Literature DB >> 11173099

Identification and analysis of eukaryotic promoters: recent computational approaches.

U Ohler1, H Niemann.   

Abstract

The DNA sequence of several higher eukaryotes is now complete, and we know the expression patterns of thousands of genes under a variety of conditions. This gives us the opportunity to identify and analyze the parts of a genome believed to be responsible for most transcription control--the promoters. This article gives a short overview of the state-of-the-art techniques for computational promoter localization and analysis, and comments on the most recent advances in the field.

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Year:  2001        PMID: 11173099     DOI: 10.1016/s0168-9525(00)02174-0

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  54 in total

1.  Deciphering genetic regulatory codes: a challenge for functional genomics.

Authors:  Alan M Michelson
Journal:  Proc Natl Acad Sci U S A       Date:  2002-01-22       Impact factor: 11.205

2.  DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.

Authors:  Yutaka Suzuki; Riu Yamashita; Kenta Nakai; Sumio Sugano
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 3.  In silico identification of metazoan transcriptional regulatory regions.

Authors:  Wyeth W Wasserman; William Krivan
Journal:  Naturwissenschaften       Date:  2003-03-27

4.  Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model.

Authors:  Marc S Halfon; Yonatan Grad; George M Church; Alan M Michelson
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

5.  An approach to identify over-represented cis-elements in related sequences.

Authors:  Jiashun Zheng; Jiajin Wu; Zhirong Sun
Journal:  Nucleic Acids Res       Date:  2003-04-01       Impact factor: 16.971

6.  Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data.

Authors:  Matthew E Hudson; Peter H Quail
Journal:  Plant Physiol       Date:  2003-12       Impact factor: 8.340

7.  PromH: Promoters identification using orthologous genomic sequences.

Authors:  V V Solovyev; I A Shahmuradov
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 8.  Computational approaches to identify promoters and cis-regulatory elements in plant genomes.

Authors:  Stephane Rombauts; Kobe Florquin; Magali Lescot; Kathleen Marchal; Pierre Rouzé; Yves van de Peer
Journal:  Plant Physiol       Date:  2003-07       Impact factor: 8.340

9.  Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay.

Authors:  Shirin Khambata-Ford; Yueyi Liu; Christopher Gleason; Mark Dickson; Russ B Altman; Serafim Batzoglou; Richard M Myers
Journal:  Genome Res       Date:  2003-06-12       Impact factor: 9.043

Review 10.  Current methods of gene prediction, their strengths and weaknesses.

Authors:  Catherine Mathé; Marie-France Sagot; Thomas Schiex; Pierre Rouzé
Journal:  Nucleic Acids Res       Date:  2002-10-01       Impact factor: 16.971

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