GeneProf data: A resource of curated, integrated and reusable high-throughput genomics experiments

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Halbritter, Florian ^a   Kousa, Anastasia I ^a   Tomlinson, Simon R ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER INTERFACE; FUNCTIONAL GENOMICS; GENE CONTROL; GENE EXPRESSION; GENEPROF DATABASE; GENETIC DATABASE; INTERNET; PRIORITY JOURNAL; RNA SEQUENCE; WEB BROWSER; ANIMAL; BINDING SITE; GENE EXPRESSION PROFILING; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; MOUSE; SEQUENCE ANALYSIS; SYSTEM ANALYSIS; DATA ANALYSIS; DATA BASE; DATA PROCESSING; INFORMATION PROCESSING; INFORMATION RETRIEVAL; ONLINE SYSTEM; PROTEIN INTERACTION; PROTEIN STRUCTURE;

TRANSCRIPTION FACTOR;

ANIMALS; BINDING SITES; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; MICE; SEQUENCE ANALYSIS, RNA; SYSTEMS INTEGRATION; TRANSCRIPTION FACTORS;

EID: 84891752912     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt966     Document Type: Article

References (28)

1. Rustici, G., Kolesnikov, N., Brandizi, M., Burdett, T., Dylag, M., Emam, I., Farne, A., Hastings, E., Ison, J., Keays, M. et al. (2013) ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res., 41, D987-D990.
2. Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
3. NCBI Resource Coordinators. (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 41, D8-D20.
4. Cochrane, G., Alako, B., Amid, C., Bower, L., Cerdeno-Tarraga, A., Cleland, I., Gibson, R., Goodgame, N., Jang, M., Kay, S. et al. (2013) Facing growth in the European Nucleotide Archive. Nucleic Acids Res., 41, D30-D35.
5. Ogasawara, O., Mashima, J., Kodama, Y., Kaminuma, E., Nakamura, Y., Okubo, K. and Takagi, T. (2013) DDBJ new system and service refactoring. Nucleic Acids Res., 41, D25-D29.
6. Halbritter, F., Vaidya, H.J. and Tomlinson, S.R. (2011) GeneProf: analysis of high-throughput sequencing experiments. Nat. Methods, 9, 7-8.
7. Goecks, J., Nekrutenko, A. and Taylor, J. (2010). Galaxy Team. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
8. Jagla, B., Wiswedel, B. and Coppee, J.Y. (2011) Extending KNIME for next-generation sequencing data analysis. Bioinformatics, 27, 2907-2909.
9. Mouse ENCODE Consortium, Stamatoyannopoulos, J.A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D.M., Groudine, M., Bender, M., Kaul, R. et al. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol., 13, 418.
10. Raney, B.J., Cline, M.S., Rosenbloom, K.R., Dreszer, T.R., Learned, K., Barber, G.P., Meyer, L.R., Sloan, C.A., Malladi, V.S., Roskin, K.M. et al. (2011) ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res., 39, D871-D875.
11. Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol., 28, 1045-1048.
12. Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
13. Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
14. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
15. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
16. Ioannidis, J.P.A., Allison, D.B., Ball, C.A., Coulibaly, I., Cui, X., Culhane, A.C., Falchi, M., Furlanello, C., Game, L., Jurman, G. et al. (2009) Repeatability of published microarray gene expression analyses. Nat. Genet., 41, 149-155.
17. Piwowar, H.A., Day, R.S. and Fridsma, D.B. (2007) Sharing detailed research data is associated with increased citation rate. PLoS One, 2, e308.
18. Flicek, P., Ahmed, I., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S. et al. (2013) Ensembl 2013. Nucleic Acids Res., 41, D48-D55.
19. Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Green, R.K., Goodsell, D.S., Prlic, A., Quesada, M. et al. (2013) The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res., 41, D475-D482.
20. Chatr-Aryamontri, A., Breitkreutz, B.-J., Heinicke, S., Boucher, L., Winter, A., Stark, C., Nixon, J., Ramage, L., Kolas, N., O'Donnell, L. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
21. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
22. Durinck, S., Bullard, J., Spellman, P.T. and Dudoit, S. (2009) GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics, 10, 2.
23. Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B. et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res., 41, D64-D69.
24. Thorvaldsdottir, H., Robinson, J.T. and Mesirov, J.P. (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinformatics, 14, 178-192.
25. Wolstencroft, K., Haines, R., Fellows, D., Williams, A., Withers, D., Owen, S., Soiland-Reyes, S., Dunlop, I., Nenadic, A., Fisher, P. et al. (2013) The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res., 41, W557-W561.
26. Chambers, I., Colby, D., Robertson, M., Nichols, J., Lee, S., Tweedie, S. and Smith, A. (2003) Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell, 113, 643-655.
27. Festuccia, N., Osorno, R., Halbritter, F., Karwacki-Neisius, V., Navarro, P., Colby, D., Wong, F., Yates, A., Tomlinson, S.R. and Chambers, I. (2012) Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells. Cell Stem Cell, 11, 477-490.
28. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.