Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set.

Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set. Research Abstract Details 

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Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set. Abstract Text:

Itsuki Ajioka,Takuya Maeda,Kazunori Nakajima,

Oligonucleotide-based microarrays, such as GeneChip, are widely used to determine the large-scale gene expression profiles. However, GeneChip only provides information on the identity of the molecules, and the investigator must obtain each cDNA clone for further analyses. In this study, we devised a program which enables us to correlate a large number of DNA accession numbers to the FANTOM (functional annotation of the mouse) full-length mouse cDNA clone set, and made a correlative table between mouse GeneChip clones and FANTOM clones. This allows easy identification of the corresponding FANTOM clone for each GeneChip clone, even if the sequence of the GeneChip clone does not directly match the FANTOM clone. Using this table, for example, a large number of in situ hybridization probes can be synthesized easily, because the FANTOM clones are flanked by T3/T7 promoters on both ends. In addition, we further developed a program which retrieves the amino acid sequence (AA Seq) for each clone, even for the FANTOM clones that lack the AA Seq description, and classifies the proteins automatically. As an example, we devised a correlation table with predictions of the secretory or transmembrane molecules. The correlation table is useful for a large-scale screening of molecules involved in cell-cell communication in various biological processes. The full correlation table for the GeneChip clones is available at http://www.kjm.keio.ac.jp/past/55/3/correlation_table1.html.

Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set. Publishing Authors By Initials

I Ajioka,T Maeda,K Nakajima,

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Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: The Keio journal of medicine

VOLUME: 55

Page Numbers: 107-10

Journal Abbreviation:

ISSN: 0022-9717

DAY: 29

MONTH: Sep

YEAR: 2006

Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set. Information

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LANGUAGE: eng

NlmUniqueID: 376354

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Grant and Affiliation Information for Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set.

AFFILIATION: Department of Anatomy, School of Medicine, Keio University, Tokyo, Japan.

Country: Japan

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MEDLINETA: Keio J Med

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