Bioinformatics Advance Access originally published online on November 5, 2004
Bioinformatics 2005 21(6):835-836; doi:10.1093/bioinformatics/bti119
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OMGProm: a database of orthologous mammalian gene promoters
Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Columbus, OH 43210, USA
*To whom correspondence should be addressed.
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Abstract |
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 TOP Abstract INTRODUCTIONDATA ACQUISITIONDATA PRESENTATIONREFERENCES |
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Summary: Sequence comparisons between human and rodents are increasingly being used for the identification of gene regulatory regions. The effectiveness of such an approach largely depends on the quality and availability of promoter sequences. We developed OMGProm by integrating three data sources: (1) experimentally supported full-length cDNA, promoter and first exon sequences; (2) homology information from HomoloGene and (3) the human and mouse genomic sequences. The current version of OMGProm contains 8550 promoter pairs of 6373 orthologous human and mouse genes, where supporting experimental evidence for transcription start site annotation exists in at least one species.
Availability: OMGProm can be accessed from http://bioinformatics.med.ohio-state.edu/OMGProm
Contact: davuluri-1{at}medctr.osu.edu
Supplementary information: Additional information on methods and implementation is available at http://bioinformatics.med.ohio-state.edu/OMGProm/si.jsp.
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INTRODUCTION |
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TOPAbstractINTRODUCTIONDATA ACQUISITIONDATA PRESENTATIONREFERENCES |
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Comparisons between human and rodent DNA sequences are widely used for the discovery of genes (Ureta-Vidal et al., 2003) and gene regulatory regions (Lenhard et al., 2003; Chapman et al., 2004). Although it is widely appreciated that the protein coding regions are significantly conserved between human and rodents, very little is known about the extent of conservation in gene regulatory regions and the capability of existing algorithms to predict regulatory elements. Even with the advent of whole-genome sequencing, there is a relative dearth of well-curated data sets that can be used to train and test these algorithms. Here, we present a database of orthologous mammalian gene promoters (OMGProm) as a platform for comparative genomics of transcriptional regulation, in order to facilitate the identification of gene regulatory elements such as core promoters and transcription factor binding sites that are conserved in the upstream regions of orthologous genes (Blanchette and Tompa, 2003; Loots et al., 2002).
Extensive molecular research in the field of transcription regulation has produced invaluable promoter sequence data that are being deposited into GenBank (Wheeler et al., 2004). In parallel, recent advances in sequencing technologies (Imanishi et al., 2004) have generated full-length cDNAs of mammalian genes. We systematically integrated the cDNA and genome sequence data and curated a set of 8550 promoters of orthologous mammalian genes. We believe that this data repository will be a valuable control set for designing novel promoter prediction tools and for testing the sensitivity of existing programs, such as FirstEF (Davuluri et al., 2001). Our database serves to complement similar databases such as DBTSS (Suzuki et al., 2002) and PromoSer (Halees and Weng, 2004).
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DATA ACQUISITION |
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TOPAbstractINTRODUCTIONDATA ACQUISITIONDATA PRESENTATIONREFERENCES |
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We developed a data-mining pipeline (Supplemental Fig. 1) that integrated data from different resources. We collected 4802 full-length cDNAs from DBTSS (Suzuki et al., 2002), 2159 full-length 5'UTR sequences from the 5'-UTR database (Davuluri et al., 2000) and human and mouse promoters from the EPD database (Schmid et al., 2004). We searched GenBank, using complex queries {e.g., ‘homo sapiens’ [ORGN] AND ("5'-UTR" [FKEY] OR promoter [FKEY] OR exon [FKEY] OR mRNA [FKEY] OR prim_transcript [FKEY])}, for retrieving experimentally supported first exons, promoters and full-length 5'-UTR sequences in humans. Then, we used a Perl script (available upon request) to parse these GenBank records into first exons, full-length mRNAs, full-length 5'-UTRs and promoter sequences that are supported by experimental evidence. The Perl script scans each GenBank nucleotide record for mRNA, exon, 5'-UTR, prim_transcript, promoter and CDS feature key annotations. If a feature was annotated as incomplete at the 5' end, e.g., ‘mRNA: <1..250’, ‘putative’ or ‘evidence = not experimental’, the record was ignored. The script also ignored those records that had identical start coordinates for both the mRNA (or first exon) and CDS. We mapped all those first exons, full-length 5'-UTR/mRNA and promoter sequences to the human (NCBI Build 34) and mouse (NCBI Build 32) genomes using BLAT (Kent and Brumbaugh, 2002). After eliminating the overlapping first exons that are mapped to the same genomic template, we had a set of 11 165 human and 7297 mouse real first exons.
