ecoli.names

1. Title: Protein Localization Sites


2. Creator and Maintainer:
	     Kenta Nakai
             Institue of Molecular and Cellular Biology
	     Osaka, University
	     1-3 Yamada-oka, Suita 565 Japan
	     nakai@imcb.osaka-u.ac.jp
             http://www.imcb.osaka-u.ac.jp/nakai/psort.html
   Donor: Paul Horton (paulh@cs.berkeley.edu)
   Date:  September, 1996
   See also: yeast database

3. Past Usage.
Reference: "A Probablistic Classification System for Predicting the Cellular 
           Localization Sites of Proteins", Paul Horton & Kenta Nakai,
           Intelligent Systems in Molecular Biology, 109-115.
	   St. Louis, USA 1996.
Results: 81% for E.coli with an ad hoc structured
	 probability model. Also similar accuracy for Binary Decision Tree and
	 Bayesian Classifier methods applied by the same authors in
	 unpublished results.

Predicted Attribute: Localization site of protein. ( non-numeric ).


4. The references below describe a predecessor to this dataset and its 
development. They also give results (not cross-validated) for classification 
by a rule-based expert system with that version of the dataset.

Reference: "Expert Sytem for Predicting Protein Localization Sites in 
           Gram-Negative Bacteria", Kenta Nakai & Minoru Kanehisa,  
           PROTEINS: Structure, Function, and Genetics 11:95-110, 1991.

Reference: "A Knowledge Base for Predicting Protein Localization Sites in
	   Eukaryotic Cells", Kenta Nakai & Minoru Kanehisa, 
	   Genomics 14:897-911, 1992.


5. Number of Instances:  336 for the E.coli dataset and 


6. Number of Attributes.
         for E.coli dataset:  8 ( 7 predictive, 1 name )

	     
7. Attribute Information.

  1.  Sequence Name: Accession number for the SWISS-PROT database
  2.  mcg: McGeoch's method for signal sequence recognition.
  3.  gvh: von Heijne's method for signal sequence recognition.
  4.  lip: von Heijne's Signal Peptidase II consensus sequence score.
           Binary attribute.
  5.  chg: Presence of charge on N-terminus of predicted lipoproteins.
	   Binary attribute.
  6.  aac: score of discriminant analysis of the amino acid content of
	   outer membrane and periplasmic proteins.
  7. alm1: score of the ALOM membrane spanning region prediction program.
  8. alm2: score of ALOM program after excluding putative cleavable signal
	   regions from the sequence.



8. Missing Attribute Values: None.


9. Class Distribution. The class is the localization site. Please see Nakai &
		       Kanehisa referenced above for more details.

  cp  (cytoplasm)                                    143
  im  (inner membrane without signal sequence)        77               
  pp  (perisplasm)                                    52
  imU (inner membrane, uncleavable signal sequence)   35
  om  (outer membrane)                                20
  omL (outer membrane lipoprotein)                     5
  imL (inner membrane lipoprotein)                     2
  imS (inner membrane, cleavable signal sequence)      2