Description Usage Details Value Source Examples
The species corresponding to an Ensembl gene identifier can typically be identified from the prefix of the identifier (e.g. ENSBTAG corresponds to Bos taurus). This table maps each known unique prefix to the corresponding species.
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C. elegans, D. melanogaster, and S. cerevisiae have atypical identifier pattern and prefixes in their Ensembl gene identifiers. However, the automatically extracted prefix for C. elegans and D. melanogaster – respectively "WBgene" and "FBgn" – can be used as such to identify datasets from those species. On the oher hand, prefixes used for the S. cerevisiae include "YHR", "YAL", and many others. Consequently, expression data from S. cerevisiae species is identified without referring to the "prefix2dataset"" table; instead, such datasets are identified if the first gene identifier in the dataset starts with "Y".
A data frame with 69 rows and 4 columns. Each row refers to one dataset in the Ensembl BioMart. The columns are described below:
dataset
contains the biomaRt dataset name.
species
contains the corresponding species name.
prefix
contains the corresponding unique prefix.
sample
contains a sample Ensembl gene identifier from this
dataset.
The prefix2dataset.build
method stored in the toolkit.R
script was used to query the Ensembl BioMart server and build this table.
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