TSSAR: TSS annotation regime for dRNA-seq data

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• 作者：Fabian Amman (30) (31)
  Michael T Wolfinger (31) (32) (33)
  Ronny Lorenz (31)
  Ivo L Hofacker (31) (34) (38)
  Peter F Stadler (30) (31) (34) (35) (36) (37)
  Sven Findei脽 (31) (38)
  
  30. Bioinformatics Group ; Department of Computer Science and the Interdisciplinary Center for Bioinformatic ; University of Leipzig ; H盲rtelstra脽e 16鈥?8 ; 04107 ; Leipzig ; Germany
  31. Institute for Theoretical Chemistry ; University of Vienna ; W盲hringerstra脽e 17 ; 1090 ; Vienna ; Austria
  32. Center for Integrative Bioinformatics Vienna (CIBIV) ; Max F. Perutz Laboratories ; University of Vienna ; Medical University of Vienna ; Dr. Bohr-Gasse 9 ; 1030 ; Vienna ; Austria
  33. Department of Biochemistry and Molecular Cell Biology ; Max F. Perutz Laboratories ; University of Vienna ; Dr. Bohr-Gasse 9 ; 1030 ; Vienna ; Austria
  34. Center for RNA in Technology and Health ; University of Copenhagen ; Gr酶nneg氓rdsvej 3 ; Frederiksberg C ; Denmark
  38. Research group Bioinformatics and Computational Biology ; Faculty of Computer Science ; University of Vienna ; W盲hringerstra脽e 29 ; 1090 ; Vienna ; Austria
  35. Max Planck Institute for Mathematics in the Sciences ; Inselstra脽e 22 ; D-04103 ; Leipzig ; Germany
  36. Fraunhofer Institute for Cell Therapy and Immunology ; Perlickstra脽e 1 ; D-04103 ; Leipzig ; Germany
  37. Santa Fe Institute ; 1399 Hyde Park Road ; Santa Fe NM ; 87501 ; USA
  
• 关键词：Differential RNA sequencing ; dRNA ; seq ; TSS ; Transcription start site annotation ; Transcriptome ; RESTful Web service ; Next generation sequencing
• 刊名：BMC Bioinformatics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：478 KB
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• 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
• 出版者：BioMed Central
• ISSN：1471-2105

文摘

Background Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) in particular. Hitherto, dRNA-seq data were analyzed by visualizing the sequencing reads mapped to the reference genome and manually annotating reliable positions. This is very labor intensive and, due to the subjectivity, biased. Results Here, we present TSSAR, a tool for automated de novo TSS annotation from dRNA-seq data that respects the statistics of dRNA-seq libraries. TSSAR uses the premise that the number of sequencing reads starting at a certain genomic position within a transcriptional active region follows a Poisson distribution with a parameter that depends on the local strength of expression. The differences of two dRNA-seq library counts thus follow a Skellam distribution. This provides a statistical basis to identify significantly enriched primary transcripts. We assessed the performance by analyzing a publicly available dRNA-seq data set using TSSAR and two simple approaches that utilize user-defined score cutoffs. We evaluated the power of reproducing the manual TSS annotation. Furthermore, the same data set was used to reproduce 74 experimentally validated TSS in H. pylori from reliable techniques such as RACE or primer extension. Both analyses showed that TSSAR outperforms the static cutoff-dependent approaches. Conclusions Having an automated and efficient tool for analyzing dRNA-seq data facilitates the use of the dRNA-seq technique and promotes its application to more sophisticated analysis. For instance, monitoring the plasticity and dynamics of the transcriptomal architecture triggered by different stimuli and growth conditions becomes possible. The main asset of a novel tool for dRNA-seq analysis that reaches out to a broad user community is usability. As such, we provide TSSAR both as intuitive RESTful Web service ( http://rna.tbi.univie.ac.at/TSSAR) together with a set of post-processing and analysis tools, as well as a stand-alone version for use in high-throughput dRNA-seq data analysis pipelines.