approach to calculate the transcript capacity
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 effe...
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| Format: | Article |
| Language: | English |
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BioMed Central
2019-09-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2019-17-3-e31.pdf |
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| author | Young-Sup Lee Kyung-Hye Won Jae-Don Oh Donghyun Shin |
| author_facet | Young-Sup Lee Kyung-Hye Won Jae-Don Oh Donghyun Shin |
| author_sort | Young-Sup Lee |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-7d4038802123409198ebaae70a2e4de0 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2019-09-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-7d4038802123409198ebaae70a2e4de02025-02-03T01:20:17ZengBioMed CentralGenomics & Informatics2234-07422019-09-0117310.5808/GI.2019.17.3.e31570approach to calculate the transcript capacityYoung-Sup LeeKyung-Hye WonJae-Don OhDonghyun ShinWe 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.http://genominfo.org/upload/pdf/gi-2019-17-3-e31.pdffatgenome-wide association study methodtranscript capacityRNA-seq |
| spellingShingle | Young-Sup Lee Kyung-Hye Won Jae-Don Oh Donghyun Shin approach to calculate the transcript capacity Genomics & Informatics fat genome-wide association study method transcript capacity RNA-seq |
| title | approach to calculate the transcript capacity |
| title_full | approach to calculate the transcript capacity |
| title_fullStr | approach to calculate the transcript capacity |
| title_full_unstemmed | approach to calculate the transcript capacity |
| title_short | approach to calculate the transcript capacity |
| title_sort | approach to calculate the transcript capacity |
| topic | fat genome-wide association study method transcript capacity RNA-seq |
| url | http://genominfo.org/upload/pdf/gi-2019-17-3-e31.pdf |
| work_keys_str_mv | AT youngsuplee approachtocalculatethetranscriptcapacity AT kyunghyewon approachtocalculatethetranscriptcapacity AT jaedonoh approachtocalculatethetranscriptcapacity AT donghyunshin approachtocalculatethetranscriptcapacity |