GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC

被引：154

作者：

Li, Ruidong ^{[1
,2
]}

Qu, Han ^{[1
]}

Wang, Shibo ^{[1
]}

Wei, Julong ^{[1
,3
]}

Zhang, Le ^{[1
,2
]}

Ma, Renyuan ^{[1
,4
]}

Lu, Jianming ^{[1
,5
]}

Zhu, Jianguo ^{[6
]}

Zhong, Wei-De ^{[5
]}

Jia, Zhenyu ^{[1
,2
]}

机构：

[1] Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA

[2] Univ Calif Riverside, Genet Gen & Bioinformat Program, Riverside, CA 92521 USA

[3] Nanjing Agr Univ, Coll Anim Sci & Technol, Nanjing 210095, Jiangsu, Peoples R China

[4] Bowdoin Coll, Dept Math, Brunswick, ME 04011 USA

[5] South China Univ Technol, Guangzhou Peoples Hosp 1, Affiliated Hosp 2, Dept Urol,Guangdong Key Lab Clin Mol Med & Diagno, Guangzhou 510180, Guangdong, Peoples R China

[6] Guizhou Prov Peoples Hosp, Dept Urol, Guiyang 550002, Guizhou, Peoples R China

来源：

BIOINFORMATICS | 2018年 / 34卷 / 14期

基金：

中国国家自然科学基金;

关键词：

D O I：

10.1093/bioinformatics/bty124

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies. Results: We have developed a user-friendly R/Bioconductor package, named GDCRNATools, for downloading, organizing and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis.

引用

页码：2515 / 2517

页数：3

共 15 条

[1] miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions [J].

Chou, Chih-Hung ;

Shrestha, Sirjana ;

Yang, Chi-Dung ;

Chang, Nai-Wen ;

Lin, Yu-Ling ;

Liao, Kuang-Wen ;

Huang, Wei-Chi ;

Sun, Ting-Hsuan ;

Tu, Siang-Jyun ;

Lee, Wei-Hsiang ;

Chiew, Men-Yee ;

Tai, Chun-San ;

Wei, Ting-Yen ;

Tsai, Tzi-Ren ;

Huang, Hsin-Tzu ;

Wang, Chung-Yu ;

Wu, Hsin-Yi ;

Ho, Shu-Yi ;

Chen, Pin-Rong ;

Chuang, Cheng-Hsun ;

Hsieh, Pei-Jung ;

Wu, Yi-Shin ;

Chen, Wen-Liang ;

Li, Meng-Ju ;

Wu, Yu-Chun ;

Huang, Xin-Yi ;

Ng, Fung Ling ;

Buddhakosai, Waradee ;

Huang, Pei-Chun ;

Lan, Kuan-Chun ;

Huang, Chia-Yen ;

Weng, Shun-Long ;

Cheng, Yeong-Nan ;

Liang, Chao ;

Hsu, Wen-Lian ;

Huang, Hsien-Da .

NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) :D296-D302

[2] TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data [J].

Colaprico, Antonio ;

Silva, Tiago C. ;

Olsen, Catharina ;

Garofano, Luciano ;

Cava, Claudia ;

Garolini, Davide ;

Sabedot, Thais S. ;

Malta, Tathiane M. ;

Pagnotta, Stefano M. ;

Castiglioni, Isabella ;

Ceccarelli, Michele ;

Bontempi, Gianluca ;

Noushmehr, Houtan .

NUCLEIC ACIDS RESEARCH, 2016, 44 (08) :e71

[3] spongeScan: A web for detecting microRNA binding elements in lncRNA sequences [J].

Furio-Tari, Pedro ;

Tarazona, Sonia ;

Gabaldon, Toni ;

Enright, Anton J. ;

Conesa, Ana .

NUCLEIC ACIDS RESEARCH, 2016, 44 (W1) :W176-W180

[4] miRcode: a map of putative microRNA target sites in the long non-coding transcriptome [J].

Jeggari, Ashwini ;

Marks, Debora S. ;

Larsson, Erik .

BIOINFORMATICS, 2012, 28 (15) :2062-2063

[5] RETRACTED: HMGA2 functions as a competing endogenous RNA to promote lung cancer progression (Retracted article. See vol. 523, 2015) [J].

Kumar, Madhu S. ;

Armenteros-Monterroso, Elena ;

East, Philip ;

Chakravorty, Probir ;

Matthews, Nik ;

Winslow, Monte M. ;

Downward, Julian .

NATURE, 2014, 505 (7482) :212-+

[6] WGCNA: an R package for weighted correlation network analysis [J].

Langfelder, Peter ;

Horvath, Steve .

BMC BIOINFORMATICS, 2008, 9 (1)

[7] starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data [J].

Li, Jun-Hao ;

Liu, Shun ;

Zhou, Hui ;

Qu, Liang-Hu ;

Yang, Jian-Hua .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D92-D97

[8] Lnc RNA HOTAIR functions as a competing endogenous RNA to regulate HER2 expression by sponging miR-331-3p in gastric cancer [J].

Liu, Xiang-hua ;

Sun, Ming ;

Nie, Feng-qi ;

Ge, Ying-bin ;

Zhang, Er-bao ;

Yin, Dan-dan ;

Kong, Rong ;

Xia, Rui ;

Lu, Kai-hua ;

Li, Jin-hai ;

De, Wei ;

Wang, Ke-ming ;

Wang, Zhao-xia .

MOLECULAR CANCER, 2014, 13

[9] Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 [J].

Love, Michael I. ;

Huber, Wolfgang ;

Anders, Simon .

GENOME BIOLOGY, 2014, 15 (12)

[10] Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer [J].

Paci, Paola ;

Colombo, Teresa ;

Farina, Lorenzo .

BMC SYSTEMS BIOLOGY, 2014, 8

← 1 2 →