Mapping Identifiers for the Integration of Genomic Datasets with the R/Bioconductor package biomaRt
Explore this paper's citation graph
Summary
It is demonstrated how to use the computational environment R to integrate and jointly analyze experimental datasets, employing BioMart web services to provide the molecule mappings.
- Type
- article
- Published
- 2009-07-01
- Cited by
- 3,765
- References
- 14
- OpenAlex
- https://openalex.org/W2045949302
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:23104199
Keywords
Ensembl, Bioconductor, Computer science, Identifier, Computational biology
References
- Bioconductor Case Studies
- Analysis of cell-based RNAi screens
- Reactome knowledgebase of human biological pathways and processes
- The HGNC Database in 2008: a resource for the human genome
- NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
- ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression
- A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.
- BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
- EnsMart: a generic system for fast and flexible access to biological data.
- Bioconductor: open software development for computational biology and bioinformatics
- The MYCN oncogene is a direct target of miR-34a
- Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
- NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
Cited by
- The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations
- Modular expression analysis reveals functional conservation between human Langerhans cells and mouse cross-priming dendritic cells
- Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2
- Genetic Drivers of Pancreatic Islet Function
- Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer
- A comprehensive manually-curated compendium of bovine transcription factors
- Hyperacute changes in blood mRNA expression profiles of rats after middle cerebral artery occlusion: Towards a stroke time signature
- A Primer on Data Analytics in Functional Genomics: How to Move from Data to Insight?
- Transcript-level regulation of MALAT1-mediated cell cycle and apoptosis genes using dual MEK/Aurora kinase inhibitor “BI-847325” on anaplastic thyroid carcinoma
- Standardized human bone marrow-derived stem cells infusion improves survival and recovery in a rat model of spinal cord injury.
- Construction and analysis of a diabetic nephropathy related protein-protein interaction network reveals nine critical and functionally associated genes
- edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology.
- MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
- Personalized diagnosis of medulloblastoma subtypes across patients and model systems.
- Études de réseaux d’expression génique : utilité pour l’élucidation des déterminants génétiques des traits complexes
- Evaluation of iTRAQ and SWATH-MS for the Quantification of Proteins Associated with Insulin Resistance in Human Duodenal Biopsy Samples
- Multivariate Statistical Methods for Testing a Set of Variables Between Groups with Application to Genomics
- How complexity increases in development: An analysis of the spatial-temporal dynamics of 1218 genes in Drosophila melanogaster.
- Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine
- Next generation sequencing of sex-specific genes in the livers of obese ZSF1 rats.
Related papers
- Improvements in the protein identifier cross-reference service
- ensembldb: an R package to create and use Ensembl-based annotation resources
- UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation
- rGREAT: an R/bioconductor package for functional enrichment on genomic regions
- gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles
- ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data
- Rtpca: an R package for differential thermal proximity coaggregation analysis
- minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information