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  Janus-a comprehensive tool investigating the two faces of transcription

Barann, M., Esser, D., Klostermeier, U. C., Lappalainen, T., Luzius, A., Kuiper, J. W. P., et al. (2013). Janus-a comprehensive tool investigating the two faces of transcription. Bioinformatics, 29(13), 1600-1606. doi:DOI 10.1093/bioinformatics/btt185.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0018-D019-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0018-D01B-7
Genre: Journal Article

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 Creators:
Barann, M., Author
Esser, D., Author
Klostermeier, U. C., Author
Lappalainen, T., Author
Luzius, A., Author
Kuiper, J. W. P., Author
Ammerpohl, O., Author
Vater, I., Author
Siebert, R., Author
Amstislavskiy, V.1, Author              
Sudbrak, R.2, Author              
Lehrach, H.2, 3, Author              
Schreiber, S., Author
Rosenstiel, P., Author
Affiliations:
1Human Chromosome 21 (Marie-Laure Yaspo), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479652              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
3Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany , ou_persistent22              

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Free keywords: classical hodgkin lymphoma antisense transcription mouse reveals genes map
 Abstract: Motivation: Protocols to generate strand-specific transcriptomes with next-generation sequencing platforms have been used by the scientific community roughly since 2008. Strand-specific reads allow for detection of antisense events and a higher resolution of expression profiles enabling extension of current transcript annotations. However, applications making use of this strandedness information are still scarce. Results: Here we present a tool (Janus), which focuses on the identification of transcriptional active regions in antisense orientation to known and novel transcribed elements of the genome. Janus can compare the antisense events of multiple samples and assigns scores to identify mutual expression of either transcript in a sense/antisense pair, which could hint to regulatory mechanisms. Janus is able to make use of single-nucleotide variant (SNV) and methylation data, if available, and reports the sense to antisense ratio of regions in the vicinity of the identified genetic and epigenetic variation. Janus interrogates positions of heterozygous SNVs to identify strand-specific allelic imbalance.

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Language(s): eng - English
 Dates: 2013-04-242013
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: Other: WOS:000321746100043
DOI: DOI 10.1093/bioinformatics/btt185
ISSN: 1367-4803
URI: ://WOS:000321746100043http://bioinformatics.oxfordjournals.org/content/29/13/1600.full.pdf
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 29 (13) Sequence Number: - Start / End Page: 1600 - 1606 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991