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Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
2004
Genome Research
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We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. ...
Despite the close evolutionary proximity of rat to mouse, we find that adding the rat sequence increases our ability to predict genomic sites that regulate gene transcription. ...
METHODS
Training Data Preparation We use whole-genome three-way human, mouse, and rat alignments as described in Blanchette et al. (2004) . ...
doi:10.1101/gr.1976004
pmid:15060013
pmcid:PMC383316
fatcat:5w64vaavcrcfzbqy36rfvgyi4y
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data
2013
Computer applications in the biosciences : CABIOS
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of human, mouse and Drosophila genomes. ...
We have developed a web-based query tool, Whole-Genome rVISTA (WGRV), that determines enrichment of transcription factors (TFs) and associated target genes in sets of co-regulated genes. ...
The capabilities of WGRV have now been significantly enhanced. WGRV is now available for human, mouse and Drosophila TF target analysis. ...
doi:10.1093/bioinformatics/btt318
pmid:23736530
pmcid:PMC3722517
fatcat:g46lgl6p4ffodnjhxxmhkijr3u
Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates
2016
Genome Biology and Evolution
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We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. ...
We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. ...
This publication was supported by the Open Access Publication Fund of the University of Wuerzburg. ...
doi:10.1093/gbe/evw103
pmid:27260203
pmcid:PMC4898815
fatcat:fv6jrg3lqjft5jcoajq5qda6z4
Whole organism lineage tracing by combinatorial and cumulative genome editing
[article]
2016
biorxiv/medrxiv
pre-print
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Genome editing of synthetic target arrays for lineage tracing (GESTALT) will help generate large-scale maps of cell lineage in multicellular systems. ...
Here we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. ...
A sample of computational times
(in hours) required to build a FlashFry database for versions of the Caenorhabditis elegans,
human, mouse, and Drosophila melanogaster genomes for common CRISPR enzymes ...
doi:10.1101/052712
fatcat:ygjezf7cjfgxxctshjhuab5niu
Finding the Needle in the Haystack: Computational Strategies for Discovering Regulatory Sequences in Genomes
2003
Current Genomics
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candidate regulatory sequences in whole genomes. ...
Historically, the functional characterization of regulatory elements has been slow, labor-intensive and inadequate to keep up with the demands of whole-genome analysis. ...
Elnitski for critical reading of the manuscript. We are grateful to JF Chang and the Berkeley PGA program for providing us with the human/mouse/ opossum/chicken GATA4 genomic sequences. ...
doi:10.2174/1389202033490169
fatcat:3t3ct3cx5jamtiwsglf42dgxzy
In Silico Identification of Regulatory Elements in Promoters
[chapter]
2011
Computational Biology and Applied Bioinformatics
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However, MAPPER database is limited to TFBSs found only in the promoter of genes from the human, mouse and D.melanogaster genomes. ...
Phylogenetic footprinting, has enormous potential in identifying new regulatory elements and completing the gene network map. ...
In Silico Identification of Regulatory Elements in Promoters, Computational Biology and Applied Bioinformatics, Prof. ...
doi:10.5772/22230
fatcat:wcruf4x7bvcsbaszaknsiejuxy
Discovery of regulatory elements in vertebrates through comparative genomics
2005
Nature Biotechnology
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The third column shows the number of genes of the cluster having any GO biological process annotation. ...
157 CCCCTCC, 235 184 Frizzled-2 signaling pathway (4, 1 × 10 −4 , 0.2) Morphogenesis (33, 6.4 × 10 −5 , 0.14) Organogenesis (29, 3.9 × 10 −5 , 0.085) Development (51, 2.7 × 10 −7 , 0.0005) Phosphatidylcholine-sterol ...
This material is based upon work supported in part by the National Science Foundation under grant DBI-0218798 and by the National Institutes of Health under grant R01 HG02602. ...
doi:10.1038/nbt1140
pmid:16211068
fatcat:ukxthkobqbdypplnd4j5lgwini
Computational prediction of transcription-factor binding site locations
2003
Genome Biology
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Identifying genomic locations of transcription-factor binding sites, particularly in higher eukaryotic genomes, has been an enormous challenge. ...
Various experimental and computational approaches have been used to detect these sites; methods involving computational comparisons of related genomes have been particularly successful. ...
