DIGGIT：一个用于推断驱动细胞表型的遗传变异的Bioconductor软件包。
DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.
作者信息
Alvarez Mariano J, Chen James C, Califano Andrea
机构信息
Department of Systems Biology and.
Department of Systems Biology and Department of Dermatology, Columbia University, New York, NY 10032 USA.
出版信息
Bioinformatics. 2015 Dec 15;31(24):4032-4. doi: 10.1093/bioinformatics/btv499. Epub 2015 Sep 2.
Abstract
UNLABELLED
Identification of driver mutations in human diseases is often limited by cohort size and availability of appropriate statistical models. We propose a method for the systematic discovery of genetic alterations that are causal determinants of disease, by prioritizing genes upstream of functional disease drivers, within regulatory networks inferred de novo from experimental data. Here we present the implementation of Driver-gene Inference by Genetical-Genomic Information Theory as an R-system package.
AVAILABILITY AND IMPLEMENTATION
The diggit package is freely available under the GPL-2 license from Bioconductor (http://www.bioconductor.org).
摘要
未标注
人类疾病中驱动突变的识别常常受到队列规模和适当统计模型可用性的限制。我们提出了一种系统发现作为疾病因果决定因素的基因改变的方法，通过在从实验数据中从头推断的调控网络内，对功能性疾病驱动因素上游的基因进行优先级排序。在此，我们展示了基于遗传基因组信息理论的驱动基因推断作为一个R系统包的实现。
可用性与实现
diggit包可在GPL-2许可下从Bioconductor（http://www.bioconductor.org）免费获取。
相似文献
1
DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.DIGGIT：一个用于推断驱动细胞表型的遗传变异的Bioconductor软件包。
Bioinformatics. 2015 Dec 15;31(24):4032-4. doi: 10.1093/bioinformatics/btv499. Epub 2015 Sep 2.
2
lpNet: a linear programming approach to reconstruct signal transduction networks.lpNet：一种用于重构信号转导网络的线性规划方法。
Bioinformatics. 2015 Oct 1;31(19):3231-3. doi: 10.1093/bioinformatics/btv327. Epub 2015 May 29.
3
HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data.希尔伯特曲线：一个用于基因组数据高分辨率可视化的 R/Bioconductor 包。
Bioinformatics. 2016 Aug 1;32(15):2372-4. doi: 10.1093/bioinformatics/btw161. Epub 2016 Mar 24.
4
netboxr: Automated discovery of biological process modules by network analysis in R.netboxr：在 R 中通过网络分析自动发现生物过程模块。
PLoS One. 2020 Nov 2;15(11):e0234669. doi: 10.1371/journal.pone.0234669. eCollection 2020.
5
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.LOLA：R和Bioconductor中基因组区域集和调控元件的富集分析。
Bioinformatics. 2016 Feb 15;32(4):587-9. doi: 10.1093/bioinformatics/btv612. Epub 2015 Oct 27.
6
Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.Seq2pathway：一个用于下一代测序数据通路分析的R/Bioconductor软件包。
Bioinformatics. 2015 Sep 15;31(18):3043-5. doi: 10.1093/bioinformatics/btv289. Epub 2015 May 15.
7
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.VariantAnnotation：一个用于探索和注释遗传变异的 Bioconductor 软件包。
Bioinformatics. 2014 Jul 15;30(14):2076-8. doi: 10.1093/bioinformatics/btu168. Epub 2014 Mar 28.
8
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.regioneR：一个用于基于排列检验进行基因组区域关联分析的R/Bioconductor软件包。
Bioinformatics. 2016 Jan 15;32(2):289-91. doi: 10.1093/bioinformatics/btv562. Epub 2015 Sep 30.
9
CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.CGHnormaliter：一个 Bioconductor 包，用于对包含多个拷贝数变异的阵列 CGH 数据进行标准化处理。
Bioinformatics. 2010 May 15;26(10):1366-7. doi: 10.1093/bioinformatics/btq155. Epub 2010 Apr 23.
10
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.DNAshapeR：一个用于DNA形状预测和特征编码的R/Bioconductor软件包。
Bioinformatics. 2016 Apr 15;32(8):1211-3. doi: 10.1093/bioinformatics/btv735. Epub 2015 Dec 14.
