title: A multi-step approach to time series analysis and gene expression clustering.
abstract: BACKGROUND
  The huge growth in gene expression data calls for the implementation of automatic tools for data processing and interpretation.
  
  
  RESULTS
  We present a new and comprehensive machine learning data mining framework consisting in a non-linear PCA neural network for feature extraction, and probabilistic principal surfaces combined with an agglomerative approach based on Negentropy aimed at clustering gene microarray data. The method, which provides a user-friendly visualization interface, can work on noisy data with missing points and represents an automatic procedure to get, with no a priori assumptions, the number of clusters present in the data. Cell-cycle dataset and a detailed analysis confirm the biological nature of the most significant clusters.
  
  
  BACKGROUND
  The software described here is a subpackage part of the ASTRONEURAL package and is available upon request from the corresponding author.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Dipartimento di Scienze Fisiche, University of Naples Federico II, Naples, Italy.
authors.forename: R
authors.initials: R
authors.lastname: Amato
authors.forename: A
authors.initials: A
authors.lastname: Ciaramella
authors.forename: N
authors.initials: N
authors.lastname: Deniskina
authors.forename: C
authors.initials: C
authors.lastname: Del Mondo
authors.forename: D
authors.initials: D
authors.lastname: di Bernardo
authors.forename: C
authors.initials: C
authors.lastname: Donalek
authors.forename: G
authors.initials: G
authors.lastname: Longo
authors.forename: G
authors.initials: G
authors.lastname: Mangano
authors.forename: G
authors.initials: G
authors.lastname: Miele
authors.forename: G
authors.initials: G
authors.lastname: Raiconi
authors.forename: A
authors.initials: A
authors.lastname: Staiano
authors.forename: R
authors.initials: R
authors.lastname: Tagliaferri
mesh_terms: D001185:Artificial Intelligence; D016000:Cluster Analysis; D003196:Computer Graphics; D003198:Computer Simulation; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D012984:Software; D013997:Time Factors; D014584:User-Computer Interface
chemical_list: D011506:Proteins