title: Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.
abstract: BACKGROUND
  Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages.
  
  
  RESULTS
  Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories.
  
  
  CONCLUSIONS
  This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.
authors.affiliation: Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark. gorodkin@genome.ku.dk
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
authors.forename: Susanna
authors.initials: S
authors.lastname: Cirera
authors.forename: Jakob
authors.initials: J
authors.lastname: Hedegaard
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: Frank
authors.initials: F
authors.lastname: Panitz
authors.forename: Claus
authors.initials: C
authors.lastname: Jørgensen
authors.forename: Karsten
authors.initials: K
authors.lastname: Scheibye-Knudsen
authors.forename: Troels
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authors.lastname: Arvin
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authors.initials: S
authors.lastname: Lumholdt
authors.forename: Milena
authors.initials: M
authors.lastname: Sawera
authors.forename: Trine
authors.initials: T
authors.lastname: Green
authors.forename: Bente J
authors.initials: BJ
authors.lastname: Nielsen
authors.forename: Jakob H
authors.initials: JH
authors.lastname: Havgaard
authors.forename: Carina
authors.initials: C
authors.lastname: Rosenkilde
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Wei
authors.initials: W
authors.lastname: Dong
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Hans-Henrik
authors.initials: HH
authors.lastname: Staefeldt
authors.forename: Rasmus
authors.initials: R
authors.lastname: Wernersson
authors.forename: Lone B
authors.initials: LB
authors.lastname: Madsen
authors.forename: Bo
authors.initials: B
authors.lastname: Thomsen
authors.forename: Henrik
authors.initials: H
authors.lastname: Hornshøj
authors.forename: Zhan
authors.initials: Z
authors.lastname: Bujie
authors.forename: Xuegang
authors.initials: X
authors.lastname: Wang
authors.forename: Xuefei
authors.initials: X
authors.lastname: Wang
authors.forename: Lars
authors.initials: L
authors.lastname: Bolund
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Christian
authors.initials: C
authors.lastname: Bendixen
authors.forename: Merete
authors.initials: M
authors.lastname: Fredholm
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D020224:Expressed Sequence Tags; D015870:Gene Expression; D020869:Gene Expression Profiling; D015723:Gene Library; D023281:Genomics; D005810:Multigene Family; D012333:RNA, Messenger / Q000378:metabolism*; D013552:Swine / Q000235:genetics*
chemical_list: D012333:RNA, Messenger