GSCALite: a web server for gene set cancer analysis

被引：863

作者：

Liu, Chun-Jie ^{[1
]}

Hu, Fei-Fei ^{[1
]}

Xia, Meng-Xuan ^{[1
]}

Han, Leng ^{[2
]}

Zhang, Qiong ^{[1
]}

Guo, An-Yuan ^{[1
]}

机构：

[1] Huazhong Univ Sci & Technol, Coll Life Sci & Technol, Hubei Bioinformat & Mol Imaging Key Lab, Key Lab Mol Biophys,Minist Educ,Dept Bioinformat, Wuhan 430074, Hubei, Peoples R China

[2] Univ Texas Hlth Sci Ctr Houston, McGovern Med Sch, Dept Biochem & Mol Biol, Houston, TX 77030 USA

来源：

BIOINFORMATICS | 2018年 / 34卷 / 21期

基金：

中国国家自然科学基金;

关键词：

EXPRESSION; RESOURCE; GENOMICS; CELLS;

D O I：

10.1093/bioinformatics/bty411

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

The availability of cancer genomic data makes it possible to analyze genes related to cancer. Cancer is usually the result of a set of genes and the signal of a single gene could be covered by background noise. Here, we present a web server named Gene Set Cancer Analysis (GSCALite) to analyze a set of genes in cancers with the following functional modules. (i) Differential expression in tumor versus normal, and the survival analysis; (ii) Genomic variations and their survival analysis; (iii) Gene expression associated cancer pathway activity; (iv) miRNA regulatory network for genes; (v) Drug sensitivity for genes; (vi) Normal tissue expression and eQTL for genes. GSCALite is a user-friendly web server for dynamic analysis and visualization of gene set in cancer and drug sensitivity correlation, which will be of broad utilities to cancer researchers.

引用

页码：3771 / 3772

页数：2

共 14 条

[1]

A pan-cancer proteomic perspective on The Cancer Genome Atlas [J].

Akbani, Rehan ;

Ng, Patrick Kwok Shing ;

Werner, Henrica M. J. ;

Shahmoradgoli, Maria ;

Zhang, Fan ;

Ju, Zhenlin ;

Liu, Wenbin ;

Yang, Ji-Yeon ;

Yoshihara, Kosuke ;

Li, Jun ;

Ling, Shiyun ;

Seviour, Elena G. ;

Ram, Prahlad T. ;

Minna, John D. ;

Diao, Lixia ;

Tong, Pan ;

Heymach, John V. ;

Hill, Steven M. ;

Dondelinger, Frank ;

Stadler, Nicolas ;

Byers, Lauren A. ;

Meric-Bernstam, Funda ;

Weinstein, John N. ;

Broom, Bradley M. ;

Verhaak, Roeland G. W. ;

Liang, Han ;

Mukherjee, Sach ;

Lu, Yiling ;

Mills, Gordon B. .

NATURE COMMUNICATIONS, 2014, 5

[2]

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans [J].

Ardlie, Kristin G. ;

DeLuca, David S. ;

Segre, Ayellet V. ;

Sullivan, Timothy J. ;

Young, Taylor R. ;

Gelfand, Ellen T. ;

Trowbridge, Casandra A. ;

Maller, Julian B. ;

Tukiainen, Taru ;

Lek, Monkol ;

Ward, Lucas D. ;

Kheradpour, Pouya ;

Iriarte, Benjamin ;

Meng, Yan ;

Palmer, Cameron D. ;

Esko, Tonu ;

Winckler, Wendy ;

Hirschhorn, Joel N. ;

Kellis, Manolis ;

MacArthur, Daniel G. ;

Getz, Gad ;

Shabalin, Andrey A. ;

Li, Gen ;

Zhou, Yi-Hui ;

Nobel, Andrew B. ;

Rusyn, Ivan ;

Wright, Fred A. ;

Lappalainen, Tuuli ;

Ferreira, Pedro G. ;

Ongen, Halit ;

Rivas, Manuel A. ;

Battle, Alexis ;

Mostafavi, Sara ;

Monlong, Jean ;

Sammeth, Michael ;

Mele, Marta ;

Reverter, Ferran ;

Goldmann, Jakob M. ;

Koller, Daphne ;

Guigo, Roderic ;

McCarthy, Mark I. ;

Dermitzakis, Emmanouil T. ;

Gamazon, Eric R. ;

Im, Hae Kyung ;

Konkashbaev, Anuar ;

Nicolae, Dan L. ;

Cox, Nancy J. ;

Flutre, Timothee ;

Wen, Xiaoquan ;

Stephens, Matthew .

