FlyAtlas 2: A new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

Nucleic Acids Research

Volumn 46, Issue D1, 2018, Pages D809-D815

  Leader, David P ^a   Krause, Sue A ^a   Pandit, Aniruddha ^a   Davies, Shireen A ^a   Dow, Julian A T ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA;

ADULT; ARTICLE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION; GENE ONTOLOGY; GENETIC TRANSCRIPTION; LARVA; MALE; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; RNA GENE; RNA SEQUENCE; ROOM TEMPERATURE; SEX DIFFERENCE; VALIDATION PROCESS; ANIMAL; COMPUTER INTERFACE; GENETICS; GROWTH, DEVELOPMENT AND AGING; SEQUENCE ANALYSIS; SEXUAL CHARACTERISTICS; WEB BROWSER;

ANIMALS; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION; LARVA; MALE; MICROARRAY ANALYSIS; MICRORNAS; RNA; SEQUENCE ANALYSIS, RNA; SEX CHARACTERISTICS; USER-COMPUTER INTERFACE; WEB BROWSER;

EID: 85040910350     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx976     Document Type: Article

References (14)

1. Chintapalli, V.R., Wang, J. and Dow, J.A.T. (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat. Genet., 39, 715-720.
2. Robinson, S.W., Herzyk, P., Dow, J.A.T. and Leader, D.P. (2013) FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster. Nucleic Acids Res., 41, D744-D750.
3. Reiter, L.T., Potocki, L., Chien, S., Gribskov, M. and Bier, E. (2001) A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster. Genome Res., 11, 1114-1125.
4. Tan, P.K., Downey, T.J., Spitznagel, E.L., Xu, P., Fu, D., Dimitrov, D.S., Lempicki, R.A., Raaka, B.M. and Cam, M.C. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res., 31, 5676-5684.
5. Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
6. Lai, E.C., Tomancak, P., Williams, R.W. and Rubin, G.M. (2003) Computational identifcation of Drosophila microRNA genes. Genome Biol., 4, R42.
7. Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L. and Pachter, L. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cuffinks. Nat. Protoc., 7, 562-578.
8. Dos Santos, G., Schroeder, A.J., Goodman, J.L., Strelets, V.B., Crosby, M.A., Thurmond, J., Emmert, D.B., Gelbart, W.M. and the FlyBase Consortium (2015) FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res., 43, D690-D697.
9. Sun, Z., Evans, J., Bhagwate, A., Middha, S., Bockol, M., Yan, H. and Kocher, J.-P. (2014) CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics, 15, 423.
10. Oliver, B. (2002) Genetic control of germline sexual dimorphism in Drosophila. Int. Rev. Cytol., 219, 1-60.
11. Fagegaltier, D., König, A., Gordon, A., Lai, E.C., Gingeras, T.R., Hannon, G.J. and Shcherbata, H.R. (2014) A genome-wide survey of sexually dimorphic expression of Drosophila miRNAs identifes the steroid hormone-induced miRNA let-7 as a regulator of sexual identity. Genetics, 198, 647-668.
12. Kent, W.J., Sugnet, Furey, C.W., Roskin, T.S., Pringle, K.M., Zahler, T.H., Haussler, A.M. and David. (2002) The Human Genome Browser at UCSC. Genome Res., 12, 996-1006.
13. Baker, B.S. (1989) Sex in fies: the splice of life. Nature, 340, 521-524.
14. Ashburner, M. and Drysdale, R. (1994) FlyBase-the Drosophila genetic database. Development, 120, 2077-2079.