modMine: flexible access to modENCODE data

被引：94

作者：

Contrino, Sergio ^{[1
]}

Smith, Richard N. ^{[1
]}

Butano, Daniela ^{[1
]}

Carr, Adrian ^{[1
]}

Hu, Fengyuan ^{[1
]}

Lyne, Rachel ^{[1
]}

Rutherford, Kim ^{[1
]}

Kalderimis, Alex ^{[1
]}

Sullivan, Julie ^{[1
]}

Carbon, Seth ^{[2
]}

Kephart, Ellen T. ^{[2
]}

Lloyd, Paul ^{[2
]}

Stinson, E. O. ^{[2
]}

Washington, Nicole L. ^{[2
]}

Perry, Marc D. ^{[3
]}

Ruzanov, Peter ^{[3
]}

Zha, Zheng ^{[3
]}

Lewis, Suzanna E. ^{[2
]}

Stein, Lincoln D. ^{[3
]}

Micklem, Gos ^{[1
]}

机构：

[1] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England

[2] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA

[3] MaRS Ctr, Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

基金：

英国惠康基金; 美国国家卫生研究院;

关键词：

GENOME DATABASE; ONTOLOGY; RESOURCE; ANNOTATIONS;

D O I：

10.1093/nar/gkr921

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：

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.

引用

页码：D1082 / D1088

页数：7

共 31 条

[1] FlyTF:: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
Adryan, Boris
Teichmann, Sarah A.
[J]. BIOINFORMATICS, 2006, 22 (12) : 1532 - 1533
[2] The Universal Protein Resource (UniProt) in 2010
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
[J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : D142 - D148
[3] The IntAct molecular interaction database in 2010
Aranda, B.
Achuthan, P.
Alam-Faruque, Y.
Armean, I.
Bridge, A.
Derow, C.
Feuermann, M.
Ghanbarian, A. T.
Kerrien, S.
Khadake, J.
Kerssemakers, J.
Leroy, C.
Menden, M.
Michaut, M.
Montecchi-Palazzi, L.
Neuhauser, S. N.
Orchard, S.
Perreau, V.
Roechert, B.
van Eijk, K.
Hermjakob, H.
[J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : D525 - D531
[4] NCBI GEO: archive for functional genomics data sets-10 years on
Barrett, Tanya
Troup, Dennis B.
Wilhite, Stephen E.
Ledoux, Pierre
Evangelista, Carlos
Kim, Irene F.
Tomashevsky, Maxim
Marshall, Kimberly A.
Phillippy, Katherine H.
Sherman, Patti M.
Muertter, Rolf N.
Holko, Michelle
Ayanbule, Oluwabukunmi
Yefanov, Andrey
Soboleva, Alexandra
[J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D1005 - D1010
[5] The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
Blake, Judith A.
Bult, Carol J.
Kadin, James A.
Richardson, Joel E.
Eppig, Janan T.
[J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D842 - D848
[6] ZFIN: enhancements and updates to the zebrafish model organism database
Bradford, Yvonne
Conlin, Tom
Dunn, Nathan
Fashena, David
Frazer, Ken
Howe, Douglas G.
Knight, Jonathan
Mani, Prita
Martin, Ryan
Moxon, Sierra A. T.
Paddock, Holly
Pich, Christian
Ramachandran, Sridhar
Ruef, Barbara J.
Ruzicka, Leyla
Schaper, Holle Bauer
Schaper, Kevin
Shao, Xiang
Singer, Amy
Sprague, Judy
Sprunger, Brock
Van Slyke, Ceri
Westerfield, Monte
[J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D822 - D829
[7] Minimum information about a microarray experiment (MIAME) - toward standards for microarray data
Brazma, A
Hingamp, P
Quackenbush, J
Sherlock, G
Spellman, P
Stoeckert, C
Aach, J
Ansorge, W
Ball, CA
Causton, HC
Gaasterland, T
Glenisson, P
Holstege, FCP
Kim, IF
Markowitz, V
Matese, JC
Parkinson, H
Robinson, A
Sarkans, U
Schulze-Kremer, S
Stewart, J
Taylor, R
Vilo, J
Vingron, M
[J]. NATURE GENETICS, 2001, 29 (04) : 365 - 371
[8] Unlocking the secrets of the genome
Celniker, Susan E.
Dillon, Laura A. L.
Gerstein, Mark B.
Gunsalus, Kristin C.
Henikoff, Steven
Karpen, Gary H.
Kellis, Manolis
Lai, Eric C.
Lieb, Jason D.
MacAlpine, David M.
Micklem, Gos
Piano, Fabio
Snyder, Michael
Stein, Lincoln
White, Kevin P.
Waterston, Robert H.
[J]. NATURE, 2009, 459 (7249) : 927 - 930
[9] The Effects of Th17 Cytokines on the Inflammatory Mediator Production and Barrier Function of ARPE-19 Cells
Chen, Ying
Yang, Peizeng
Li, Fuzhen
Kijlstra, Aize
[J]. PLOS ONE, 2011, 6 (03):
[10] Reactome: a database of reactions, pathways and biological processes
Croft, David
O'Kelly, Gavin
Wu, Guanming
Haw, Robin
Gillespie, Marc
Matthews, Lisa
Caudy, Michael
Garapati, Phani
Gopinath, Gopal
Jassal, Bijay
Jupe, Steven
Kalatskaya, Irina
Mahajan, Shahana
May, Bruce
Ndegwa, Nelson
Schmidt, Esther
Shamovsky, Veronica
Yung, Christina
Birney, Ewan
Hermjakob, Henning
D'Eustachio, Peter
Stein, Lincoln
[J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D691 - D697

← 1 2 3 4 →