title: EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.
abstract: The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool designated EZ-Retrieve that can: (i) retrieve any particular region of human genome sequence from the NCBI database and (ii) analyze retrieved sequences for putative transcription factor-binding sites (TFBSs) as they appear on the TRANSFAC database. The tool is web-based, user-friendly and offers both batch sequence retrieval and batch TFBS prediction. A major application of EZ-Retrieve is the analysis of co-expressed genes that are highlighted as expression clusters in DNA microarray experiments.
authors.affiliation: Center for Applied Genomics, Public Health Research Institute, 225 Warren Street, ICPH W420M, Newark, NJ 07103, USA.
authors.forename: Haibo
authors.initials: H
authors.lastname: Zhang
authors.forename: Y
authors.initials: Y
authors.lastname: Ramanathan
authors.forename: Patricia
authors.initials: P
authors.lastname: Soteropoulos
authors.forename: Michael L
authors.initials: ML
authors.lastname: Recce
authors.forename: Peter P
authors.initials: PP
authors.lastname: Tolias
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D018797:Cell Cycle Proteins; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D004268:DNA-Binding Proteins; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D050684:E2F Transcription Factors; D005786:Gene Expression Regulation; D017344:Genes, Insect / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D020218:Response Elements / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; D050684:E2F Transcription Factors; D014157:Transcription Factors; D004247:DNA