ArticleBMC genomics2011
TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 4 of them syntheses that pooled it.
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Who cites it
23 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Pooled it
- Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype.Human molecular genetics · 2016Pooled it
- Pooled it
- A quantitative transcriptome reference map of the normal human brain.Neurogenetics · 2014Pooled it
- Gene Expression Studies in Down Syndrome: What Do They Tell Us about Disease Phenotypes?International journal of molecular sciences · 2024Review
- Zinc metabolism and its role in immunity status in subjects with trisomy 21: chromosomal dosage effect.Frontiers in immunology · 2024Article
- The transcriptome profile of human trisomy 21 blood cells.Human genomics · 2021Article
- The Role of Artificial Intelligence in the Diagnosis and Prognosis of Renal Cell Tumors.Diagnostics (Basel, Switzerland) · 2021Review
- Dysregulation of NIPBL leads to impaired RUNX1 expression and haematopoietic defects.Journal of cellular and molecular medicine · 2020Article
- Reference quantitative transcriptome dataset for adultData in brief · 2019Article
- Dataset of differential gene expression between total normal human thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma.Data in brief · 2019Article
- On the length, weight and GC content of the human genome.BMC research notes · 2019Article
- Article
- Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells.Frontiers in genetics · 2018Article
- Network-based co-expression analysis for exploring the potential diagnostic biomarkers of metastatic melanoma.PloS one · 2018Article
- A molecular view of the normal human thyroid structure and function reconstructed from its reference transcriptome map.BMC genomics · 2017Article
- Systematic identification of human housekeeping genes possibly useful as references in gene expression studies.Molecular medicine reports · 2017Article
- Weighted gene co-expression network analysis reveals key genes involved in pancreatic ductal adenocarcinoma development.Cellular oncology (Dordrecht, Netherlands) · 2016Article
- Systematic large-scale meta-analysis identifies a panel of two mRNAs as blood biomarkers for colorectal cancer detection.Oncotarget · 2016Article
- Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral 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.
resultsTRAM (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.
conclusionsTRAM 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.