README TRAM 1.3 On December 26, 2017, TRAM 1.3 version replaced the 1.2.1 version. A version with some revisions in the English language was distributed on May 27, 2018. A version for Windows has been released on May 27, 2018. A bug hampering "Export" function (TRAM Home) has been fixed on February 22, 2019. We discourage use of previous versions of the TRAM software that are archived in the site only for historical purposes, having been used in previous articles. However, subsequent changes in the NCBI database format now make them not usable for the Set Up process needed to fill the tool with gene information. A pre-loaded version of TRAM 1.3 is supplied only for H. sapiens (November 2017 data). 1. Import of data about Genes from "NCBI Gene" during TRAM Set Up procedure has been updated to reflect recent availability of the "NCBI Gene" "Tabular" format. This also improved the assignment of the chromosomal "Location" for each gene. 2. A new parameter is available in the "Map" and "Cluster" analyses: "Sample Number", allowing the inclusion in the analysis only of genes having at least "n" values across the analyzed datasets (when dataset number is greater than 1). n=3 is suggested in a typical meta-analysis. 3. A protocol is provided to include all GenBank Accession numbers available for RNA and RefSeq RNA sequences related to a given locus in the "NCBI Gene" database to improve probe assignment to the corresponding locus. See Guide section 1.3, c). 4. A new procedure is provided to assign each probe to the relative locus. Essentially, priority is given to GenBank sequences related to a given locus in the "NCBI Gene" database; if this fails the "Gene Symbol" annotation provided by the platform is used, if this fails the UniGene Cluster ID is used; if there is no way to assign the probe to a locus the GenBank accession itself will be used. If you use this software, please cite: Pelleri MC, Cattani C, Vitale L, Antonaros A, Strippoli P, Locatelli C, Cocchi G, Piovesan A and Caracusi M. Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells Front Genet, April 24, 2018 - https://doi.org/10.3389/fgene.2018.00125 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 12:121, 2011. --- README TRAM 1.2.1 On January 23, 2015, TRAM 1.2.1 version replaced the 1.2 version. A pre-loaded version of TRAM 1.2.1 is supplied only for H. sapiens (June 2013 or January 2015 data). 1. Import of data about Genes from "NCBI Gene" during TRAM Set Up procedure has been updated to reflect recent changes in "NCBI Gene" Summary format. In addition, information about Strand "+" or "-" ("complement") is now processed for each gene, and it is displayed in the TRAM "Genes" Table. 2. The chromosomal Location of each "Segment" in the "Map" Layouts is now displayed if at least one of the genes within the Segment, and not only the first, has a Location assigned to it in the "Genes" Table. 3. A bug causing the display of an error message during the use of the "Help with data" function while preparing gene expression data for the import, or during the "Set Up" of "Platforms", has been fixed. 4. A minor bug hampering the display of the execution time used to "Recalculate" the analysis with different parameters in the "Cluster" Layouts has been fixed. If you use this software, please cite: 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 12:121, 2011. --- README TRAM 1.2 On April 26, 2014, TRAM 1.2 version replaced the 1.1 version. It is again released as a FileMaker Pro 12 template, along with a runtime application able to run "FileMaker Pro" at the core of the software. A pre-loaded version of TRAM 1.2 is supplied only for H. sapiens (June 2013 or April 2014 data). 1. The gene data download procedure has been revised, due to changes of the NCBI format for the "Gene" Entrez database. 2. The mitochondrion genes are now parsed and mapped. However, the corresponding entries were removed from "Chromosomes", "Genes" and "Gene Aliases" TRAM Tables of the pre-loaded version for H. sapiens (2013 or 2014) to avoid mapping errors because no platform included in this version contained probes for human mitochondrion genes. 3. Two new commands: "Export Main Tables" and "Import Main Tables" have been released to import Results into a TRAM (empty) template that may display the results as graphics (see Section 4.3 of the Guide). If you use this software, please cite: 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 12:121, 2011. --- README TRAM 1.1 On June 13, 2013 TRAM 1.1 version ("TRAM 2013") replaced the 1.0.1 version. It is now released as a FileMaker Pro 12 template, along with a runtime application able to run "FileMaker Pro" at the core of the software. 1. The conversion of each probe identifier to the corresponding Gene Symbol has been much improved by implementing conversion of all possible alias symbols of each gene to the corresponding, updated Gene Symbol provided by Entrez Gene. Clone names may be also converted to the corresponding Gene Symbols. 2. A utility useful for automatic download of Gene Expression Omnibus (GEO) sample data is now provided ("GEO_Download" for Macintosh, Windows and UNIX operating systems), along with a detailed protocol for conducting meta-analysis by TRAM. 3. The chromosome data set up procedure has been revised, due to relevant changes of the NCBI format for the "Genome" Entrez database. 4. Improved functions for preparing expression data files ("Help with data" utility): fixing of a bug causing transformation in "1" of lacking expression values when back-transforming logarithmic data, improved automatic removal of the header lines lacking gene expression values and retention of the platform code only in the first line of the final processed text file(s). 5. These warnings have been added to the Guide: "Do not move the "TRAM" folder while the software is open, and run the "TRAM" software from a local hard disk and not from a network drive". "If a TRAM analysis aborts unexpectedly, it is advisable to restart it in a fresh TRAM copy". 6. Removal of previously imported Platforms or Samples has been made more effective and faster. 7. The software documents ("Guide" and "About") are now stored only online, and they are no longer available within the software folders. TRAM can access these documents on line. 8. An updated pre-loaded version (June 2013) is supplied only for H. sapiens. If you use this software, please cite: 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 12:121, 2011.