Genomics Inform.  2019 Sep;17(3):e31. 10.5808/GI.2019.17.3.e31.

In silico approach to calculate the transcript capacity

• Lee YS
• Won KH
• Oh JD
• Shin D

• KMID: 2462045
• DOI: http://doi.org/10.5808/GI.2019.17.3.e31

Abstract

We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation. We used the genome-wide association study (GWAS) beta effect and transcription level in RNA-sequencing to estimate TC. The trait was body fat percent and the transcript reads were obtained from the human protein atlas. The assumption was that the GWAS beta effect is the gene's effect and TC was related to the corresponding gene effect and transcript reads. Further, we surveyed gene ontology (GO) in the highest TC and the lowest TC genes. The most frequent GOs with the highest TC were neuronal-related and cell projection organization related. The most frequent GOs with the lowest TC were wound-healing related and embryo development related. We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.

Keyword

fat; genome-wide association study; in silico method; transcript capacity; RNA-seq

MeSH Terms

Adipose Tissue
Computational Biology
Computer Simulation*
Embryonic Development
Female
Gene Ontology
Genome-Wide Association Study
Humans
Methods
Pregnancy