Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for analysis of CAGE data
| Autor: | Nikos Perdikopanis, Georgios Georgakilas, Artemis G. Hatzigeorgiou |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Gene isoform
Computer science Gene regulatory network Locus (genetics) Machine learning computer.software_genre 01 natural sciences Annotation 010104 statistics & probability 03 medical and health sciences Exon Transcription (biology) Gene expression medicine 0101 mathematics 030304 developmental biology 0303 health sciences business.industry Intron medicine.disease Quantitative Biology::Genomics Cap analysis gene expression Identification (information) ComputingMethodologies_PATTERNRECOGNITION RNA splicing Benchmark (computing) Artificial intelligence business Algorithm computer Transcriptional noise |
| Zdroj: | bioRxiv UnpayWall Microsoft Academic Graph |
| DOI: | 10.1101/752253 |
| Popis: | Cap Analysis of Gene Expression (CAGE) experimental protocol has emerged as a powerful experimental technique for assisting in the identification of transcription start sites (TSSs). There is strong evidence that CAGE also identifies capping sites along various other locations of transcribed loci such as splicing byproducts, alternative isoforms and capped molecules overlapping introns and exons. We present ADAPT-CAGE, a Machine Learning framework which is trained to distinguish between CAGE signal derived from TSSs and transcriptional noise. ADAPT-CAGE provides annotation-agnostic, highly accurate and single-nucleotide resolution experimentally derived TSSs on a genome-wide scale. It has been specifically designed aiming for flexibility and ease-of-use by only requiring aligned CAGE data and the underlying genomic sequence. When compared to existing algorithms, ADAPT-CAGE exhibits improved performance on every benchmark that we designed based on both annotation- and experimentally-driven strategies. This performance boost brings ADAPT-CAGE in the spotlight as a computational framework that is able to assist in the refinement of gene regulatory networks, the incorporation of accurate information of gene expression regulators and alternative promoter usage in both physiological and pathological conditions. |
| Databáze: | OpenAIRE |
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