c,g,t} @attribute 'p-41' {a,c,g,t} @attribute 'p-40' {a,c,g,t} @attribute 'p-39' {a,c,g,t} @attribute 'p-38' {a,c,g,t} @attribute 'p-37' {a,c,g,t} @attribute 'p-36' {a,c,g,t} @attribute 'p-35' {a,c,g,t} @attribute 'p-34' {a,c,g,t} @attribute 'p-33' {a,c,g,t} @attribute 'p-32' {a,c,g,t} @attribute 'p-31' {a,c,g,t} @attribute 'p-30' {a,c,g,t} @attribute 'p-29' {a,c,g,t} @attribute 'p-28' {a,c,g,t} @attribute 'p-27' {a,c,g,t} @attribute 'p-26' {a,c,g,t} @attribute 'p-25' {a,c,g,t} @attribute 'p-24' {a,c,g,t} @attribute 'p-23' {a,c,g,t} @attribute 'p-22' {a,c,g,t} @attribute 'p-21' {a,c,g,t} @attribute 'p-20' {a,c,g,t} @attribute 'p-19' {a,c,g,t} @attribute 'p-18' {a,c,g,t} @attribute 'p-17' {a,c,g,t} @attribute 'p-16' {a,c,g,t} @attribute 'p-15' {a,c,g,t} @attribute 'p-14' {a,c,g,t} @attribute 'p-13' {a,c,g,t} @attribute 'p-12' {a,c,g,t} @attribute 'p-11' {a,c,g,t} @attribute 'p-10' {a,c,g,t} @attribute 'p-9' {a,c,g,t} @attribute 'p-8' {a,c,g,t} @attribute 'p-7' {a,c,g,t} @attribute 'p-6' {a,c,g,t} @attribute 'p-5' {a,c,g,t} @attribute 'p-4' {a,c,g,t} @attribute 'p-3' {a,c,g,t} @attribute 'p-2' {a,c,g,t} @attribute 'p-1' {a,c,g,t} @attribute 'p1' {a,c,g,t} @attribute 'p2' {a,c,g,t} @attribute 'p3' {a,c,g,t} @attribute 'p4' {a,c,g,t} @attribute 'p5' {a,c,g,t} @attribute 'p6' {a,c,g,t} @attribute 'p7' {a,c,g,t} @data +,S10,t,a,c,t,a,g,c,a,a,t,a,c,g,c,t,t,g,c,g,t,t,c,g,g,t,g,g,t,t,a,a,g,t,a,t,g,t,a,t,a,a,t,g,c,g,c,g,g,g,c,t,t,g,t,c,g,t +,AMPC,t,g,c,t,a,t,c,c,t,g,a,c,a,g,t,t,g,t,c,a,c,g,c,t,g,a,t,t,g,g,t,g,t,c,g,t,t,a,c,a,a,t,c,t,a,a,c,g,c,a,t,c,g,c,c,a,a +,AROH,g,t,a,c,t,a,g,a,g,a,a,c,t,a,g,t,g,c,a,t,t,a,g,c,t,t,a,t,t,t,t,t,t,t,g,t,t,a,t,c,a,t,g,c,t,a,a,c,c,a,c,c,c,g,g,c,g +,DEOP2,a,a,t,t,g,t,g,a,t,g,t,g,t,a,t,c,g,a,a,g,t,g,t,g,t,t,g,c,g,g,a,g,t,a,g,a,t,g,t,t,a,g,a,a,t,a,c,t,a,a,c,a,a,a,c,t,c +,LEU1_TRNA,t,c,g,a,t,a,a,t,t,a,a,c,t,a,t,t,g,a,c,g,a,a,a,a,g,c,t,g,a,a,a,a,c,c,a,c,t,a,g,a,a,t,g,c,g,c,c,t,c,c,g,t,g,g,t,a,g 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-,867,a,t,a,t,g,a,a,c,g,t,t,g,a,g,a,c,t,g,c,c,g,c,t,g,a,g,t,t,a,t,c,a,g,c,t,g,t,g,a,a,c,g,a,c,a,t,t,c,t,g,g,c,g,t,c,t,a -,1169,c,g,a,a,c,g,a,g,t,c,a,a,t,c,a,g,a,c,c,g,c,t,t,t,g,a,c,t,c,t,g,g,t,a,t,t,a,c,t,g,t,g,a,a,c,a,t,t,a,t,t,c,g,t,c,t,c -,802,c,a,a,t,g,g,c,c,t,c,t,a,a,a,c,g,g,g,t,c,t,t,g,a,g,g,g,g,t,t,t,t,t,t,g,c,t,g,a,a,a,g,g,a,g,g,a,a,c,t,a,t,a,t,g,c,g -,521,t,t,g,a,c,c,t,a,c,t,a,c,g,c,c,a,g,c,a,t,t,t,t,g,g,c,g,g,t,g,t,a,a,g,c,t,a,a,c,c,a,t,t,c,c,g,g,t,t,g,a,c,t,c,a,a,t -,918,c,g,t,c,t,a,t,c,g,g,t,g,a,a,c,c,t,c,c,g,g,t,a,t,c,a,a,c,g,c,t,g,g,a,a,g,g,t,g,a,c,g,c,t,a,a,c,g,c,a,g,a,t,g,c,a,g -,1481,g,c,c,a,a,t,c,a,a,t,c,a,a,g,a,a,c,t,t,g,a,a,g,g,g,t,g,g,t,a,t,c,a,g,c,c,a,a,c,a,g,c,c,t,g,a,c,a,t,c,c,t,t,c,g,t,t -,1024,t,g,g,a,t,g,g,a,c,g,t,t,c,a,a,c,a,t,t,g,a,g,g,a,a,g,g,c,a,t,a,a,c,g,c,t,a,c,t,a,c,c,t,g,a,t,g,t,t,t,a,c,t,c,c,a,a -,1149,g,a,g,g,t,g,g,c,t,a,t,g,t,g,t,a,t,g,a,c,c,g,a,a,c,g,a,g,t,c,a,a,t,c,a,g,a,c,c,g,c,t,t,t,g,a,c,t,c,t,g,g,t,a,t,t,a 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-,753,a,a,g,t,g,c,t,t,a,g,c,t,t,c,a,a,g,g,t,c,a,c,g,g,a,t,a,c,g,a,c,c,g,a,a,g,c,g,a,g,c,c,t,c,g,t,c,c,t,c,a,a,t,g,g,c,c -,630,g,a,a,g,a,c,c,a,c,g,c,c,t,c,g,c,c,a,c,c,g,a,g,t,a,g,a,c,c,c,t,t,a,g,a,g,a,g,c,a,t,g,t,c,a,g,c,c,t,c,g,a,c,a,a,c,t -,660,t,t,a,g,a,g,a,g,c,a,t,g,t,c,a,g,c,c,t,c,g,a,c,a,a,c,t,t,g,c,a,t,a,a,a,t,g,c,t,t,t,c,t,t,g,t,a,g,a,c,g,t,g,c,c,c,t -,1216,t,a,t,t,c,g,t,c,t,c,c,g,c,g,a,c,t,a,c,g,a,t,g,a,g,a,t,g,c,c,t,g,a,g,t,g,c,t,t,c,c,g,t,t,a,c,t,g,g,a,t,t,g,t,c,a,c -,835,t,g,c,t,g,a,a,a,g,g,a,g,g,a,a,c,t,a,t,a,t,g,c,g,c,t,c,a,t,a,c,g,a,t,a,t,g,a,a,c,g,t,t,g,a,g,a,c,t,g,c,c,g,c,t,g,a -,35,c,a,t,g,a,a,c,t,c,a,a,g,g,c,t,g,a,t,a,c,g,g,c,g,a,g,a,c,t,t,g,c,g,a,g,c,c,t,t,g,t,c,c,t,t,g,c,g,g,t,a,c,a,c,a,g,c -,1218,t,t,c,g,t,c,t,c,c,g,c,g,a,c,t,a,c,g,a,t,g,a,g,a,t,g,c,c,t,g,a,g,t,g,c,t,t,c,c,g,t,t,a,c,t,g,g,a,t,t,g,t,c,a,c,c,a -,668,c,a,t,g,t,c,a,g,c,c,t,c,g,a,c,a,a,c,t,t,g,c,a,t,a,a,a,t,g,c,t,t,t,c,t,t,g,t,a,g,a,c,g,t,g,c,c,c,t,a,c,g,c,g,c,t,t -,413,a,g,g,a,g,g,a,a,c,t,a,c,g,c,a,a,g,g,t,t,g,g,a,a,c,a,t,c,g,g,a,g,a,g,a,t,g,c,c,a,g,c,c,a,g,c,g,c,a,c,c,t,g,c,a,c,g -,991,t,c,t,c,a,a,c,a,a,g,a,t,t,a,a,c,c,g,a,c,a,g,a,t,t,c,a,a,t,c,t,c,g,t,g,g,a,t,g,g,a,c,g,t,t,c,a,a,c,a,t,t,g,a,g,g,a -,751,t,g,a,a,g,t,g,c,t,t,a,g,c,t,t,c,a,a,g,g,t,c,a,c,g,g,a,t,a,c,g,a,c,c,g,a,a,g,c,g,a,g,c,c,t,c,g,t,c,c,t,c,a,a,t,g,g -,850,c,t,a,t,a,t,g,c,g,c,t,c,a,t,a,c,g,a,t,a,t,g,a,a,c,g,t,t,g,a,g,a,c,t,g,c,c,g,c,t,g,a,g,t,t,a,t,c,a,g,c,t,g,t,g,a,a -,93,g,c,g,g,c,a,g,c,a,c,g,t,t,t,c,c,a,c,g,c,g,g,t,g,a,g,a,g,c,c,t,c,a,g,g,a,t,t,c,a,t,g,t,c,g,a,t,g,t,c,t,t,c,c,g,g,t -,1108,a,t,c,c,c,t,a,a,t,g,t,c,t,a,c,t,t,c,c,g,g,t,c,a,a,t,c,c,a,t,c,t,a,c,g,t,t,a,a,c,c,g,a,g,g,t,g,g,c,t,a,t,g,t,g,t,a -,915,t,g,g,c,g,t,c,t,a,t,c,g,g,t,g,a,a,c,c,t,c,c,g,g,t,a,t,c,a,a,c,g,c,t,g,g,a,a,g,g,t,g,a,c,g,c,t,a,a,c,g,c,a,g,a,t,g -,1019,t,c,t,c,g,t,g,g,a,t,g,g,a,c,g,t,t,c,a,a,c,a,t,t,g,a,g,g,a,a,g,g,c,a,t,a,a,c,g,c,t,a,c,t,a,c,c,t,g,a,t,g,t,t,t,a,c -,19,t,a,t,t,g,g,c,t,t,g,c,t,c,a,a,g,c,a,t,g,a,a,c,t,c,a,a,g,g,c,t,g,a,t,a,c,g,g,c,g,a,g,a,c,t,t,g,c,g,a,g,c,c,t,t,g,t -,1320,t,a,g,a,g,g,g,t,g,t,a,c,t,c,c,a,a,g,a,a,g,a,g,g,a,a,g,a,t,g,a,g,g,c,t,a,g,a,c,g,t,c,t,c,t,g,c,a,t,g,g,a,g,t,a,t,g -,91,c,a,g,c,g,g,c,a,g,c,a,c,g,t,t,t,c,c,a,c,g,c,g,g,t,g,a,g,a,g,c,c,t,c,a,g,g,a,t,t,c,a,t,g,t,c,g,a,t,g,t,c,t,t,c,c,g -,217,t,t,a,c,g,t,t,g,g,c,g,a,c,c,g,c,t,a,g,g,a,c,t,t,t,c,t,t,g,t,t,g,a,t,t,t,t,c,c,a,t,g,c,g,g,t,g,t,t,t,t,g,c,g,c,a,a -,957,a,c,g,c,t,a,a,c,g,c,a,g,a,t,g,c,a,g,c,g,a,a,c,g,c,t,c,g,g,c,g,t,a,t,t,c,t,c,a,a,c,a,a,g,a,t,t,a,a,c,c,g,a,c,a,g,a -,260,g,g,t,g,t,t,t,t,g,c,g,c,a,a,t,g,t,t,a,a,t,c,g,c,t,t,t,g,t,a,c,a,c,c,t,c,a,g,g,c,a,t,g,t,a,a,a,c,g,t,c,t,t,c,g,t,a -,557,a,a,c,c,a,t,t,c,c,g,g,t,t,g,a,c,t,c,a,a,t,g,a,g,c,a,t,c,t,c,g,a,t,g,c,a,g,c,g,t,a,c,t,c,c,t,a,c,a,t,g,a,a,t,a,g,a -,1355,a,g,a,c,g,t,c,t,c,t,g,c,a,t,g,g,a,g,t,a,t,g,a,g,a,t,g,g,a,c,t,a,c,g,g,t,g,g,g,t,a,c,a,a,t,a,t,g,c,t,g,g,a,t,g,g,a -,244,t,g,t,t,g,a,t,t,t,t,c,c,a,t,g,c,g,g,t,g,t,t,t,t,g,c,g,c,a,a,t,g,t,t,a,a,t,c,g,c,t,t,t,g,t,a,c,a,c,c,t,c,a,g,g,c,a -,464,t,g,c,a,c,g,g,g,t,t,g,c,g,a,t,a,g,c,c,t,c,a,g,c,g,t,a,t,t,c,a,g,g,t,g,c,g,a,g,t,t,c,g,a,t,a,g,t,c,t,c,a,g,a,g,t,c -,296,a,g,g,c,a,t,g,t,a,a,a,c,g,t,c,t,t,c,g,t,a,g,c,g,c,a,t,c,a,g,t,g,c,t,t,t,c,t,t,a,c,t,g,t,g,a,g,t,a,c,g,c,a,c,c,a,g -,648,c,c,g,a,g,t,a,g,a,c,c,c,t,t,a,g,a,g,a,g,c,a,t,g,t,c,a,g,c,c,t,c,g,a,c,a,a,c,t,t,g,c,a,t,a,a,a,t,g,c,t,t,t,c,t,t,g -,230,c,g,c,t,a,g,g,a,c,t,t,t,c,t,t,g,t,t,g,a,t,t,t,t,c,c,a,t,g,c,g,g,t,g,t,t,t,t,g,c,g,c,a,a,t,g,t,t,a,a,t,c,g,c,t,t,t -,1163,t,a,t,g,a,c,c,g,a,a,c,g,a,g,t,c,a,a,t,c,a,g,a,c,c,g,c,t,t,t,g,a,c,t,c,t,g,g,t,a,t,t,a,c,t,g,t,g,a,a,c,a,t,t,a,t,t -,1321,a,g,a,g,g,g,t,g,t,a,c,t,c,c,a,a,g,a,a,g,a,g,g,a,a,g,a,t,g,a,g,g,c,t,a,g,a,c,g,t,c,t,c,t,g,c,a,t,g,g,a,g,t,a,t,g,a -,663,g,a,g,a,g,c,a,t,g,t,c,a,g,c,c,t,c,g,a,c,a,a,c,t,t,g,c,a,t,a,a,a,t,g,c,t,t,t,c,t,t,g,t,a,g,a,c,g,t,g,c,c,c,t,a,c,g -,799,c,c,t,c,a,a,t,g,g,c,c,t,c,t,a,a,a,c,g,g,g,t,c,t,t,g,a,g,g,g,g,t,t,t,t,t,t,g,c,t,g,a,a,a,g,g,a,g,g,a,a,c,t,a,t,a,t -,987,g,t,a,t,t,c,t,c,a,a,c,a,a,g,a,t,t,a,a,c,c,g,a,c,a,g,a,t,t,c,a,a,t,c,t,c,g,t,g,g,a,t,g,g,a,c,g,t,t,c,a,a,c,a,t,t,g -,1226,c,g,c,g,a,c,t,a,c,g,a,t,g,a,g,a,t,g,c,c,t,g,a,g,t,g,c,t,t,c,c,g,t,t,a,c,t,g,g,a,t,t,g,t,c,a,c,c,a,a,g,g,c,t,t,c,c -,794,c,t,c,g,t,c,c,t,c,a,a,t,g,g,c,c,t,c,t,a,a,a,c,g,g,g,t,c,t,t,g,a,g,g,g,g,t,t,t,t,t,t,g,c,t,g,a,a,a,g,g,a,g,g,a,a,c -,1442,t,a,a,c,a,t,t,a,a,t,a,a,a,t,a,a,g,g,a,g,g,c,t,c,t,a,a,t,g,g,c,a,c,t,c,a,t,t,a,g,c,c,a,a,t,c,a,a,t,c,a,a,g,a,a,c,t