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All datasets containing annotation files that did not include gene symbols for at least 90% of the probes present in the data were removed.
The above data set [see Additional file 7: BED format files, some with extra columns containing annotation] was the basis for overlap queries following filtering performed with bedops, followed by Fisher's exact tests or logistic regression modelling in R. For example, TPM-annotated promoters were filtered by TPM >1 to generate the subset of expressed promoters.
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This method is evaluated using the QUWI database, which is the only available public dataset containing annotations regarding gender, age range, and nationality.
This method is evaluated using the QUWI database, which is the only publicly available dataset containing annotations regarding gender, age range, and nationality.
Following the experimental setup employed by Rocktäschel et al. [16] in evaluating their ChemSpot tool, we trained a CRF model on the SCAI training corpus containing annotations for systematic names.
A file containing annotations for the Mouse 430_2 array was downloaded from Affymetrix.
Surprisingly, amongst the recovered sequences for the Rd.HMM, those containing annotations were soluble inorganic pyrophosphatases.
Annotation summary reports in the form of a spreadsheet containing annotations for all 47 publications were generated regularly from the Phenoscape Knowledgebase to review annotation consistency.
The output from the analyses are Genbank files containing annotations.
The online database containing annotations of cDNA transcripts with exonized L1 sequences [ 22] is a read-only version of the annotation system.
The regulation of sex-specific gene expression was represented by two clusters, one containing annotations for alternative splicing and the other for RNA editing.
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