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Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

D. Kolbe
2004 Genome Research  
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

Inna Dubchak, Matthew Munoz, Alexandre Poliakov, Nathan Salomonis, Simon Minovitsky, Rolf Bodmer, Alexander C. Zambon
2013 Computer applications in the biosciences : CABIOS  
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

Frédéric G. Brunet, Jean-Nicolas Volff, Manfred Schartl
2016 Genome Biology and Evolution  
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]

Aaron McKenna, Gregory Findlay, James A Gagnon, Marshall Horwitz, Alexander Franz F Schier, Jay Shendure
2016 biorxiv/medrxiv   pre-print
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

Ivan Ovcharenko, Gabriela Loots
2003 Current Genomics  
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]

Vikrant Nain, Shakti Sahi, Polumetla Ananda
2011 Computational Biology and Applied Bioinformatics  
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

Amol Prakash, Martin Tompa
2005 Nature Biotechnology  
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

Martha L Bulyk
2003 Genome Biology  
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

Inna Dubchak, Kelly Frazer
2003 Genome Biology  
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

T. Sauer, E. Shelest, E. Wingender
2005 Bioinformatics  
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

D. Forest, R. Nishikawa, H. Kobayashi, A. Parton, C. J. Bayne, D. W. Barnes
2007 Proceedings of the National Academy of Sciences of the United States of America  
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

D. C. King
2005 Genome Research  
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

D. Boffelli
2003 Science  
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

Bernardo Lemos, José; Andrés Yunes, Fernando R. Vargas, Miguel A.M. Moreira, Angelo A. Cardoso, Héctor N. Seuánez
2004 Genomics  
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

Tae-Woo Ryu, Se-Joon Lee, Cheol-Goo Hur, Do-Heon Lee
2009 BMB Reports  
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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