Dataset Information

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons.

ABSTRACT: The accurate characterization of RNA transcripts and expression levels across species is critical for understanding transcriptome evolution. As available RNA-seq data accumulate rapidly, there is a great demand for tools that build gene annotations for cross-species RNA-seq analysis. However, prevailing methods of ortholog annotation for RNA-seq analysis between closely-related species do not take inter-species variation in mappability into consideration.Here we present XSAnno, a computational framework that integrates previous approaches with multiple filters to improve the accuracy of inter-species transcriptome comparisons. The implementation of this approach in comparing RNA-seq data of human, chimpanzee, and rhesus macaque brain transcriptomes has reduced the false discovery of differentially expressed genes, while maintaining a low false negative rate.The present study demonstrates the utility of the XSAnno pipeline in building ortholog annotations and improving the accuracy of cross-species transcriptome comparisons.

SUBMITTER: Zhu Y

PROVIDER: S-EPMC4035071 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons.

Zhu Ying Y Li Mingfeng M Sousa André M M AM Sestan Nenad N

BMC genomics 20140507

<h4>Background</h4>The accurate characterization of RNA transcripts and expression levels across species is critical for understanding transcriptome evolution. As available RNA-seq data accumulate rapidly, there is a great demand for tools that build gene annotations for cross-species RNA-seq analysis. However, prevailing methods of ortholog annotation for RNA-seq analysis between closely-related species do not take inter-species variation in mappability into consideration.<h4>Results</h4>Here w ...[more]

PMID: 24884593

Similar Datasets

Project description:Chemotaxis is the process by which motile bacteria sense their chemical environment and move towards more favourable conditions. Escherichia coli utilises a single sensory pathway, but little is known about signalling pathways in species with more complex systems.To investigate whether chemotaxis pathways in other bacteria follow the E. coli paradigm, we analysed 206 species encoding at least 1 homologue of each of the 5 core chemotaxis proteins (CheA, CheB, CheR, CheW and CheY). 61 species encode more than one of all of these 5 proteins, suggesting they have multiple chemotaxis pathways. Operon information is not available for most bacteria, so we developed a novel statistical approach to cluster che genes into putative operons. Using operon-based models, we reconstructed putative chemotaxis pathways for all 206 species. We show that cheA-cheW and cheR-cheB have strong preferences to occur in the same operon as two-gene blocks, which may reflect a functional requirement for co-transcription. However, other che genes, most notably cheY, are more dispersed on the genome. Comparison of our operons with shuffled equivalents demonstrates that specific patterns of genomic location may be a determining factor for the observed in vivo chemotaxis pathways. We then examined the chemotaxis pathways of Rhodobacter sphaeroides. Here, the PpfA protein is known to be critical for correct partitioning of proteins in the cytoplasmically-localised pathway. We found ppfA in che operons of many species, suggesting that partitioning of cytoplasmic Che protein clusters is common. We also examined the apparently non-typical chemotaxis components, CheA3, CheA4 and CheY6. We found that though variants of CheA proteins are rare, the CheY6 variant may be a common type of CheY, with a significantly disordered C-terminal region which may be functionally significant.We find that many bacterial species potentially have multiple chemotaxis pathways, with grouping of che genes into operons likely to be a major factor in keeping signalling pathways distinct. Gene order is highly conserved with cheA-cheW and cheR-cheB blocks, perhaps reflecting functional linkage. CheY behaves differently to other Che proteins, both in its genomic location and its putative protein interactions, which should be considered when modelling chemotaxis pathways.

Dataset Information

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons.

Publications

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets