Literature DB >> 14681463

PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries.

Hirohide Uenishi1, Tomoko Eguchi, Kohei Suzuki, Tetsuya Sawazaki, Daisuke Toki, Hiroki Shinkai, Naohiko Okumura, Noriyuki Hamasima, Takashi Awata.   

Abstract

We generated the PEDE (Pig EST Data Explorer; http://pede.dna.affrc.go.jp/) database using sequences assembled from porcine 5' ESTs from oligo-capped full-length cDNA libraries. Thus far we have performed EST analysis of various organs (thymus, spleen, uterus, lung, liver, ovary and peripheral blood mononuclear cells) and assembled 68,076 high-quality sequences into 5546 contigs and 28,461 singlets. PEDE provides a search interface for getting results of homology searches and enables users to obtain information on sequence data and cDNA clones of interest. Single-nucleotide polymorphisms detected through comparison of the EST sequences are classified by origin (western and oriental breeds) and are searchable in the database. This database system can accelerate analyses of livestock traits and yields information that can lead to new applications in pigs as model systems for medical research.

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Year:  2004        PMID： 14681463      PMCID： PMC308771          DOI： 10.1093/nar/gkh037

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  21 in total

1.  CAP3: A DNA sequence assembly program.

Authors:  X Huang; A Madan
Journal:  Genome Res       Date:  1999-09       Impact factor: 9.043

Review 2.  The immunological barrier to xenotransplantation.

Authors:  M Cascalho; J L Platt
Journal:  Immunity       Date:  2001-04       Impact factor: 31.745

3.  TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

Authors:  Geo Pertea; Xiaoqiu Huang; Feng Liang; Valentin Antonescu; Razvan Sultana; Svetlana Karamycheva; Yuandan Lee; Joseph White; Foo Cheung; Babak Parvizi; Jennifer Tsai; John Quackenbush
Journal:  Bioinformatics       Date:  2003-03-22       Impact factor: 6.937

4.  Construction of a new porcine whole-genome framework map using a radiation hybrid panel.

Authors:  N Hamasima; H Suzuki; A Mikawa; T Morozumi; G Plastow; T Mitsuhashi
Journal:  Anim Genet       Date:  2003-06       Impact factor: 3.169

5.  A linkage map of 243 DNA markers in an intercross of Göttingen miniature and Meishan pigs.

Authors:  S Mikawa; T Akita; N Hisamatsu; Y Inage; Y Ito; E Kobayashi; H Kusumoto; T Matsumoto; H Mikami; M Minezawa; M Miyake; S Shimanuki; C Sugiyama; Y Uchida; Y Wada; S Yanai; H Yasue
Journal:  Anim Genet       Date:  1999-12       Impact factor: 3.169

6.  Sequence of the swine major histocompatibility complex region containing all non-classical class I genes.

Authors:  P Chardon; C Rogel-Gaillard; L Cattolico; S Duprat; M Vaiman; C Renard
Journal:  Tissue Antigens       Date:  2001-01

7.  Sequence of the pig major histocompatibility region containing the classical class I genes.

Authors:  C Renard; M Vaiman; N Chiannilkulchai; L Cattolico; C Robert; P Chardon
Journal:  Immunogenetics       Date:  2001-08       Impact factor: 2.846

8.  The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.

Authors:  J Quackenbush; J Cho; D Lee; F Liang; I Holt; S Karamycheva; B Parvizi; G Pertea; R Sultana; J White
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

9.  Database resources of the National Center for Biotechnology.

Authors:  David L Wheeler; Deanna M Church; Scott Federhen; Alex E Lash; Thomas L Madden; Joan U Pontius; Gregory D Schuler; Lynn M Schriml; Edwin Sequeira; Tatiana A Tatusova; Lukas Wagner
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

Review 10.  Genomic organization of the mammalian MHC.

Authors:  Attila Kumánovics; Toyoyuki Takada; Kirsten Fischer Lindahl
Journal:  Annu Rev Immunol       Date:  2001-12-19       Impact factor: 28.527
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  22 in total

1.  Development of dense microsatellite markers in the entire SLA region and evaluation of their polymorphisms in porcine breeds.

Authors:  Maiko Tanaka; Asako Ando; Christine Renard; Patrick Chardon; Michiko Domukai; Naohiko Okumura; Takashi Awata; Hirohide Uenishi
Journal:  Immunogenetics       Date:  2005-10-18       Impact factor: 2.846

2.  Biased distribution of single nucleotide polymorphisms (SNPs) in porcine Toll-like receptor 1 (TLR1), TLR2, TLR4, TLR5, and TLR6 genes.

Authors:  Hiroki Shinkai; Maiko Tanaka; Takeya Morozumi; Tomoko Eguchi-Ogawa; Naohiko Okumura; Yoshihiro Muneta; Takashi Awata; Hirohide Uenishi
Journal:  Immunogenetics       Date:  2006-04-05       Impact factor: 2.846

3.  Sequencing and characterization of the porcine α-galactosidase A gene: towards the generation of a porcine model for Fabry disease.

Authors:  Makoto Yoshimitsu; Koji Higuchi; Xin Fan; Sonshin Takao; Jeffrey A Medin; Chuwa Tei; Toshihiro Takenaka
Journal:  Mol Biol Rep       Date:  2010-02-04       Impact factor: 2.316

4.  A study of alternative splicing in the pig.

Authors:  Ann-Britt Nygard; Susanna Cirera; Michael J Gilchrist; Jan Gorodkin; Claus B Jørgensen; Merete Fredholm
Journal:  BMC Res Notes       Date:  2010-05-05

5.  Trans-species polymorphism and selection in the MHC class II DRA genes of domestic sheep.

Authors:  Keith T Ballingall; Mara S Rocchi; Declan J McKeever; Frank Wright
Journal:  PLoS One       Date:  2010-06-30       Impact factor: 3.240

6.  The Pig Genome Database (PiGenome): an integrated database for pig genome research.

Authors:  Dajeong Lim; Yong-Min Cho; Kyung-Tai Lee; Yeonkyung Kang; Samsun Sung; Jungrye Nam; Eung-Woo Park; Sung-Jong Oh; Seok-Ki Im; Heebal Kim
Journal:  Mamm Genome       Date:  2008-12-10       Impact factor: 2.957

7.  Characterization of porcine TAP genes: alternative splicing of TAP1.

Authors:  Carmen N García-Borges; Bounleut Phanavanh; Mark D Crew
Journal:  Immunogenetics       Date:  2006-03-23       Impact factor: 2.846

8.  Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG.

Authors:  Lilin Ye; Wenbin Tuo; Xindong Liu; Neil E Simister; Xiaoping Zhu
Journal:  Dev Comp Immunol       Date:  2008-02-20       Impact factor: 3.636

9.  Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence.

Authors:  Hirohide Uenishi; Takeya Morozumi; Daisuke Toki; Tomoko Eguchi-Ogawa; Lauretta A Rund; Lawrence B Schook
Journal:  BMC Genomics       Date:  2012-11-15       Impact factor: 3.969

10.  Purification of Ovine Respiratory Complex I Results in a Highly Active and Stable Preparation.

Authors:  James A Letts; Gianluca Degliesposti; Karol Fiedorczuk; Mark Skehel; Leonid A Sazanov
Journal:  J Biol Chem       Date:  2016-09-26       Impact factor: 5.157
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