Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS)
Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease marked by motor neuron degeneration and complex genetic underpinnings. Despite growing research into its molecular pathology, the role of codon usage bias (CUB) in ALS-related genes remains largely unexplored. In this...
| Autore principale: | |
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| Natura: | Tesi |
| Lingua: | inglese |
| Pubblicazione: |
AUW
2025
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| Accesso online: | https://repository.auw.edu.bd/handle/123456789/541 |
| _version_ | 1857448961515716608 |
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| author | Marwa, Safa |
| author_facet | Marwa, Safa |
| author_sort | Marwa, Safa |
| collection | institutional Repository |
| description | Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease marked by
motor neuron degeneration and complex genetic underpinnings. Despite growing research into
its molecular pathology, the role of codon usage bias (CUB) in ALS-related genes remains
largely unexplored. In this study, we analyzed 607 ALS-associated genes and compared them
with 138 human housekeeping genes to examine differences in codon usage. Using tools such as
CAIcal and CodonW, we assessed nucleotide composition, GC content, RSCU values, ENC,
neutrality plots, and parity plots. Statistical testing (Mann–Whitney U test) revealed 15 codons
with significant usage differences between ALS and non-disease genes. These codons were
further used as features in machine learning models (KNN, SVM, RF), where Random Forest
achieved the highest classification accuracy (85.9%). Our results indicate that ALS genes are
characterized by GC-rich codon preferences influenced by natural selection and functional
constraints, likely related to translational efficiency and gene expression optimization. This
codon-level distinction has implications for ALS biomarker discovery and the rational design of
therapeutic gene constructs. |
| format | Thesis |
| id | 123456789-541 |
| institution | Asian University for Women |
| language | English |
| publishDate | 2025 |
| publisher | AUW |
| record_format | dspace |
| spelling | 123456789-5412026-02-18T06:09:56Z Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS) Marwa, Safa Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease marked by motor neuron degeneration and complex genetic underpinnings. Despite growing research into its molecular pathology, the role of codon usage bias (CUB) in ALS-related genes remains largely unexplored. In this study, we analyzed 607 ALS-associated genes and compared them with 138 human housekeeping genes to examine differences in codon usage. Using tools such as CAIcal and CodonW, we assessed nucleotide composition, GC content, RSCU values, ENC, neutrality plots, and parity plots. Statistical testing (Mann–Whitney U test) revealed 15 codons with significant usage differences between ALS and non-disease genes. These codons were further used as features in machine learning models (KNN, SVM, RF), where Random Forest achieved the highest classification accuracy (85.9%). Our results indicate that ALS genes are characterized by GC-rich codon preferences influenced by natural selection and functional constraints, likely related to translational efficiency and gene expression optimization. This codon-level distinction has implications for ALS biomarker discovery and the rational design of therapeutic gene constructs. 2025-07-13T07:03:32Z 2025-07-13T07:03:32Z 2025-04 Thesis https://repository.auw.edu.bd/handle/123456789/541 en application/pdf AUW |
| spellingShingle | Marwa, Safa Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS) |
| title | Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS) |
| title_full | Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS) |
| title_fullStr | Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS) |
| title_full_unstemmed | Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS) |
| title_short | Analysis Of Codon Usage Patterns In Genes Related To Amyotrophic Lateral Sclerosis (ALS) |
| title_sort | analysis of codon usage patterns in genes related to amyotrophic lateral sclerosis als |
| url | https://repository.auw.edu.bd/handle/123456789/541 |
| work_keys_str_mv | AT marwasafa analysisofcodonusagepatternsingenesrelatedtoamyotrophiclateralsclerosisals |