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

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Lenzi, Luca ^a   Facchin, Federica ^a   Piva, Francesco ^b   Giulietti, Matteo ^b   Pelleri, Maria C ^a   Frabetti, Flavia ^a   Vitale, Lorenza ^a   Casadei, Raffaella ^a   Canaider, Silvia ^a   Bortoluzzi, Stefania ^c   Coppe, Alessandro ^c   Danieli, Gian A ^c   Principato, Giovanni ^b   Ferrari, Sergio ^d   Strippoli, Pierluigi ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

^c UNIVERSITY OF PADOVA   (Italy)

^d UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CALCULATION; CELL DIFFERENTIATION; CHROMOSOMAL LOCALIZATION; COMPUTER PROGRAM; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCATION; GENE MAPPING; GENETIC DATABASE; HEMATOPOIETIC STEM CELL; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; MEGAKARYOCYTE; NONHUMAN; PHENOTYPE; QUANTITATIVE ANALYSIS; BIOLOGICAL MODEL; BIOLOGY; CLUSTER ANALYSIS; COMPUTER INTERFACE; DATA BASE; GENE EXPRESSION PROFILING; INTERNET; METHODOLOGY;

DANIO RERIO;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; INTERNET; MODELS, BIOLOGICAL; USER-COMPUTER INTERFACE;

EID: 79951559163     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-121     Document Type: Article

References (41)

