ArticleGenome research2004
Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 54 citations in OpenAlex.
- Bi-alignments with affine gaps costs.Algorithms for molecular biology : AMB · 2022Article
- The LMO2 -25 Region Harbours GATA2-Dependent Myeloid Enhancer and RUNX-Dependent T-Lymphoid Repressor Activity.PloS one · 2015Article
- Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.BMC bioinformatics · 2014Article
- Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms.Molecular bioSystems · 2014Article
- Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression.Molecular and cellular biology · 2013Article
- The transcriptional programme controlled by Runx1 during early embryonic blood development.Developmental biology · 2012Article
- Integration of Elf-4 into stem/progenitor and erythroid regulatory networks through locus-wide chromatin studies coupled with in vivo functional validation.Molecular and cellular biology · 2012Article
- Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators.Developmental cell · 2011Article
- Genome-wide analysis of transcriptional reprogramming in mouse models of acute myeloid leukaemia.PloS one · 2011Article
- cis-Regulatory remodeling of the SCL locus during vertebrate evolution.Molecular and cellular biology · 2010Article
- EKLF directly activates the p21WAF1/CIP1 gene by proximal promoter and novel intronic regulatory regions during erythroid differentiation.Molecular and cellular biology · 2010Article
- Genomic approaches uncover increasing complexities in the regulatory landscape at the human SCL (TAL1) locus.PloS one · 2010Article
- TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements.BMC genomics · 2007Article
- Article
- The SCL transcriptional network and BMP signaling pathway interact to regulate RUNX1 activity.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.Genome research · 2006Article
- Close sequence comparisons are sufficient to identify human cis-regulatory elements.Genome research · 2006Article
- Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence.Genome biology · 2006Article
- Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.Genome research · 2005Article
- Subtree power analysis and species selection for comparative genomics.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Comparative analysis of genomic sequences is becoming a standard technique for studying gene regulation. However, only a limited number of tools are currently available for the analysis of multiple genomic sequences. An extensive data set for the testing and training of such tools is provided by the SCL gene locus. Here we have expanded the data set to eight vertebrate species by sequencing the dog SCL locus and by annotating the dog and rat SCL loci. To provide a resource for the bioinformatics community, all SCL sequences and functional annotations, comprising a collation of the extensive experimental evidence pertaining to SCL regulation, have been made available via a Web server. A Web interface to new tools specifically designed for the display and analysis of multiple sequence alignments was also implemented. The unique SCL data set and new sequence comparison tools allowed us to perform a rigorous examination of the true benefits of multiple sequence comparisons. We demonstrate that multiple sequence alignments are, overall, superior to pairwise alignments for identification of mammalian regulatory regions. In the search for individual transcription factor binding sites, multiple alignments markedly increase the signal-to-noise ratio compared to pairwise alignments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.