IMPRes-Pro: A high dimensional multiomics integration method for in silico hypothesis generation
| Autor: | Duolin Wang, Dong Xu, Trupti Joshi, Yuexu Jiang |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Proteomics
Background information Computer science In silico Breast Neoplasms computer.software_genre Machine learning General Biochemistry Genetics and Molecular Biology 03 medical and health sciences Health informatics tools Computer Graphics Humans Computer Simulation Molecular Biology 030304 developmental biology TRACE (psycholinguistics) 0303 health sciences business.industry Gene Expression Profiling 030302 biochemistry & molecular biology Computational Biology Visualization Dynamic programming Female Artificial intelligence Noise (video) Web service business computer Algorithms Software |
| Zdroj: | Methods. 173:16-23 |
| ISSN: | 1046-2023 |
| Popis: | Nowadays, large amounts of omics data have been generated and contributed to increasing knowledge about associated biological mechanisms. A new challenge coming along is how to identify the active pathways and extract useful insights from these data with huge background information and noise. Although biologically meaningful modules can often be detected by many existing informatics tools, it is still hard to interpret or make use of the results towards in silico hypothesis generation and testing. To address this gap, we previously developed the IMPRes (Integrative MultiOmics Pathway Resolution) v 1.0 algorithm, a new step-wise active pathway detection method using a dynamic programming approach. This approach enables the network detection one step at a time, making it easy for researchers to trace the pathways, and leading to more accurate drug design and more effective treatment strategies. In this paper, we present IMPRes-Pro, an enhancement to IMPRes v1.0 by integrating proteomics data along with transcriptomics data and constructing a heterogeneous background network. The evaluation experiment conducted on human primary breast cancer dataset has shown the advantage over the original IMPRes v1.0 method. Furthermore, a case study on human metastatic breast cancer dataset was performed and we have provided several insights regarding the selection of optimal therapy strategy. IMPRes-Pro algorithm and visualization tool is available as a web service at http://digbio.missouri.edu/impres. |
| Databáze: | OpenAIRE |
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