1. Michalak P. Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 2008, 91:243-248. 10.1016/j.ygeno.2007.11.002, 18082363.
2. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voûte PA, Heisterkamp S, van Kampen A, Versteeg R. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 2001, 291:1289-1292. 10.1126/science.1056794, 11181992.
3. Lercher MJ, Urrutia AO, Hurst LD. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31:180-183. 10.1038/ng887, 11992122.
4. Lee JM, Sonnhammer EL. Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 2003, 13:875-882. 10.1101/gr.737703, 430880, 12695325.
5. Yamashita T, Honda M, Takatori H, Nishino R, Hoshino N, Kaneko S. Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes. Genomics 2004, 84:867-875. 10.1016/j.ygeno.2004.08.008, 15475266.
6. Nei M. Genome evolution: let's stick together. Heredity 2003, 90:411-412. 10.1038/sj.hdy.6800287, 12764410.
7. Yi G, Sze SH, Thon MR. Identifying clusters of functionally related genes in genomes. Bioinformatics 2007, 23:1053-1060. 10.1093/bioinformatics/btl673, 17237058.
8. Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AH. The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res 2003, 13:1998-2004. 10.1101/gr.1649303, 403669, 12915492.
9. Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G. Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 2004, 5:151. 10.1186/1471-2105-5-151, 528725, 15488149.
10. Coppe A, Danieli GA, Bortoluzzi S. REEF: searching REgionally Enriched Features in genomes. BMC Bioinformatics 2006, 7:453-460. 10.1186/1471-2105-7-453, 1624853, 17042935.
11. Diacovo TG, de Fougerolles AR, Bainton DF, Springer TA. A functional integrin ligand on the surface of platelets: intercellular adhesion molecule-2. J Clin Invest 1994, 94:1243-1251. 10.1172/JCI117442, 295209, 8083366.
12. Tunnacliffe A, Majumdar S, Yan B, Poncz M. Genes for beta-thromboglobulin and platelet factor 4 are closely linked and form part of a cluster of related genes on chromosome 4. Blood 1992, 79:2896-2900.
13. Italiano JE, Patel-Hett S, Hartwig JH. Mechanics of proplatelet elaboration. J Thromb Haemost 2007, 5:18-23. 10.1111/j.1538-7836.2007.02487.x, 17635704.
14. Vainchenker W, Bouguet J, Guichard J, Breton-Gorius J. Megakaryocyte colony formation from human bone marrow precursors. Blood 1979, 54:940-945.
15. Deshmukh L, Tyukhtenko S, Liu J, Fox JE, Qin J, Vinogradova O. Structural insight into the interaction between platelet integrin alphaIIbbeta3 and cytoskeletal protein skelemin. J Biol Chem 2007, 282:32349-32356. 10.1074/jbc.M704666200, 17804417.
16. Chen Z, Shivdasani RA. Regulation of platelet biogenesis: insights from the May-Hegglin anomaly and other MYH9-related disorders. J Thromb Haemost 2009, 7:272-276. 10.1111/j.1538-7836.2009.03425.x, 19630815.
17. Wong ET, Jenne DE, Zimmer M, Porter SD, Gilks CB. Changes in chromatin organization at the neutrophil elastase locus associated with myeloid cell differentiation. Blood 1999, 94:3730-3736.
18. Fuhrken PG, Chen C, Apostolidis PA, Wang M, Miller WM, Papoutsakis ET. Gene Ontology-driven transcriptional analysis of CD34+ cell-initiated megakaryocytic cultures identifies new transcriptional regulators of megakaryopoiesis. Physiol Genomics 2008, 33:159-169. 10.1152/physiolgenomics.00127.2007, 18252802.
19. Ferrari F, Bortoluzzi S, Coppe A, Basso D, Bicciato S, Zini R, Gemelli C, Danieli GA, Ferrari S. Genomic expression during human myelopoiesis. BMC Genomics 2007, 8:264-283. 10.1186/1471-2164-8-264, 2045681, 17683550.
20. Giammona LM, Fuhrken PG, Papoutsakis ET, Miller WM. Nicotinamide (vitamin B3) increases the polyploidisation and proplatelet formation of cultured primary human megakaryocytes. Br J Haematol 2006, 135:554-566. 10.1111/j.1365-2141.2006.06341.x, 17054670.
21. Tenedini E, Fagioli ME, Vianelli N, Tazzari PL, Ricci F, Tagliafico E, Ricci P, Gugliotta L, Martinelli G, Tura S, Baccarani M, Ferrari S, Catani L. Gene expression profiling of normal and malignant CD34-derived megakaryocytic cells. Blood 2004, 104:3126-3135. 10.1182/blood-2003-07-2597, 15271793.
22. Fuhrken PG, Chen C, Miller WM, Papoutsakis ET. Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation. Exp Hematol 2007, 35:476-489. 10.1016/j.exphem.2006.10.017, 17309828.
23. Guglielmelli P, Zini R, Bogani C, Salati S, Pancrazzi A, Bianchi E, Mannelli F, Ferrari S, Le Bousse-Kerdilès MC, Bosi A, Barosi G, Migliaccio AR, Manfredini R, Vannucchi AM. Molecular profiling of CD34+ cells in idiopathic myelofibrosis identifies a set of disease-associated genes and reveals the clinical significance of Wilms' tumor gene 1 (WT1). Stem Cells 2007, 25:165-173. 10.1634/stemcells.2006-0351, 16990584.
24. Neumann F, Teutsch N, Kliszewski S, Bork S, Steidl U, Brors B, Schimkus N, Roes N, Germing U, Hildebrandt B, Royer-Pokora B, Eils R, Gattermann N, Haas R, Kronenwett R. Gene expression profiling of Philadelphia chromosome (Ph)-negative CD34+ hematopoietic stem and progenitor cells of patients with Ph-positive CML in major molecular remission during therapy with imatinib. Leukemia 2005, 19:458-460. 10.1038/sj.leu.2403615, 15618956.
25. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
26. Sohal D, Yeatts A, Ye K, Pellagatti A, Zhou L, Pahanish P, Mo Y, Bhagat T, Mariadason J, Boultwood J, Melnick A, Greally J, Verma A. Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration. PLoS One 2008, 3:e2965. 10.1371/journal.pone.0002965, 2495035, 18698424.
27. Mar JC, Kimura Y, Schroder K, Irvine KM, Hayashizaki Y, Suzuki H, Hume D, Quackenbush J. Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics 2009, 10:110. 10.1186/1471-2105-10-110, 2680405, 19374774.
28. Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S. MACAT--microarray chromosome analysis tool. Bioinformatics 2005, 21:2112-2113. 10.1093/bioinformatics/bti183, 15572464.
29. Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, Behm FG, Raimondi SC, Relling MV, Patel A, Cheng C, Campana D, Wilkins D, Zhou X, Li J, Liu H, Pui CH, Evans WE, Naeve C, Wong L, Downing JR. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 2002, 1:133-143. 10.1016/S1535-6108(02)00032-6, 12086872.
30. Luo J, Schumacher M, Scherer A, Sanoudou D, Megherbi D, Davison T, Shi T, Tong W, Shi L, Hong H, Zhao C, Elloumi F, Shi W, Thomas R, Lin S, Tillinghast G, Liu G, Zhou Y, Herman D, Li Y, Deng Y, Fang H, Bushel P, Woods M, Zhang J. A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. Pharmacogenomics J 2010, 10:278-291. 10.1038/tpj.2010.57, 2920074, 20676067.
31. Pignatelli M, Serras F, Moya A, Guigó R, Corominas M. CROC: finding chromosomal clusters in eukaryotic genomes. Bioinformatics 2009, 25:1552-1553. 10.1093/bioinformatics/btp248, 19389737.
32. Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 2009, 25:2730-2731. 10.1093/bioinformatics/btp472, 2759552, 19654113.
33. Kim J, Chung HJ, Park CH, Park WY, Kim JH. ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics. Bioinformatics 2004, 20:1191-1192. 10.1093/bioinformatics/bth052, 14764551.
34. D'Addabbo P, Lenzi L, Facchin F, Casadei R, Canaider S, Vitale L, Frabetti F, Carinci P, Zannotti M, Strippoli P. GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers. Bioinformatics 2004, 20:2883-2885.
35. Lenzi L, Frabetti F, Facchin F, Casadei R, Vitale L, Canaider S, Carinci P, Zannotti M, Strippoli P. UniGene Tabulator: a full parser for the UniGene format. Bioinformatics 2006, 22:2570-2571. 10.1093/bioinformatics/btl425, 16895929.
36. TRAM home page. , http://apollo11.isto.unibo.it/software/
37. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, 37:D885-890. 10.1093/nar/gkn764, 2686538, 18940857.
38. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2007, 35:D26-31. 10.1093/nar/gkl993, 1761442, 17148475.
39. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2010, 38:D5-16. 10.1093/nar/gkp967, 2808881, 19910364.
40. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2009, 37:D755-761. 10.1093/nar/gkn875, 2686463, 18996895.
41. Quackenbush J. Microarray data normalization and transformation. Nat Genet 2002, 32:496-501. 10.1038/ng1032, 12454644.