In-silico identification of chicken immune-related genes.
In order to increase the resources available in chicken, a large-scale expressed sequence tag (EST) project was recently undertaken, resulting in the addition of more than 330,000 sequences to the databases. With the sequencing of further EST collections, there are now more than 460,000 chicken EST sequences publicly available (http://www.ncbi.nlm.nih.gov/). Previous analyses of the EST data estimate that the chicken genome may contain up to 35,000 genes. However, human data indicate that there may only be around 25,000, although there may be many more transcripts than actual genes. Here we describe how we used a bioinformatics approach with this large EST collection in order to identify immune-related genes, many of which were previously unreported in the chicken. The ESTs include cytokines, chemokines, antigens, cell surface proteins, receptors and MHC-associated genes. The identification of these kinds of genes will allow further study of avian immunology and will pave the way for large-scale immune-related microarray experiments, giving new insight into functional and evolutionary studies.
Smith
Jacqueline
J
Division of Genomics and Bioinformatics, Roslin Institute, EH25 9PS, Roslin (Edinburgh), Midlothian, UK. Jacqueline.Smith@bbsrc.ac.uk
Speed
David
D
Law
Andrew S
AS
Glass
Elizabeth J
EJ
Burt
David W
DW
D000818:Animals; D000941:Antigens / Q000235:genetics; D018925:Chemokines / Q000235:genetics; D002645:Chickens / Q000276:immunology*; D019295:Computational Biology; D016207:Cytokines / Q000235:genetics; D016208:Databases, Factual; D020224:Expressed Sequence Tags; D005802:Genes, MHC Class II; D016678:Genome; D007107:Immune System / Q000502:physiology; D008285:Major Histocompatibility Complex / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D010802:Phylogeny
D000941:Antigens; D018925:Chemokines; D016207:Cytokines; D008565:Membrane Proteins