Suppr超能文献

通过社区融合来识别癌症组学的共性和差异。

Identification of cancer omics commonality and difference via community fusion.

机构信息

Center for Applied Statistics, Renmin University of China, Beijing, China.

School of Statistics, Renmin University of China, Beijing, China.

出版信息

Stat Med. 2019 Mar 30;38(7):1200-1212. doi: 10.1002/sim.8027. Epub 2018 Nov 12.

Abstract

The analysis of cancer omics data is a "classic" problem; however, it still remains challenging. Advancing from early studies that are mostly focused on a single type of cancer, some recent studies have analyzed data on multiple "related" cancer types/subtypes, examined their commonality and difference, and led to insightful findings. In this article, we consider the analysis of multiple omics datasets, with each dataset on one type/subtype of "related" cancers. A Community Fusion (CoFu) approach is developed, which conducts marker selection and model building using a novel penalization technique, informatively accommodates the network community structure of omics measurements, and automatically identifies the commonality and difference of cancer omics markers. Simulation demonstrates its superiority over direct competitors. The analysis of TCGA lung cancer and melanoma data leads to interesting findings.

摘要

癌症组学数据分析是一个“经典”问题;然而,它仍然具有挑战性。从早期主要集中在单一类型癌症的研究进展,一些最近的研究分析了多种“相关”癌症类型/亚型的数据,检查了它们的共性和差异,并得出了有见地的发现。在本文中,我们考虑了多个组学数据集的分析,每个数据集都是一种“相关”癌症的一种类型/亚型。我们开发了一种社区融合(CoFu)方法,该方法使用一种新颖的惩罚技术进行标记选择和模型构建,信息性地适应了组学测量的网络社区结构,并自动识别癌症组学标记的共性和差异。模拟表明它优于直接竞争对手。对 TCGA 肺癌和黑色素瘤数据的分析得出了有趣的发现。

相似文献

1
Identification of cancer omics commonality and difference via community fusion.
Stat Med. 2019 Mar 30;38(7):1200-1212. doi: 10.1002/sim.8027. Epub 2018 Nov 12.
2
An integrative sparse boosting analysis of cancer genomic commonality and difference.
Stat Methods Med Res. 2020 May;29(5):1325-1337. doi: 10.1177/0962280219859026. Epub 2019 Jul 7.
4
Multi-omic and multi-view clustering algorithms: review and cancer benchmark.
Nucleic Acids Res. 2018 Nov 16;46(20):10546-10562. doi: 10.1093/nar/gky889.
5
Integrative analysis of high-throughput cancer studies with contrasted penalization.
Genet Epidemiol. 2014 Feb;38(2):144-51. doi: 10.1002/gepi.21781. Epub 2014 Jan 6.
6
Multi-omics facilitated variable selection in Cox-regression model for cancer prognosis prediction.
Methods. 2017 Jul 15;124:100-107. doi: 10.1016/j.ymeth.2017.06.010. Epub 2017 Jun 13.
7
Omics Pipe: a community-based framework for reproducible multi-omics data analysis.
Bioinformatics. 2015 Jun 1;31(11):1724-8. doi: 10.1093/bioinformatics/btv061. Epub 2015 Jan 30.
8
Integrating multidimensional omics data for cancer outcome.
Biostatistics. 2016 Oct;17(4):605-18. doi: 10.1093/biostatistics/kxw010. Epub 2016 Mar 14.
9
Integrative Analysis of Cancer Omics Data for Prognosis Modeling.
Genes (Basel). 2019 Aug 9;10(8):604. doi: 10.3390/genes10080604.
10
Onco-Multi-OMICS Approach: A New Frontier in Cancer Research.
Biomed Res Int. 2018 Oct 3;2018:9836256. doi: 10.1155/2018/9836256. eCollection 2018.

引用本文的文献

1
Biomarker-guided heterogeneity analysis of genetic regulations via multivariate sparse fusion.
Stat Med. 2021 Jul 30;40(17):3915-3936. doi: 10.1002/sim.9006. Epub 2021 Apr 27.
2
Integrative sparse partial least squares.
Stat Med. 2021 Apr;40(9):2239-2256. doi: 10.1002/sim.8900. Epub 2021 Feb 8.
3
An integrative sparse boosting analysis of cancer genomic commonality and difference.
Stat Methods Med Res. 2020 May;29(5):1325-1337. doi: 10.1177/0962280219859026. Epub 2019 Jul 7.
4
Penalized integrative semiparametric interaction analysis for multiple genetic datasets.
Stat Med. 2019 Jul 30;38(17):3221-3242. doi: 10.1002/sim.8172. Epub 2019 Apr 16.

本文引用的文献

1
Promoting Similarity of Sparsity Structures in Integrative Analysis with Penalization.
J Am Stat Assoc. 2017;112(517):342-350. doi: 10.1080/01621459.2016.1139497. Epub 2017 May 3.
2
Network-based machine learning and graph theory algorithms for precision oncology.
NPJ Precis Oncol. 2017 Aug 8;1(1):25. doi: 10.1038/s41698-017-0029-7. eCollection 2017.
4
Analysis of cancer gene expression data with an assisted robust marker identification approach.
Genet Epidemiol. 2017 Dec;41(8):779-789. doi: 10.1002/gepi.22066. Epub 2017 Sep 14.
9
Identification of TRA2B-DNAH5 fusion as a novel oncogenic driver in human lung squamous cell carcinoma.
Cell Res. 2016 Oct;26(10):1149-1164. doi: 10.1038/cr.2016.111. Epub 2016 Sep 27.
10
Promoting similarity of model sparsity structures in integrative analysis of cancer genetic data.
Stat Med. 2017 Feb 10;36(3):509-559. doi: 10.1002/sim.7138. Epub 2016 Sep 25.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验