引用本文的文献
1
DDX54 downregulation enhances anti-PD1 therapy in immune-desert lung tumors with high tumor mutational burden.DDX54表达下调增强了对肿瘤突变负荷高的免疫“冷”肺肿瘤的抗PD1治疗效果。
Proc Natl Acad Sci U S A. 2025 Apr 8;122(14):e2412310122. doi: 10.1073/pnas.2412310122. Epub 2025 Apr 2.
2
Multi-Omics Analysis Reveals Clinical Value and Possible Mechanisms of ATAD1 Down-Regulation in Human Prostate Adenocarcinoma.多组学分析揭示ATAD1下调在人前列腺腺癌中的临床价值及可能机制。
Life (Basel). 2022 Oct 30;12(11):1742. doi: 10.3390/life12111742.
3
SYSMut: decoding the functional significance of rare somatic mutations in cancer.SYSMut：解码癌症中罕见体细胞突变的功能意义。
Brief Bioinform. 2022 Jul 18;23(4). doi: 10.1093/bib/bbac280.
4
Untangling a complex web: Computational analyses of tumor molecular profiles to decode driver mechanisms.解开复杂的谜团：计算分析肿瘤分子谱以解码驱动机制。
J Genet Genomics. 2020 Oct 20;47(10):595-609. doi: 10.1016/j.jgg.2020.11.001. Epub 2020 Nov 28.
5
DriverDBv3: a multi-omics database for cancer driver gene research.DriverDBv3：一个用于癌症驱动基因研究的多组学数据库。
Nucleic Acids Res. 2020 Jan 8;48(D1):D863-D870. doi: 10.1093/nar/gkz964.
6
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.社区评估在药物基因组筛选中推进癌症药物组合的计算预测。
Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2.
7
Differential gene regulatory networks in development and disease.发育和疾病中的差异基因调控网络。
Cell Mol Life Sci. 2018 Mar;75(6):1013-1025. doi: 10.1007/s00018-017-2679-6. Epub 2017 Oct 10.
8
The recurrent architecture of tumour initiation, progression and drug sensitivity.肿瘤起始、进展和药物敏感性的复发结构。
Nat Rev Cancer. 2017 Feb;17(2):116-130. doi: 10.1038/nrc.2016.124. Epub 2016 Dec 15.
本文引用的文献
1
Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks.通过调控网络的系统水平分析鉴定人类疾病的因果遗传驱动因素。
Cell. 2014 Oct 9;159(2):402-14. doi: 10.1016/j.cell.2014.09.021.
2
Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.跨物种调控网络分析鉴定出 FOXM1 和 CENPF 之间的协同相互作用，该作用驱动前列腺癌恶性进展。
Cancer Cell. 2014 May 12;25(5):638-651. doi: 10.1016/j.ccr.2014.03.017.
3
Mutational heterogeneity in cancer and the search for new cancer-associated genes.癌症中的突变异质性与新的癌症相关基因的寻找。
Nature. 2013 Jul 11;499(7457):214-218. doi: 10.1038/nature12213. Epub 2013 Jun 16.
4
Apolipoprotein E and Alzheimer disease: risk, mechanisms and therapy.载脂蛋白 E 与阿尔茨海默病：风险、机制与治疗。
Nat Rev Neurol. 2013 Feb;9(2):106-18. doi: 10.1038/nrneurol.2012.263. Epub 2013 Jan 8.
5
Leveraging models of cell regulation and GWAS data in integrative network-based association studies.在基于整合网络的关联研究中利用细胞调控模型和全基因组关联研究（GWAS）数据。
Nat Genet. 2012 Jul 27;44(8):841-7. doi: 10.1038/ng.2355.
6
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.人类 B 细胞相互作用组鉴定出 MYB 和 FOXM1 作为生发中心增殖的主要调节因子。
Mol Syst Biol. 2010 Jun 8;6:377. doi: 10.1038/msb.2010.31.
7
The transcriptional network for mesenchymal transformation of brain tumours.脑肿瘤间质转化的转录网络。
Nature. 2010 Jan 21;463(7279):318-25. doi: 10.1038/nature08712. Epub 2009 Dec 23.
8
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.人类B细胞中转录因子活性的翻译后调节因子的全基因组鉴定。
Nat Biotechnol. 2009 Sep;27(9):829-39. doi: 10.1038/nbt.1563. Epub 2009 Sep 9.
9
Reverse engineering of regulatory networks in human B cells.人类B细胞中调控网络的逆向工程
Nat Genet. 2005 Apr;37(4):382-90. doi: 10.1038/ng1532. Epub 2005 Mar 20.
Zotero 插件