Plant DirectBioinformaticsPeer-reviewed journal article
A reference-free algorithm discovers regulation in the plant transcriptome
Elisabeth A. MeyeriD, Evan V. SaldivariD, Marek KokotiD, Bo XueiD, Sebastian DeorowicziD, Seung Y. RheeiD, Julia SalzmaniD
Abstract
Most plant genomes and their regulation remain unknown. We used SPLASH - a new, reference-genome free sequence variation detection algorithm - to analyze transcriptional and post-transcriptional regulation from RNA-seq data. We discovered differential homolog expression during maize pollen development, and imbibition-dependent cryptic splicing in Arabidopsis seeds. SPLASH enables discovery of novel regulatory mechanisms, including differential regulation of genes from hybrid parental haplotypes, without the use of alignment to a reference genome.
- organism: Arabidopsis
- assay: bulk RNA-seq
- research focus: differential expression
- research focus: gene regulatory network inference
- approach: statistical model
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- Field percentile
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