Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://pede.dna.affrc.go.jp/
Full name: Pig Expression Data Explorer
Description: PEDE comprised 68‚ÄČ076 high-quality Pig ESTs obtained by using full-length-enriched cDNA libraries derived from seven tissues.
Year founded: 2007
Last update: 2014-06-25
Version:
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Japan
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:
EST

Contact information

University/Institution: National Institute of Agrobiological Sciences
Address: 2 Ikenodai, Tsukuba, Ibaraki 305-8602, Japan
City: Tsukuba
Province/State:
Country/Region: Japan
Contact name (PI/Team): Hirohide Uenishi
Contact email (PI/Helpdesk): huenishi@affrc.go.jp

Publications

17145712
PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. [PMID: 17145712]
Uenishi H, Eguchi-Ogawa T, Shinkai H, Okumura N, Suzuki K, Toki D, Hamasima N, Awata T.

We formerly released the porcine expressed sequence tag (EST) database Pig EST Data Explorer (PEDE; http://pede.dna.affrc.go.jp/), which comprised 68,076 high-quality ESTs obtained by using full-length-enriched cDNA libraries derived from seven tissues. We have added eight tissues and cell types to the EST analysis and have integrated 94,555 additional high-quality ESTs into the database. We also fully sequenced the inserts of 10,147 of the cDNA clones that had undergone EST analysis; the sequences and annotation of the cDNA clones were stored in the database. Further, we constructed an interface that can be used to perform various searches in the database. The PEDE database is the primary resource of expressed pig genes that are supported by full-length cDNA sequences. This resource not only enables us to pick cDNA clones of interest for a particular analysis, but it also confirms and thus contributes to the sequencing integrity of the pig genome, which is now being compiled by an international consortium (http://www.piggenome.org/). PEDE has therefore evolved into what we now call 'Pig Expression Data Explorer'.

Nucleic Acids Res. 2007:35(Database issue) | 37 Citations (from Europe PMC, 2021-06-19)
14681463
PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. [PMID: 14681463]
Uenishi H, Eguchi T, Suzuki K, Sawazaki T, Toki D, Shinkai H, Okumura N, Hamasima N, Awata T.

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.

Nucleic Acids Res. 2004:32(Database issue) | 50 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
1452/5061 (71.33%)
Genotype phenotype and variation:
204/705 (71.206%)
1452
Total Rank
87
Citations
5.118
z-index

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Record metadata

Created on: 2015-08-10
Curated by:
Dong Zou [2018-02-07]
Shixiang Sun [2015-11-20]