The Pancreatic Expression database: 2011 update

被引：24

作者：

Cutts, Rosalind J. ^{[1
,2
]}

Gadaleta, Emanuela ^{[1
,2
]}

Hahn, Stephan A. ^{[3
]}

Crnogorac-Jurcevic, Tatjana ^{[1
,2
]}

Lemoine, Nicholas R. ^{[1
,2
]}

Chelala, Claude ^{[1
,2
]}

机构：

[1] Queen Mary Univ London, Inst Canc, Ctr Mol Oncol & Imaging, London EC1M 6BQ, England

[2] Queen Mary Univ London, CR UK Ctr, Barts & London Sch Med & Dent, London EC1M 6BQ, England

[3] Ruhr Univ Bochum, D-44780 Bochum, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

关键词：

ARCHIVE; BIOMART;

D O I：

10.1093/nar/gkq937

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 Pancreatic Expression database (PED, http://www.pancreasexpression.org) has established itself as the main repository for pancreatic-derived -omics data. For the past 3 years, its data content and access have increased substantially. Here we describe several of its new and improved features, such as data content, which now includes over 60 000 measurements derived from transcriptomics, proteomics, genomics and miRNA profiles from various pancreas-centred reports on a broad range of specimen and experimental types. We also illustrate the capabilities of its interface, which allows integrative queries that can combine PED data with a growing number of biological resources such as NCBI, Ensembl, UniProt and Reactome. Thus, PED is capable of retrieving and integrating different types of -omics, annotations and clinical data. We also focus on the importance of data sharing and interoperability in the cancer field, and the integration of PED into the International Cancer Genome Consortium (ICGC) data portal.

引用

页码：D1023 / D1028

页数：6

共 18 条

[1] The Universal Protein Resource (UniProt) in 2010 [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Barrell, Daniel ;

Bely, Benoit ;

Bingley, Mark ;

Binns, David ;

Bower, Lawrence ;

Browne, Paul ;

Chan, Wei Mun ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fedotov, Alexander ;

Foulger, Rebecca ;

Garavelli, John ;

Huntley, Rachael ;

Jacobsen, Julius ;

Kleen, Michael ;

Laiho, Kati ;

Leinonen, Rasko ;

Legge, Duncan ;

Lin, Quan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Poggioli, Diego ;

Pruess, Manuela ;

Corbett, Matt ;

di Martino, Giuseppe ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Bairoch, Amos ;

Bougueleret, Lydie ;

Xenarios, Ioannis ;

Altairac, Severine ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bolleman, Jerven ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D142-D148

[2] NCBI GEO: archive for high-throughput functional genomic data [J].

Barrett, Tanya ;

Troup, Dennis B. ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Rudnev, Dmitry ;

Evangelista, Carlos ;

Kim, Irene F. ;

Soboleva, Alexandra ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Muertter, Rolf N. ;

Edgar, Ron .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D885-D890

[3]

Blankenberg D., CURR PROTOC MOL BIOL

[4] Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets [J].

Chelala, Claude ;

Hahn, Stephan A. ;

Whiteman, Hannah J. ;

Barry, Sayka ;

Hariharan, Deepak ;

Radon, Tomasz P. ;

Lemoine, Nicholas R. ;

Crnogorac-Jurcevic, Tatjana .

BMC GENOMICS, 2007, 8 (1)

[5] Integration of biological networks and gene expression data using Cytoscape [J].

Cline, Melissa S. ;

Smoot, Michael ;

Cerami, Ethan ;

Kuchinsky, Allan ;

Landys, Nerius ;

Workman, Chris ;

Christmas, Rowan ;

Avila-Campilo, Iliana ;

Creech, Michael ;

Gross, Benjamin ;

Hanspers, Kristina ;

Isserlin, Ruth ;

Kelley, Ryan ;

Killcoyne, Sarah ;

Lotia, Samad ;

Maere, Steven ;

Morris, John ;

Ono, Keiichiro ;

Pavlovic, Vuk ;

Pico, Alexander R. ;

Vailaya, Aditya ;

Wang, Peng-Liang ;

Adler, Annette ;

Conklin, Bruce R. ;

Hood, Leroy ;

Kuiper, Martin ;

Sander, Chris ;

Schmulevich, Ilya ;

Schwikowski, Benno ;

Warner, Guy J. ;

Ideker, Trey ;

Bader, Gary D. .

NATURE PROTOCOLS, 2007, 2 (10) :2366-2382

[6] The Distributed Annotation System [J].

Dowell, Robin D. ;

Jokerst, Rodney M. ;

Day, Allen ;

Eddy, Sean R. ;

Stein, Lincoln .

BMC BIOINFORMATICS, 2001, 2 (1)

[7] BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis [J].

Durinck, S ;

Moreau, Y ;

Kasprzyk, A ;

Davis, S ;

De Moor, B ;

Brazma, A ;

Huber, W .

BIOINFORMATICS, 2005, 21 (16) :3439-3440

[8]

Goonetilleke K S, 2008, Int J Surg, V6, P81, DOI 10.1016/j.ijsu.2006.09.001

[9] BioMart Central Portal-unified access to biological data [J].

Haider, Syed ;

Ballester, Benoit ;

Smedley, Damian ;

Zhang, Junjun ;

Rice, Peter ;

Kasprzyk, Arek .

NUCLEIC ACIDS RESEARCH, 2009, 37 :W23-W27

[10] Analysis of mortality rates for pancreatic cancer across the world [J].

Hariharan, D. ;

Saied, A. ;

Kocher, H. M. .

HPB, 2008, 10 (01) :58-62

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