Simple method for cutoff point identification in descriptive high-throughput biological studies
Abstract Background Rapid development of high-throughput omics technologies generates an increasing interest in algorithms for cutoff point identification. Existing cutoff methods and tools identify cutoff points based on an association of continuous variables with another variable, such as phenotyp...
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| Format: | Article |
| Language: | English |
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BMC
2022-03-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08427-6 |
| _version_ | 1818673428141441024 |
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| author | Alexander Suvorov |
| author_facet | Alexander Suvorov |
| author_sort | Alexander Suvorov |
| collection | DOAJ |
| description | Abstract Background Rapid development of high-throughput omics technologies generates an increasing interest in algorithms for cutoff point identification. Existing cutoff methods and tools identify cutoff points based on an association of continuous variables with another variable, such as phenotype, disease state, or treatment group. These approaches are not applicable for descriptive studies in which continuous variables are reported without known association with any biologically meaningful variables. Results The most common shape of the ranked distribution of continuous variables in high-throughput descriptive studies corresponds to a biphasic curve, where the first phase includes a big number of variables with values slowly growing with rank and the second phase includes a smaller number of variables rapidly growing with rank. This study describes an easy algorithm to identify the boundary between these phases to be used as a cutoff point. Discussion The major assumption of that approach is that a small number of variables with high values dominate the biological system and determine its major processes and functions. This approach was tested on three different datasets: human genes and their expression values in the human cerebral cortex, mammalian genes and their values of sensitivity to chemical exposures, and human proteins and their expression values in the human heart. In every case, the described cutoff identification method produced shortlists of variables (genes, proteins) highly relevant for dominant functions/pathways of the analyzed biological systems. Conclusions The described method for cutoff identification may be used to prioritize variables in descriptive omics studies for a focused functional analysis, in situations where other methods of dichotomization of data are inaccessible. |
| first_indexed | 2024-12-17T07:55:38Z |
| format | Article |
| id | doaj.art-b1bbad66170147bd9b21c4d48f2fb8b2 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T07:55:38Z |
| publishDate | 2022-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b1bbad66170147bd9b21c4d48f2fb8b22022-12-21T21:57:42ZengBMCBMC Genomics1471-21642022-03-012311610.1186/s12864-022-08427-6Simple method for cutoff point identification in descriptive high-throughput biological studiesAlexander Suvorov0Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of MassachusettsAbstract Background Rapid development of high-throughput omics technologies generates an increasing interest in algorithms for cutoff point identification. Existing cutoff methods and tools identify cutoff points based on an association of continuous variables with another variable, such as phenotype, disease state, or treatment group. These approaches are not applicable for descriptive studies in which continuous variables are reported without known association with any biologically meaningful variables. Results The most common shape of the ranked distribution of continuous variables in high-throughput descriptive studies corresponds to a biphasic curve, where the first phase includes a big number of variables with values slowly growing with rank and the second phase includes a smaller number of variables rapidly growing with rank. This study describes an easy algorithm to identify the boundary between these phases to be used as a cutoff point. Discussion The major assumption of that approach is that a small number of variables with high values dominate the biological system and determine its major processes and functions. This approach was tested on three different datasets: human genes and their expression values in the human cerebral cortex, mammalian genes and their values of sensitivity to chemical exposures, and human proteins and their expression values in the human heart. In every case, the described cutoff identification method produced shortlists of variables (genes, proteins) highly relevant for dominant functions/pathways of the analyzed biological systems. Conclusions The described method for cutoff identification may be used to prioritize variables in descriptive omics studies for a focused functional analysis, in situations where other methods of dichotomization of data are inaccessible.https://doi.org/10.1186/s12864-022-08427-6CutoffDichotomizationDescriptive genomicsThreshold-omics |
| spellingShingle | Alexander Suvorov Simple method for cutoff point identification in descriptive high-throughput biological studies BMC Genomics Cutoff Dichotomization Descriptive genomics Threshold -omics |
| title | Simple method for cutoff point identification in descriptive high-throughput biological studies |
| title_full | Simple method for cutoff point identification in descriptive high-throughput biological studies |
| title_fullStr | Simple method for cutoff point identification in descriptive high-throughput biological studies |
| title_full_unstemmed | Simple method for cutoff point identification in descriptive high-throughput biological studies |
| title_short | Simple method for cutoff point identification in descriptive high-throughput biological studies |
| title_sort | simple method for cutoff point identification in descriptive high throughput biological studies |
| topic | Cutoff Dichotomization Descriptive genomics Threshold -omics |
| url | https://doi.org/10.1186/s12864-022-08427-6 |
| work_keys_str_mv | AT alexandersuvorov simplemethodforcutoffpointidentificationindescriptivehighthroughputbiologicalstudies |