Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
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Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. / Gorodkin, Jan; Cirera, Susanna; Hedegaard, Jakob; Gilchrist, Michael J; Panitz, Frank; Jørgensen, Claus; Scheibye-Knudsen, Karsten; Arvin, Troels; Lumholdt, Steen; Sawera, Milena; Green, Trine; Nielsen, Bente; Havgaard, Jakob H; Rosenkilde, Carina; Wang, Jun; Li, Heng; Li, Ruiqiang; Liu, Bin; Hu, Songnian; Dong, Wei; Li, Wei; Yu, Jun; Wang, Jian; Staefeldt, Hans-Henrik; Wernersson, Rasmus; Madsen, Lone B; Thomsen, Bo Stjerne; Hornshøj, Henrik; Bujie, Zhan; Wang, Xuegang; Wang, Xuefei; Bolund, Lars; Brunak, Søren; Yang, Huanming; Bendixen, Christian; Fredholm, Merete.
In: Genome Biology, Vol. 8, No. R45, 2007, p. R45.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
AU - Gorodkin, Jan
AU - Cirera, Susanna
AU - Hedegaard, Jakob
AU - Gilchrist, Michael J
AU - Panitz, Frank
AU - Jørgensen, Claus
AU - Scheibye-Knudsen, Karsten
AU - Arvin, Troels
AU - Lumholdt, Steen
AU - Sawera, Milena
AU - Green, Trine
AU - Nielsen, Bente
AU - Havgaard, Jakob H
AU - Rosenkilde, Carina
AU - Wang, Jun
AU - Li, Heng
AU - Li, Ruiqiang
AU - Liu, Bin
AU - Hu, Songnian
AU - Dong, Wei
AU - Li, Wei
AU - Yu, Jun
AU - Wang, Jian
AU - Staefeldt, Hans-Henrik
AU - Wernersson, Rasmus
AU - Madsen, Lone B
AU - Thomsen, Bo Stjerne
AU - Hornshøj, Henrik
AU - Bujie, Zhan
AU - Wang, Xuegang
AU - Wang, Xuefei
AU - Bolund, Lars
AU - Brunak, Søren
AU - Yang, Huanming
AU - Bendixen, Christian
AU - Fredholm, Merete
N1 - Paper id:: R45.1-R45.16
PY - 2007
Y1 - 2007
N2 - 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.Conclusion: 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.
AB - 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.Conclusion: 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.
KW - Animals
KW - Cluster Analysis
KW - Computational Biology
KW - Expressed Sequence Tags
KW - Gene Expression
KW - Gene Expression Profiling
KW - Gene Library
KW - Genomics
KW - Multigene Family
KW - RNA, Messenger
KW - Swine
U2 - 10.1186/gb-2007-8-4-r45
DO - 10.1186/gb-2007-8-4-r45
M3 - Journal article
C2 - 17407547
VL - 8
SP - R45
JO - Genome Biology (Online Edition)
JF - Genome Biology (Online Edition)
SN - 1474-7596
IS - R45
ER -
ID: 8067734