NexGenEx-Tom: A gene expression platform to investigate the functionalities of the tomato genome

BMC Plant Biology

Volumn 15, Issue 1, 2015, Pages

  Bostan, Hamed ^a   Chiusano, Maria Luisa ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

Expression Atlas; Gene expression comparison; Gene expression profiling; NGS data analysis; Tomato expression database

Indexed keywords

TRANSCRIPTOME;

COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; INTERNET; PLANT GENOME; TOMATO;

DATABASES, GENETIC; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; LYCOPERSICON ESCULENTUM; SOFTWARE; TRANSCRIPTOME;

EID: 84924028481     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-014-0412-2     Document Type: Article

References (46)

1. Jimenez-Lopez JC, Gachomo EW, Sharma S, Kotchoni SO. Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases. Am J Mol Biol. 2013;3:115.
2. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet. 2009;11:31-46.
3. Leinonen R, Sugawara H, Shumway M. The sequence read archive. Nucleic Acids Res. 2011;39:D19-21.
4. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, et al. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res. 2007;35:D760-5.
5. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17:10-2.
6. Andrews S: FastQC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 2010.
7. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644-52.
8. Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012;28:1086-92.
9. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9.
10. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
11. Anders S: Analysing RNA-Seq data with the DESeq package. Molecular biology 2010:1-17
12. Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc. 2013;8:1765-86.
13. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451-5.
14. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nat Genet. 2006;38:500-1.
15. Boria I, Pesole G, Mignone F. NGS TREX: next generation sequences transcriptome profile explorer. EMBnet journal. 2012;18:93.
16. Coletta A, Molter C, Duqué R, Steenhoff D, Taminau J, De Schaetzen V, et al. InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. Genome Biol. 2012;13:R104.
17. Forsberg R, Mønsted S, Hein AM: CLC Bio Integrated Platform for Handling and Analysis of Tag Sequencing Data. Tag-Based Next Generation Sequencing (eds M Harbers and G Kahl), Wiley-VCH Verlag GmbH and Co KGaA, Weinheim, Germany 2011:393-405.
18. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178-92.
19. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, et al. The generic genome browser: a building block for a model organism system database. Genome Res. 2002;12:1599-610.
20. Nussbaumer T, Kugler KG, Bader KC, Sharma S, Seidel M, Mayer KF. RNASeqExpressionBrowser-A web interface to browse and visualize high-throughput expression data. Bioinformatics. 2014;30:2519-20.
21. Fernández XM, Birney E: Ensembl Genome Browser. In Vogel and Motulsky's Human Genetics. Springer Berlin Heidelberg; 2010: 923-939
22. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12:996-1006.
23. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, et al. The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 2007;35:D883-7.
24. Grant D, Nelson RT, Cannon SB, Shoemaker RC. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2009;38:D843-846.
25. Hirsch CD, Hamilton JP, Childs KL, Cepela J, Crisovan E, Vaillancourt B, Hirsch CN, Habermann M, Neal B, Buell CR: Spud DB: A resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding. The Plant Genome 2014, 7
26. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562-78.
27. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621-8.
28. Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, et al. Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One. 2013;8:e61005.
29. Jamie A, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson SA, et al. An RNA-Seq based gene expression atlas of the common bean. BMC Genomics. 2014;15:866.
30. Consortium TG. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485:635-41.
31. Consortium PGS. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475:189-95.
32. Kim S, Park M, Yeom S-I, Kim Y-M, Lee JM, Lee H-A, et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet. 2014;46:270-8.
33. Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H: Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World. DNA Research 2014:1-12.
34. Zhong S, Fei Z, Chen Y-R, Zheng Y, Huang M, Vrebalov J, et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. 2013;31:154-9.
35. Fei Z, Joung J-G, Tang X, Zheng Y, Huang M, Lee JM, et al. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res. 2011;39:D1156-63.
36. Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, et al. The SOL Genomics Network. A comparative resource for Solanaceae biology and beyond. Plant Physiol. 2005;138:1310-7.
37. Suresh BV, Roy R, Sahu K, Misra G, Chattopadhyay D. Tomato Genomic Resources Database: An Integrated Repository of Useful Tomato Genomic Information for Basic and Applied Research. PLoS One. 2014;9:e86387.
38. Fruhwirt P, Huber M, Mulazzani M, Weippl ER. Innodb database forensics. In: Advanced Information Networking and Applications (AINA), 2010 24th IEEE International Conference on; 20-23 April 2010. Perth, Western Australia: IEEE; 2010. p. 1028-36.
39. Bayer R: The universal B-tree for multidimensional indexing: General concepts. In. Mathematisches Institut und Institut für Informatik der Technischen Universität München: Springer; 1997: 198-209
40. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal. 2012;6:1621-4.
41. Trim Galore [ http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ]
42. A Python framework to work with high-throughput sequencing data, Bioinformatics, in print, online at doi:10.1093/bioinformatics/btu638 2014.
43. Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database. 2011;2011:030.
44. Seo S: A review and comparison of methods for detecting outliers in univariate data sets. University of Pittsburgh, Pennsylvania, Graduate School of Public Health, Biostatistics; 2006.
45. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009;25:288-9.
46. Chiusano ML, D'Agostino N, Traini A, Licciardello C, Raimondo E, Aversano M, et al. ISOL@: an Italian SOLAnaceae genomics resource. BMC Bioinformatics. 2008;9:S7.