We used the HomoloGene database (Wheeler et al., 2004) to obtain orthologous gene counterparts for all the genes in our database that have real first exons. We found 9330 orthologous mouse promoters for 6688 human genes, and 5618 orthologous human promoters for 4253 mouse genes. We then aligned the real first exon and promoter sequence of a gene in one species with the 5' upstream region of its orthologous counterpart as follows. We retrieved two sequences, Seq-1 (–5 to +2 kb relative to the TSS of the real first exon of human/mouse) and Seq-2 (–20 to +2 kb relative to the 5' end of the annotated first exon of the mouse/human orthologous counterpart). We aligned Seq-1 and Seq-2 using BLASTZ (Schwartz et al., 2003). As Seq-1 has real first exon coordinates, this sequence is analogous to a template that is used to annotate the first exon of the orthologous gene in Seq-2. The degree of conservation of the core promoter (–35 to +35 bp) and donor site in the BLASTZ alignment determined the readjusted position of the TSS and donor site in Seq-2. The alignment was further refined by an additional alignment of Seq-1 and Seq-2 by ClustalW (Thompson et al., 1994). We found 6251 (67%) human promoters conserved in mouse and 4288 (76%) mouse promoters conserved in human. In the combined set of 10 539 first exons, if any two first exons of a gene overlapped and the distance between transcription start sites was less than 50 bp, we eliminated the shorter first exon. This resulted in 8550 promoter pairs, which include alternative promoters, for 6373 unique gene pairs (Supplemental Table 1).
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DATA PRESENTATION |
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TOPAbstractINTRODUCTIONDATA ACQUISITIONDATA PRESENTATIONREFERENCES |
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The OMGProm database is presented via an interactive and easy-to-use web interface. The data are displayed with links to the raw data and related references. A user may query the database with a Unigene ID, Gene Symbol or GenBank accession number of interest. Each record displays information about a pair of promoters of orthologous genes. We provide the BLASTZ and ClustalW alignments of orthologous sequences, in which the first exons are displayed in different color. Additionally, CpG island and human–mouse sequence conservation tracks are presented as annotated in the UCSC genome database (Karolchik et al., 2003). We implemented the database in MYSQL, and the web-interface and promoter visualization using GDVTK (Sun and Davuluri, 2004). For the convenience of our users, we have also run the promoter sequences through the RepeatMasker program (Smit, A.F.A. and Green, P.; http://repeatmasker.org), and these masked sequences are also available for downloading.
We will periodically update OMGProm by including additional organisms such as rat and chimpanzee, and by continuously updating the data utilizing our data-mining pipeline. The results of different phylogenetic footprinting and sequence alignment programs will be included in the future updates of OMGProm.
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Acknowledgments |
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We thank the anonymous reviewers for their constructive suggestions, Twyla Pohar for editing the manuscript and Sang-Gook Han for assistance with web implementation.
Received on May 21, 2004; revised on October 1, 2004; accepted on October 20, 2004
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REFERENCES |
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TOPAbstractINTRODUCTIONDATA ACQUISITIONDATA PRESENTATIONREFERENCES |
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Blanchette, M. and Tompa, M. (2003) FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Res., 31, 3840–3842
Chapman, M.A., Donaldson, I.J., Gilbert, J., Grafham, D., Rogers, J., Green, A.R., Gottgens, B. (2004) Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. Genome Res., 14, 313–318
Davuluri, R.V., Suzuki, Y., Sugano, S., Zhang, M.Q. (2000) CART classification of human 5' UTR sequences. Genome Res., 10, 1807–1816
Davuluri, R.V., Grosse, I., Zhang, M.Q. (2001) Computational identification of promoters and first exons in the human genome. Nat. Genet., 29, 412–417[CrossRef][ISI][Medline].
Halees, A.S. and Weng, Z. (2004) PromoSer: improvements to the algorithm, visualization and accessibility. Nucleic Acids Res., 32, W191–W194
Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PloS Biol., 2, 3–20[CrossRef].
Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51–54
Kent, W.J. and Brumbaugh, H. (2002) BLAT—the BLAST-like alignment tool. Genome Res., 12, 656–664
Lenhard, B., Sandelin, A., Mendoza, L., Engstrom, P., Jareborg, N., Wasserman, W.W. (2003) Identification of conserved regulatory elements by comparative genome analysis. J. Biol., 2, 13[CrossRef][Medline].
Loots, G.G., Ovcharenko, I., Pachter, L., Dubchak, I., Rubin, E.M. (2002) rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res., 12, 832–839
Schmid, C.D., Praz, V., Delorenzi, M., Perier, R., Bucher, P. (2004) The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res., 32, D82–D85
Schwartz, S., Kent, W.J., Smith, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., Miller, W. (2003) Human–mouse alignments with BLASTZ. Genome Res., 13, 103–107.
Sun, H. and Davuluri, R.V. (2004) Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics, 20, 727–734
Suzuki, Y., Yamashita, R., Nakai, N., Sugano, S. (2002) DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res., 30, 328–331
Thompson, J.D., Higgins, D.G., Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673–4680
Ureta-Vidal, A., Ettwiller, L., Birney, E. (2003) Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet., 4, 251–262[ISI][Medline].
Wheeler, D.L., Church, D.M., Edgar, R., Federhen, S., Helmberg, W., Madden, T.L., Pontius, J.U., Schuler, G.D., Schriml, L.M., Sequeira, E., et al. (2004) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res., 32, D35–D40
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