Phylogenetic footprinting in other organisms Similar phylogenetic footprinting approaches have been taken to try to identify regulatory elements in the noncoding portions of other genomes. ...
doi:10.1186/gb-2003-5-1-201
pmid:14709165
pmcid:PMC395725
fatcat:7fm4f2xygbbyjf4egpfcbbtlx4
Multi-species sequence comparison: the next frontier in genome annotation
2003
Genome Biology
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and the development of new algorithms for alignment, analysis of conservation, and visualization of results. ...
Most current computational tools have been designed for pairwise comparisons, and efficient extension of these tools to multiple species will require knowledge of the ideal evolutionary distance to choose ...
ID was partially supported by the Programs for Genomic Applications grant from the NHLBI/NIH. ...
doi:10.1186/gb-2003-4-12-122
pmid:14659006
pmcid:PMC329408
fatcat:sttdlxf5cnbnfgyxufhxw5bema
Evaluating phylogenetic footprinting for human-rodent comparisons
2005
Bioinformatics
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Motivation: 'Phylogenetic footprinting' is a widely applied approach to identify regulatory regions and potential transcription factor binding sites (TFBSs) using alignments of non-coding orthologous regions ...
Results: In this paper we use 2678 human, mouse and rat TFBSs from the TRANSFAC Ò database for this evaluation. ...
ACKNOWLEDGEMENTS This work was supported by the Bioinformatics Competence Center 'Intergenomics' using a grant of the German Ministry of Education and Research (grant no. 031U210A). ...
doi:10.1093/bioinformatics/bti819
pmid:16332706
fatcat:ymuzqsd5azb37megq64sqoeckm
RNA expression in a cartilaginous fish cell line reveals ancient 3' noncoding regions highly conserved in vertebrates
2007
Proceedings of the National Academy of Sciences of the United States of America
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Our results indicate that highly conserved gene sequences dating from the appearance of jawed vertebrates and representing potential cis-regulatory elements can be identified through the use of cartilaginous ...
Although these genomic analyses are informative, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. ...
Susumu Hyodo of the University of Tokyo (Tokyo, Japan) for kind help, advice, and contribution of materials allowing the work with C. milii. ...
doi:10.1073/pnas.0610350104
pmid:17227856
pmcid:PMC1770858
fatcat:dnnsqi334fevnjwdk756k3hghu
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
2005
Genome Research
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Different analytical methods score distinctive features of whole-genome alignments among human, mouse, and rat to predict functional regions. ...
Of the 95,000 bp in the HBB gene complex, 33,642 bp (35%) are in the whole-genome human-mouse-rat alignments, similar to the fraction obtained genome-wide (Gibbs et al. 2004) . ...
doi:10.1101/gr.3642605
pmid:16024817
pmcid:PMC1182217
fatcat:36jqdvackra3rdubsjsid4upyq
Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome
2003
Science
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We developed a variant of phylogenetic footprinting, which we termed phylogenetic shadowing. ...
Phylogenetic footprinting (5, 6) has been used to identify highly conserved putative regulatory elements, exploiting alignments across numerous evolutionarily distant species. ...
genome, many of which are likely to be missed by human-mouse comparisons. ...
doi:10.1126/science.1081331
pmid:12610304
fatcat:5cge6lmeknhmpo7d2ssels7tqi
Phylogenetic footprinting reveals extensive conservation of Sonic Hedgehog (SHH) regulatory elements
2004
Genomics
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Using a Bayesian alignment algorithm for phylogenetic footprinting we analyzed~28 kb of noncoding DNA in the SHH locus of human and mouse. ...
Human-mouse analysis was complemented by sequencing in apes, monkeys, rodents, and bats, thus further confirming the evolutionary conservation of some segments. ...
Ranz for their reading of an earlier draft of the manuscript and for useful comments. We are also indebted to Cibele R. ...
doi:10.1016/j.ygeno.2004.05.009
pmid:15498458
fatcat:aj7fl5pgh5fj5bsayvyranrh6u
CONVIRT: A web-based tool for transcriptional regulatory site identification using a conserved virtual chromosome
2009
BMB Reports
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CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. ...
However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. ...
The conservation information is from the human-mouse netted alignment. ...
doi:10.5483/bmbrep.2009.42.12.823
pmid:20044955
fatcat:xxw6vcynjnhgrhvgl6g7lmflsu
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