tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Por:
L. DE LA FUENTE, A. ARZALLUZ-LUQUE, M. TARDAGUILA, H. DEL RISCO, C. MARTI, S. TARAZONA, P. SALGUERO, R. SCOTT, A. LERMA, A. ALASTRUE-AGUDO, P. BONILLA, J. NEWMAN, S. KOSUGI, L. MCINTYRE, V. MORENO-MANZANO and A. CONESA
Publicada:
18 may 2020
Resumen:
Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at .
Filiaciones:
:
Prince Felipe Res Ctr, Genom Gene Express Lab, Valencia, Spain
IIS Fdn Jimenez Diaz, Bioinformat Unit, Madrid, Spain
:
Univ Politecn Valencia, Dept Stat & Operat Res, Valencia, Spain
M. TARDAGUILA:
Univ Florida, Inst Food & Agr Sci, Dept Microbiol & Cell Sci, Gainesville, FL 32611 USA
Wellcome Trust Sanger Inst, Human Genet Dept, Cambridge, England
H. DEL RISCO:
Univ Florida, Inst Food & Agr Sci, Dept Microbiol & Cell Sci, Gainesville, FL 32611 USA
:
Prince Felipe Res Ctr, Genom Gene Express Lab, Valencia, Spain
:
Univ Politecn Valencia, Dept Stat & Operat Res, Valencia, Spain
:
Prince Felipe Res Ctr, Genom Gene Express Lab, Valencia, Spain
R. SCOTT:
Univ Florida, Inst Food & Agr Sci, Dept Microbiol & Cell Sci, Gainesville, FL 32611 USA
:
Prince Felipe Res Ctr, Genom Gene Express Lab, Valencia, Spain
:
Wellcome Trust Sanger Inst, Human Genet Dept, Cambridge, England
:
Wellcome Trust Sanger Inst, Human Genet Dept, Cambridge, England
J. NEWMAN:
Univ Florida, Genet Inst, Gainesville, FL 32611 USA
Univ Florida, Dept Pathol, Gainesville, FL 32611 USA
S. KOSUGI:
Univ Florida, Genet Inst, Gainesville, FL 32611 USA
RIKEN, Lab Stat & Translat Genet, Ctr Integrat Med Sci, Wako, Saitama, Japan
L. MCINTYRE:
Univ Florida, Genet Inst, Gainesville, FL 32611 USA
Univ Florida, Dept Mol Genet & Microbiol, Gainesville, FL USA
:
Prince Felipe Res Ctr, Neural Regenerat Lab, Valencia, Spain
:
Univ Florida, Inst Food & Agr Sci, Dept Microbiol & Cell Sci, Gainesville, FL 32611 USA
Univ Florida, Genet Inst, Gainesville, FL 32611 USA
Gold, Green Published
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