Word-based characterization of promoters involved in human DNA repair pathways Export

@article{citeulike:5926597, abstract = {BACKGROUND:DNA repair genes provide an important contribution towards the surveillance and repair of DNA damage. These genes produce a large network of interacting proteins whose mRNA expression is likely to be regulated by similar regulatory factors. Full characterization of promoters of DNA repair genes and the similarities among them will more fully elucidate the regulatory networks that activate or inhibit their expression. To address this goal, the authors introduce a technique to find regulatory genomic signatures, which represents a specific application of the genomic signature methodology to classify DNA sequences as putative functional elements within a single organism.RESULTS:The effectiveness of the regulatory genomic signatures is demonstrated via analysis of promoter sequences for genes in DNA repair pathways of humans. The promoters are divided into two classes, the bidirectional promoters and the unidirectional promoters, and distinct genomic signatures are calculated for each class. The genomic signatures include statistically overrepresented words, word clusters, and co-occurring words. The robustness of this method is confirmed by the ability to identify sequences that exist as motifs in TRANSFAC and JASPAR databases, and in overlap with verified binding sites in this set of promoter regions.CONCLUSION:The word-based signatures are shown to be effective by finding occurrences of known regulatory sites. Moreover, the signatures of the bidirectional and unidirectional promoters of human DNA repair pathways are clearly distinct, exhibiting virtually no overlap. In addition to providing an effective characterization method for related DNA sequences, the signatures elucidate putative regulatory aspects of DNA repair pathways, which are notably under-characterized.}, author = {Lichtenberg, Jens and Jacox, Edwin and Welch, Joshua and Kurz, Kyle and Liang, Xiaoyu and Yang, Mary and Drews, Frank and Ecker, Klaus and Lee, Stephen and Elnitski, Laura and Welch, Lonnie}, citeulike-article-id = {5926597}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-10-S1-S18}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19594877}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19594877}, doi = {10.1186/1471-2164-10-S1-S18}, issn = {1471-2164}, journal = {BMC Genomics}, keywords = {bidirectional, discovery, dna\_damage, dna\_repair\_genes, dna\_repair\_pathways, dna\_sequences, functional\_elements, genomic, human\_dna\_repair, jaspar, motif, pattern, promoter\_regions, promoter\_sequences, promoters, regulatory, regulatory\_aspects, regulatory\_factors, regulatory\_networks, signature, transfac, word\_clusters}, number = {Suppl 1}, pages = {S18+}, posted-at = {2009-10-12 13:24:11}, priority = {0}, title = {Word-based characterization of promoters involved in human DNA repair pathways}, url = {http://dx.doi.org/10.1186/1471-2164-10-S1-S18}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:5926597 L3 - citeulike-article-id:5926597 N2 - BACKGROUND:DNA repair genes provide an important contribution towards the surveillance and repair of DNA damage. These genes produce a large network of interacting proteins whose mRNA expression is likely to be regulated by similar regulatory factors. Full characterization of promoters of DNA repair genes and the similarities among them will more fully elucidate the regulatory networks that activate or inhibit their expression. To address this goal, the authors introduce a technique to find regulatory genomic signatures, which represents a specific application of the genomic signature methodology to classify DNA sequences as putative functional elements within a single organism.RESULTS:The effectiveness of the regulatory genomic signatures is demonstrated via analysis of promoter sequences for genes in DNA repair pathways of humans. The promoters are divided into two classes, the bidirectional promoters and the unidirectional promoters, and distinct genomic signatures are calculated for each class. The genomic signatures include statistically overrepresented words, word clusters, and co-occurring words. The robustness of this method is confirmed by the ability to identify sequences that exist as motifs in TRANSFAC and JASPAR databases, and in overlap with verified binding sites in this set of promoter regions.CONCLUSION:The word-based signatures are shown to be effective by finding occurrences of known regulatory sites. Moreover, the signatures of the bidirectional and unidirectional promoters of human DNA repair pathways are clearly distinct, exhibiting virtually no overlap. In addition to providing an effective characterization method for related DNA sequences, the signatures elucidate putative regulatory aspects of DNA repair pathways, which are notably under-characterized. IS - Suppl 1 JF - BMC Genomics SN - 1471-2164 TI - Word-based characterization of promoters involved in human DNA repair pathways VL - 10 SP - S18 KW - bidirectional KW - discovery KW - dna_damage KW - dna_repair_genes KW - dna_repair_pathways KW - dna_sequences KW - functional_elements KW - genomic KW - human_dna_repair KW - jaspar KW - motif KW - pattern KW - promoter_regions KW - promoter_sequences KW - promoters KW - regulatory KW - regulatory_aspects KW - regulatory_factors KW - regulatory_networks KW - signature KW - transfac KW - word_clusters AU - Lichtenberg, Jens AU - Jacox, Edwin AU - Welch, Joshua AU - Kurz, Kyle AU - Liang, Xiaoyu AU - Yang, Mary AU - Drews, Frank AU - Ecker, Klaus AU - Lee, Stephen AU - Elnitski, Laura AU - Welch, Lonnie PY - 2009/// UR - http://dx.doi.org/10.1186/1471-2164-10-S1-S18 ER -