- author = "William B. Langdon and J. Rowsell and A. P. Harrison",
- title = "Creating Regular Expressions as {mRNA} Motifs with {GP} to Predict Human Exon Splitting",
- booktitle = "GECCO '09: Proceedings of the 11th Annual conference on Genetic and evolutionary computation",
- year = "2009",
- editor = "Guenther Raidl and Franz Rothlauf and Giovanni Squillero and Rolf Drechsler and Thomas Stuetzle and Mauro Birattari and Clare Bates Congdon and Martin Middendorf and Christian Blum and Carlos Cotta and Peter Bosman and Joern Grahl and Joshua Knowles and David Corne and Hans-Georg Beyer and Ken Stanley and Julian F. Miller and Jano {van Hemert} and Tom Lenaerts and Marc Ebner and Jaume Bacardit and Michael O'Neill and Massimiliano {Di Penta} and Benjamin Doerr and Thomas Jansen and Riccardo Poli and Enrique Alba",
- pages = "1789--1790",
- address = "Montreal",
- month = "8-12 " # jul,
- organisation = "SIGEVO",
- publisher = "ACM",
- publisher_address = "New York, NY, USA",
- keywords = "genetic algorithms, genetic programming, Poster, Gene expression and regulation, alternative splicing, Microarray analysis, Integration of genetic programming into bioinformatics, Biological interpretation of computer generated motifs, Bioinformatics, Affymetrix GeneChip, strongly typed genetic programming, grammar, regular expression, Alternative splicing of Homosapiens exons, HDONA",
- isbn13 = "978-1-60558-325-9",
-
URL = "
http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/papers/langdon_2009_gecco.pdf",
-
DOI = "
doi:10.1145/1569901.1570162",
-
data_url = "
http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp-code/tr-09-02.tar.gz",
- size = "2 pages",
-
abstract = "RNAnet \cite{CES-486}
http://bioinformatics.essex.ac.uk/users/wlangdon/rnanet/
allows the user to calculate correlations of gene
expression, both between genes and between components
within genes. We investigate all of Ensembl
http://www.ensembl.org and find all the Homo Sapiens
exons for which there are sufficient robust Affymetrix
HG-U133 Plus 2 GeneChip probes. Calculating correlation
between mRNA probe measurements for the same exon shows
many exons whose components are consistently up
regulated and down regulated. However we identify other
Ensembl exons where sub-regions within them are self
consistent but these transcript blocks are not well
correlated with other blocks in the same exon. We
suggest many current Ensembl exon definitions are
incomplete.
Secondly, having identified exon with substructure we use machine learning to try and identify patterns in the DNA sequence lying between blocks of high correlation which might yield biological or technological explanations. A Backus-Naur form (BNF) context-free grammar constrains strongly typed genetic programming (STGP) to evolve biological motifs in the form of regular expressions (RE) (e.g. TCTTT) which classify gene exons with potential alternative mRNA expression from those without. We show biological patterns can be data mined by a GP written in gawk and using egrep from NCBI's GEO http://www.ncbi.nlm.nih.gov/geo/ database. The automatically produced DNA motifs suggest that alternative polyadenylation is not responsible. (Full version in TR-09-02 \cite{langdon:2009:TR-09-02}.)
Blocky exons can be found in (broken see data_url) http://bioinformatics.essex.ac.uk/users/wlangdon/tr-09-02.tar.gz",
-
notes = "t03p220. Longer version in
\cite{langdon:2009:TR-09-02}.
GECCO-2009 A joint meeting of the eighteenth international conference on genetic algorithms (ICGA-2009) and the fourteenth annual genetic programming conference (GP-2009).
ACM Order Number 910092. Also known as \cite{DBLP:conf/gecco/LangdonRH09}",
