ArticleBMC bioinformatics2009
BASE--2nd generation software for microarray data management and analysis.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed.
- Assessment of early response biomarkers in relation to long-term survival in patients with HER2-negative breast cancer receiving neoadjuvant chemotherapy plus bevacizumab: Results from the Phase II PROMIX trial.International journal of cancer · 2018Trial
- Efficient arsenic metabolism--the AS3MT haplotype is associated with DNA methylation and expression of multiple genes around AS3MT.PloS one · 2013Trial
- Clinical associations of ESR2 (estrogen receptor beta) expression across thousands of primary breast tumors.Scientific reports · 2022Article
- Daily Rhythms of TNFα Expression and Food Intake Regulate Synchrony of Plasmodium Stages with the Host Circadian Cycle.Cell host & microbe · 2018Article
- Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.The British journal of surgery · 2018Article
- Hypoxia regulates global membrane protein endocytosis through caveolin-1 in cancer cells.Nature communications · 2016Article
- Article
- SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.International journal of environmental research and public health · 2015Article
- The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine.Genome medicine · 2015Article
- Systemic Monocytic-MDSCs Are Generated from Monocytes and Correlate with Disease Progression in Breast Cancer Patients.PloS one · 2015Article
- Article
- VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.Nucleic acids research · 2015Article
- STATegra EMS: an Experiment Management System for complex next-generation omics experiments.BMC systems biology · 2014Article
- Data management strategies for multinational large-scale systems biology projects.Briefings in bioinformatics · 2014Review
- A digital repository with an extensible data model for biobanking and genomic analysis management.BMC genomics · 2014Article
- Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.BMC genomics · 2013Article
- N-6-adenine-specific DNA methyltransferase 1 (N6AMT1) polymorphisms and arsenic methylation in Andean women.Environmental health perspectives · 2013Article
- Djeen (Database for Joomla!'s Extensible Engine): a research information management system for flexible multi-technology project administration.BMC research notes · 2013Article
- Polymorphisms in iron homeostasis genes and urinary cadmium concentrations among nonsmoking women in Argentina and Bangladesh.Environmental health perspectives · 2013Article
- XperimentR: painless annotation of a biological experiment for the laboratory scientist.BMC bioinformatics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2.
resultsThe new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE.
conclusionBASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.
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Registered trials
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.