ArticleGenome biology2007
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- Genome-wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis.Developmental biology · 2015Article
- Structured RNAs and synteny regions in the pig genome.BMC genomics · 2014Article
- Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis.Physiological genomics · 2014Article
- Transcriptional regulation of Caenorhabditis elegans FOXO/DAF-16 modulates lifespan.Longevity & healthspan · 2014Article
- Rapid cohort generation and analysis of disease spectrum of large animal model of cone dystrophy.PloS one · 2013Article
- Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence.BMC genomics · 2012Article
- A gene expression atlas of the domestic pig.BMC biology · 2012Article
- Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae.BMC genomics · 2012Article
- Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species.BMC genomics · 2012Article
- Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.BMC genomics · 2012Article
- Organization, complexity and allelic diversity of the porcine (Sus scrofa domestica) immunoglobulin lambda locus.Immunogenetics · 2012Article
- Evolution of the porcine (Sus scrofa domestica) immunoglobulin kappa locus through germline gene conversion.Immunogenetics · 2012Article
- Study of the differential transcription in liver of growth hormone receptor (GHR), insulin-like growth factors (IGF1, IGF2) and insulin-like growth factor receptor (IGF1R) genes at different postnatal developmental ages in pig breeds.Molecular biology reports · 2012Article
- From structure prediction to genomic screens for novel non-coding RNAs.PLoS computational biology · 2011Review
- An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua).Marine biotechnology (New York, N.Y.) · 2011Article
- Transgenic pigs as models for translational biomedical research.Journal of molecular medicine (Berlin, Germany) · 2010Review
- A study of alternative splicing in the pig.BMC research notes · 2010Article
- Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies.Genome biology · 2010Article
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Authors and funding
36 authors.
Funding
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Abstract
backgroundKnowledge 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.
resultsUsing 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.
conclusionThis 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.
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