TITLE

[X]uniqMAP: unique gene sequence regions in the human and mouse genomes

AUTHOR(S)
Jimenez, Jose L; Durbin, Richard
PUB. DATE
January 2006
SOURCE
BMC Genomics;2006, Vol. 7, p249
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Current approaches for genome-wise functional analyses, such as microarray and RNA interference studies, rely on the specificity of oligonucleotide sequences to selectively target cellular transcripts. The design of specific oligos involves the determination of unique DNA regions in the gene/transcripts of interest from the targeted organism. This process is tedious, time consuming and it does not scale up for high-throughput studies. Description: Taking advantage of the availability of complete genome sequence information for mouse and human, the most widely used systems for the study of mammalian genetics, we have built a database, [X]uniqMAP, that stores the precalculated unique regions for all transcripts of these two organisms. For each gene, the database discriminates between those unique regions that are shared by all transcripts and those exclusive to single transcripts. In addition, it also provides those unique regions that are shared between orthologous genes from the two organisms. The database is updated regularly to reflect changes in genome assemblies and gene builds. Conclusion: Over 85% of genes have unique regions at least 19 bases long, with the majority being unique over 60% of their lengths. 14482 human genes share exactly at least a unique region with mouse genes, though such regions are typically under 40 bases long. The full data are publicly accessible online both interactively and for download. They should facilitate (i) the design of probes, primers and siRNAs for both small- and large-scale projects; and (ii) the identification of regions for the design of oligos that could be re-used to target equivalent gene/transcripts from human and mouse.
ACCESSION #
28858709

 

Related Articles

  • Genome-wide transcription and the implications for genomic organization. Kapranov, Philipp; Willingham, Aarron T.; Gingeras, Thomas R. // Nature Reviews Genetics;Jun2007, Vol. 8 Issue 6, p413 

    Recent evidence of genome-wide transcription in several species indicates that the amount of transcription that occurs cannot be entirely accounted for by current sets of genome-wide annotations. Evidence indicates that most of both strands of the human genome might be transcribed, implying...

  • A context-based approach to identify the most likely mapping for RNA-seq experiments. Bonfert, Thomas; Csaba, Gergely; Zimmer, Ralf; Friedel, Caroline C. // BMC Bioinformatics;2012 Supplement 6, Vol. 13 Issue Suppl 6, p1 

    Background: Sequencing of mRNA (RNA-seq) by next generation sequencing technologies is widely used for analyzing the transcriptomic state of a cell. Here, one of the main challenges is the mapping of a sequenced read to its transcriptomic origin. As a simple alignment to the genome will fail to...

  • The regulated retrotransposon transcriptome of mammalian cells. Faulkner, Geoffrey J.; Kimura, Yasumasa; Daub, Carsten O.; Shivangi Wani; Plessy, Charles; Irvine, Katharine M.; Schroder, Kate; Cloonan, Nicole; Steptoe, Anita L.; Lassmann, Timo; Waki, Kazunori; Hornig, Nadine; Arakawa, Takahiro; Takahashi, Hazuki; Kawai, Jun; Forrest, Alistair R. R.; Suzuki, Harukazu; Hayashizaki, Yoshihide; Hume, David A.; Orlando, Valerio // Nature Genetics;May2009, Vol. 41 Issue 5, p563 

    Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6–30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of...

  • Nucleosome Positioning. Nishida, Hiromi // ISRN Molecular Biology;2012, p1 

    Nucleosome positioning is not only related to genomic DNA compaction but also to other biological functions. After the chromatin is digested by micrococcal nuclease, nucleosomal (nucleosome-bound) DNA fragments can be sequenced and mapped on the genomic DNA sequence. Due to the development of...

  • Novel definition files for human GeneChips based on GeneAnnot. Ferrari, Francesco; Bortoluzzi, Stefania; Coppe, Alessandro; Sirota, Alexandra; Safran, Marilyn; Shmoish, Michael; Ferrari, Sergio; Lancet, Doron; Danieli, Gian Antonio; Bicciato, Silvio // BMC Bioinformatics;2007 Supplement 2, Vol. 8, p446 

    Background: Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of...

  • Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches. Chen, Geng; Wang, Charles; Shi, Leming; Tong, Weida; Qu, Xiongfei; Chen, Jiwei; Yang, Jianmin; Shi, Caiping; Chen, Long; Zhou, Peiying; Lu, Bingxin; Shi, Tieliu // Human Genetics;Aug2013, Vol. 132 Issue 8, p899 

    The human reference genome is still incomplete and a number of gene sequences are missing from it. The approaches to uncover them, the reasons causing their absence and their functions are less explored. Here, we comprehensively identified and characterized the missing genes of human reference...

  • Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data. Quinn, Emma M.; Cormican, Paul; Kenny, Elaine M.; Hill, Matthew; Anney, Richard; Gill, Michael; Corvin, Aiden P.; Morris, Derek W. // PLoS ONE;Mar2013, Vol. 8 Issue 3, p1 

    Next-generation RNA sequencing (RNA-seq) maps and analyzes transcriptomes and generates data on sequence variation in expressed genes. There are few reported studies on analysis strategies to maximize the yield of quality RNA-seq SNP data. We evaluated the performance of different SNP-calling...

  • Perfect Hamming code with a hash table for faster genome mapping. Takenaka, Yoichi; Seno, Shigeto; Matsuda, Hideo // BMC Genomics;2011 Supplement 3, Vol. 12 Issue Suppl 3, p1 

    Background: With the advent of next-generation sequencers, the growing demands to map short DNA sequences to a genome have promoted the development of fast algorithms and tools. The tools commonly used today are based on either a hash table or the suffix array/Burrow-Wheeler transform. These...

  • Detection of identity by descent using next-generation whole genome sequencing data.  // BMC Bioinformatics;2012, Vol. 13 Issue 1, p121 

    The article presents a study focusing on Identity by descent (IBD). It states that IBD has played an important role in the discovery of genetic loci underlying human diseases. It further discusses the DNA sequencing which enables the comprehensive analysis of genomes. It also mentions that IBD...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics