Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells

被引：88

作者：

Li, Jian-Rong ^{[1
,2
]}

Sun, Chuan-Hu ^{[1
]}

Li, Wenyuan ^{[3
]}

Chao, Rou-Fang ^{[1
]}

Huang, Chieh-Chen ^{[4
]}

Zhou, Xianghong Jasmine ^{[3
]}

Liu, Chun-Chi ^{[1
,2
]}

机构：

[1] Natl Chung Hsing Univ, Inst Genom & Bioinformat, Taichung 402, Taiwan

[2] Natl Chung Hsing Univ, PhD Program Med Biotechnol, Taichung 402, Taiwan

[3] Univ So Calif, Mol & Computat Biol, Los Angeles, CA 90089 USA

[4] Natl Chung Hsing Univ, Dept Life Sci, Taichung 402, Taiwan

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

基金：

美国国家卫生研究院;

关键词：

HUMAN GENOME; C-MYC; EXPRESSION; CARCINOMA; P63; GENES; CCAT1; QUANTIFICATION; DELTA-NP63; DISCOVERY;

D O I：

10.1093/nar/gkv1282

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The genome-wide transcriptome profiling of cancerous and normal tissue samples can provide insights into the molecular mechanisms of cancer initiation and progression. RNA Sequencing (RNA-Seq) is a revolutionary tool that has been used extensively in cancer research. However, no existing RNA-Seq database provides all of the following features: (i) large-scale and comprehensive data archives and analyses, including coding-transcript profiling, long non-coding RNA (lncRNA) profiling and coexpression networks; (ii) phenotype-oriented data organization and searching and (iii) the visualization of expression profiles, differential expression and regulatory networks. We have constructed the first public database that meets these criteria, the Cancer RNASeq Nexus (CRN, http://syslab4.nchu.edu.tw/CRN). CRN has a user-friendly web interface designed to facilitate cancer research and personalized medicine. It is an open resource for intuitive data exploration, providing coding-transcript/lncRNA expression profiles to support researchers generating new hypotheses in cancer research and personalized medicine.

引用

页码：D944 / D951

页数：8

共 35 条

[1] Differential expression of colon cancer associated transcript1 (CCAT1) along the colonic adenoma-carcinoma sequence [J].

Alaiyan, Bilal ;

Ilyayev, Nadia ;

Stojadinovic, Alexander ;

Izadjoo, Mina ;

Roistacher, Marina ;

Pavlov, Vera ;

Tzivin, Victoria ;

Halle, David ;

Pan, Honguang ;

Trink, Barry ;

Gure, Ali O. ;

Nissan, Aviram .

BMC CANCER, 2013, 13

[2] Loss of p63 leads to increased cell migration and up-regulation of genes involved in invasion and metastasis [J].

Barbieri, Christopher E. ;

Tang, Luo Jia ;

Brown, Kimberly A. ;

Pietenpol, Jennifer A. .

CANCER RESEARCH, 2006, 66 (15) :7589-7597

[3] NCBI GEO: archive for functional genomics data sets-update [J].

Barrett, Tanya ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Evangelista, Carlos ;

Kim, Irene F. ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Holko, Michelle ;

Yefanov, Andrey ;

Lee, Hyeseung ;

Zhang, Naigong ;

Robertson, Cynthia L. ;

Serova, Nadezhda ;

Davis, Sean ;

Soboleva, Alexandra .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D991-D995

[4] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].

BENJAMINI, Y ;

HOCHBERG, Y .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300

[5] p40 (ΔNp63) is superior to p63 for the diagnosis of pulmonary squamous cell carcinoma [J].

Bishop, Justin A. ;

Teruya-Feldstein, Julie ;

Westra, William H. ;

Pelosi, Giuseppe ;

Travis, William D. ;

Rekhtman, Natasha .

MODERN PATHOLOGY, 2012, 25 (03) :405-415

[6] 8q24 amplified segments involve novel fusion genes between NSMCE2 and long noncoding RNAs in acute myelogenous leukemia [J].

Chinen, Yoshiaki ;

Sakamoto, Natsumi ;

Nagoshi, Hisao ;

Taki, Tomohiko ;

Maegawa, Saori ;

Tatekawa, Shotaro ;

Tsukamoto, Taku ;

Mizutani, Shinsuke ;

Shimura, Yuji ;

Yamamoto-Sugitani, Mio ;

Kobayashi, Tsutomu ;

Matsumoto, Yosuke ;

Horiike, Shigeo ;

Kuroda, Junya ;

Taniwaki, Masafumi .

JOURNAL OF HEMATOLOGY & ONCOLOGY, 2014, 7

[7] GENCODE: The reference human genome annotation for The ENCODE Project [J].

Harrow, Jennifer ;

Frankish, Adam ;

Gonzalez, Jose M. ;

Tapanari, Electra ;

Diekhans, Mark ;

Kokocinski, Felix ;

Aken, Bronwen L. ;

Barrell, Daniel ;

Zadissa, Amonida ;

Searle, Stephen ;

Barnes, If ;

Bignell, Alexandra ;

Boychenko, Veronika ;

Hunt, Toby ;

Kay, Mike ;

Mukherjee, Gaurab ;

Rajan, Jeena ;

Despacio-Reyes, Gloria ;

Saunders, Gary ;

Steward, Charles ;

Harte, Rachel ;

Lin, Michael ;

Howald, Cedric ;

Tanzer, Andrea ;

Derrien, Thomas ;

Chrast, Jacqueline ;

Walters, Nathalie ;

Balasubramanian, Suganthi ;

Pei, Baikang ;

Tress, Michael ;

Manuel Rodriguez, Jose ;

Ezkurdia, Iakes ;

van Baren, Jeltje ;

Brent, Michael ;

Haussler, David ;

Kellis, Manolis ;

Valencia, Alfonso ;

Reymond, Alexandre ;

Gerstein, Mark ;

Guigo, Roderic ;

Hubbard, Tim J. .

GENOME RESEARCH, 2012, 22 (09) :1760-1774

[8] RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing [J].

Krupp, Markus ;

Marquardt, Jens U. ;

Sahin, Ugur ;

Galle, Peter R. ;

Castle, John ;

Teufel, Andreas .

BIOINFORMATICS, 2012, 28 (08) :1184-1185

[9] Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data [J].

Kupershmidt, Ilya ;

Su, Qiaojuan Jane ;

Grewal, Anoop ;

Sundaresh, Suman ;

Halperin, Inbal ;

Flynn, James ;

Shekar, Mamatha ;

Wang, Helen ;

Park, Jenny ;

Cui, Wenwu ;

Wall, Gregory D. ;

Wisotzkey, Robert ;

Alag, Satnam ;

Akhtari, Saeid ;

Ronaghi, Mostafa .

PLOS ONE, 2010, 5 (09)

[10] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [J].

Langmead, Ben ;

Trapnell, Cole ;

Pop, Mihai ;

Salzberg, Steven L. .

GENOME BIOLOGY, 2009, 10 (03)

← 1 2 3 4 →