SCIENCE, 2015, 348 (6235) :648-660

[3]

An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules [J].

Basu, Amrita ;

Bodycombe, Nicole E. ;

Cheah, Jaime H. ;

Price, Edmund V. ;

Liu, Ke ;

Schaefer, Giannina I. ;

Ebright, Richard Y. ;

Stewart, Michelle L. ;

Ito, Daisuke ;

Wang, Stephanie ;

Bracha, Abigail L. ;

Liefeld, Ted ;

Wawer, Mathias ;

Gilbert, Joshua C. ;

Wilson, Andrew J. ;

Stransky, Nicolas ;

Kryukov, Gregory V. ;

Dancik, Vlado ;

Barretina, Jordi ;

Garraway, Levi A. ;

Hon, C. Suk-Yee ;

Munoz, Benito ;

Bittker, Joshua A. ;

Stockwell, Brent R. ;

Khabele, Dineo ;

Stern, Andrew M. ;

Clemons, Paul A. ;

Shamji, Alykhan F. ;

Schreiber, Stuart L. .

CELL, 2013, 154 (05) :1151-1161

[4]

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data [J].

Cerami, Ethan ;

Gao, Jianjiong ;

Dogrusoz, Ugur ;

Gross, Benjamin E. ;

Sumer, Selcuk Onur ;

Aksoy, Buelent Arman ;

Jacobsen, Anders ;

Byrne, Caitlin J. ;

Heuer, Michael L. ;

Larsson, Erik ;

Antipin, Yevgeniy ;

Reva, Boris ;

Goldberg, Arthur P. ;

Sander, Chris ;

Schultz, Nikolaus .

CANCER DISCOVERY, 2012, 2 (05) :401-404

[5]

Expanding the computational toolbox for mining cancer genomes [J].

Ding, Li ;

Wendl, Michael C. ;

McMichael, Joshua F. ;

Raphael, Benjamin J. .

NATURE REVIEWS GENETICS, 2014, 15 (08) :556-570

[6]

A Pan-cancer Analysis of the Expression and Clinical Relevance of Small Nucleolar RNAs in Human Cancer [J].

Gong, Jing ;

Li, Yajuan ;

Liu, Chun-Jie ;

Xiang, Yu ;

Li, Chunlai ;

Ye, Youqiong ;

Zhang, Zhao ;

Hawke, David H. ;

Park, Peter K. ;

Diao, Lixia ;

Putkey, John A. ;

Yang, Liuqing ;

Guo, An-Yuan ;

Lin, Chunru ;

Han, Leng .

CELL REPORTS, 2017, 21 (07) :1968-1981

[7]

The Hippo pathway and human cancer [J].

Harvey, Kieran F. ;

Zhang, Xiaomeng ;

Thomas, David M. .

NATURE REVIEWS CANCER, 2013, 13 (04) :246-257

[8]

Mayakonda A, 2016, BIORXIV

[9]

Oncomine 3.0: Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles [J].

Rhodes, Daniel R. ;

Kalyana-Sundaram, Shanker ;

Mahavisno, Vasudeva ;

Varambally, Radhika ;

Yu, Jianjun ;

Briggs, Benjamin B. ;

Barrette, Terrence R. ;

Anstet, Matthew J. ;

Kincead-Beal, Colleen ;

Kulkarni, Prakash ;

Varambally, Sooryanaryana ;

Ghoshy, Debashis ;

Chinnaiyan, Arul M. .

NEOPLASIA, 2007, 9 (02) :166-180

[10]

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses [J].

Tang, Zefang ;

Li, Chenwei ;

Kang, Boxi ;

Gao, Ge ;

Li, Cheng ;

Zhang, Zemin .

NUCLEIC ACIDS RESEARCH, 2017, 45 (W1) :W98-W102

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