A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics
In cancer genomics research, gene expressions provide clues to gene regulations implicating patients’ risk of survival. Gene expressions, however, fluctuate due to noises arising internally and externally, making their use to infer gene associations, hence regulation mechanisms, problematic. Here, w...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/13/6/1331 |
| _version_ | 1797593823034998784 |
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| author | Wei-Quan Fang Yu-Le Wu Ming-Jing Hwang |
| author_facet | Wei-Quan Fang Yu-Le Wu Ming-Jing Hwang |
| author_sort | Wei-Quan Fang |
| collection | DOAJ |
| description | In cancer genomics research, gene expressions provide clues to gene regulations implicating patients’ risk of survival. Gene expressions, however, fluctuate due to noises arising internally and externally, making their use to infer gene associations, hence regulation mechanisms, problematic. Here, we develop a new regression approach to model gene association networks while considering uncertain biological noises. In a series of simulation experiments accounting for varying levels of biological noises, the new method was shown to be robust and perform better than conventional regression methods, as judged by a number of statistical measures on unbiasedness, consistency and accuracy. Application to infer gene associations in germinal-center B cells led to the discovery of a three-by-two regulatory motif gene expression and a three-gene prognostic signature for diffuse large B-cell lymphoma. |
| first_indexed | 2024-03-11T02:14:55Z |
| format | Article |
| id | doaj.art-e0c5e895f43443dd9ebf7e174d42207d |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-11T02:14:55Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-e0c5e895f43443dd9ebf7e174d42207d2023-11-18T11:17:49ZengMDPI AGLife2075-17292023-06-01136133110.3390/life13061331A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma TranscriptomicsWei-Quan Fang0Yu-Le Wu1Ming-Jing Hwang2Institute of Biomedical Sciences, Academia Sinica, Taipei 115, TaiwanInstitute of Biomedical Sciences, Academia Sinica, Taipei 115, TaiwanInstitute of Biomedical Sciences, Academia Sinica, Taipei 115, TaiwanIn cancer genomics research, gene expressions provide clues to gene regulations implicating patients’ risk of survival. Gene expressions, however, fluctuate due to noises arising internally and externally, making their use to infer gene associations, hence regulation mechanisms, problematic. Here, we develop a new regression approach to model gene association networks while considering uncertain biological noises. In a series of simulation experiments accounting for varying levels of biological noises, the new method was shown to be robust and perform better than conventional regression methods, as judged by a number of statistical measures on unbiasedness, consistency and accuracy. Application to infer gene associations in germinal-center B cells led to the discovery of a three-by-two regulatory motif gene expression and a three-gene prognostic signature for diffuse large B-cell lymphoma.https://www.mdpi.com/2075-1729/13/6/1331cancer prognostic genesgene association networkdiffuse large B-cell lymphomabiological noises |
| spellingShingle | Wei-Quan Fang Yu-Le Wu Ming-Jing Hwang A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics Life cancer prognostic genes gene association network diffuse large B-cell lymphoma biological noises |
| title | A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics |
| title_full | A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics |
| title_fullStr | A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics |
| title_full_unstemmed | A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics |
| title_short | A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics |
| title_sort | noise tolerating gene association network uncovering an oncogenic regulatory motif in lymphoma transcriptomics |
| topic | cancer prognostic genes gene association network diffuse large B-cell lymphoma biological noises |
| url | https://www.mdpi.com/2075-1729/13/6/1331 |
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