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Lenzi L, Facchin F, Piva F, et al. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics. 2011;12:121doi: 10.1186/1471-2164-12-121.
Lenzi, L., Facchin, F., Piva, F., Giulietti, M., Pelleri, M. C., Frabetti, F., Vitale, L., Casadei, R., Canaider, S., Bortoluzzi, S., Coppe, A., Danieli, G. A., Principato, G., Ferrari, S., & Strippoli, P. (2011). TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC genomics, 12121. https://doi.org/10.1186/1471-2164-12-121
Lenzi, Luca, et al. "TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources." BMC genomics vol. 12 (2011): 121. doi: https://doi.org/10.1186/1471-2164-12-121
Lenzi L, Facchin F, Piva F, Giulietti M, Pelleri MC, Frabetti F, Vitale L, Casadei R, Canaider S, Bortoluzzi S, Coppe A, Danieli GA, Principato G, Ferrari S, Strippoli P. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics. 2011 Feb 18;12:121. doi: 10.1186/1471-2164-12-121. PMID: 21333005; PMCID: PMC3052188.
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BMC Genomics. 2011 Feb 18;12:121. doi: 10.1186/1471-2164-12-121.

TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources.

BMC genomics

Luca Lenzi, Federica Facchin, Francesco Piva, Matteo Giulietti, Maria Chiara Pelleri, Flavia Frabetti, Lorenza Vitale, Raffaella Casadei, Silvia Canaider, Stefania Bortoluzzi, Alessandro Coppe, Gian Antonio Danieli, Giovanni Principato, Sergio Ferrari, Pierluigi Strippoli

Affiliations

  1. Center for Research in Molecular Genetics Fondazione CARISBO, Department of Histology, Embryology and Applied Biology, University of Bologna - Via Belmeloro, 8 - 40126 - Bologna, Italy.

PMID: 21333005 PMCID: PMC3052188 DOI: 10.1186/1471-2164-12-121

Abstract

BACKGROUND: Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input.

RESULTS: TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified.

CONCLUSIONS: TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes.

References

  1. Nat Genet. 2002 Jun;31(2):180-3 - PubMed
  2. J Clin Invest. 1994 Sep;94(3):1243-51 - PubMed
  3. BMC Bioinformatics. 2004 Oct 15;5:151 - PubMed
  4. Exp Hematol. 2007 Mar;35(3):476-489 - PubMed
  5. Leukemia. 2005 Mar;19(3):458-60 - PubMed
  6. Physiol Genomics. 2008 Apr 22;33(2):159-69 - PubMed
  7. J Thromb Haemost. 2009 Jul;7 Suppl 1:272-6 - PubMed
  8. Bioinformatics. 2006 Oct 15;22(20):2570-1 - PubMed
  9. BMC Bioinformatics. 2009 Apr 19;10:110 - PubMed
  10. Genome Res. 2003 Sep;13(9):1998-2004 - PubMed
  11. Blood. 1992 Jun 1;79(11):2896-900 - PubMed
  12. PLoS One. 2008 Aug 13;3(8):e2965 - PubMed
  13. Bioinformatics. 2004 May 1;20(7):1191-2 - PubMed
  14. Bioinformatics. 2009 Oct 15;25(20):2730-1 - PubMed
  15. Bioinformatics. 2007 May 1;23(9):1053-60 - PubMed
  16. Genomics. 2004 Nov;84(5):867-75 - PubMed
  17. J Thromb Haemost. 2007 Jul;5 Suppl 1:18-23 - PubMed
  18. Cancer Cell. 2002 Mar;1(2):133-43 - PubMed
  19. Br J Haematol. 2006 Nov;135(4):554-66 - PubMed
  20. Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16 - PubMed
  21. Bioinformatics. 2009 Jun 15;25(12):1552-3 - PubMed
  22. Bioinformatics. 2004 Nov 1;20(16):2883-5 - PubMed
  23. Stem Cells. 2007 Jan;25(1):165-73 - PubMed
  24. J Biol Chem. 2007 Nov 2;282(44):32349-56 - PubMed
  25. Nucleic Acids Res. 2009 Jan;37(Database issue):D885-90 - PubMed
  26. Blood. 2004 Nov 15;104(10):3126-35 - PubMed
  27. Genome Res. 2003 May;13(5):875-82 - PubMed
  28. Nucleic Acids Res. 2007 Jan;35(Database issue):D26-31 - PubMed
  29. Bioinformatics. 2005 May 1;21(9):2112-3 - PubMed
  30. Nucleic Acids Res. 2009 Jan;37(Database issue):D755-61 - PubMed
  31. Blood. 1979 Oct;54(4):940-5 - PubMed
  32. Bioinformatics. 2003 Jan 22;19(2):185-93 - PubMed
  33. Nat Genet. 2002 Dec;32 Suppl:496-501 - PubMed
  34. Pharmacogenomics J. 2010 Aug;10(4):278-91 - PubMed
  35. BMC Bioinformatics. 2006 Oct 16;7:453 - PubMed
  36. Blood. 1999 Dec 1;94(11):3730-6 - PubMed
  37. Science. 2001 Feb 16;291(5507):1289-92 - PubMed
  38. Heredity (Edinb). 2003 Jun;90(6):411-2 - PubMed
  39. BMC Genomics. 2007 Aug 03;8:264 - PubMed
  40. Genomics. 2008 Mar;91(3):243-8 - PubMed

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