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About 7% of the RNA-Seq reads could be matched to multiple locations in the genome.
The NCDR holds information about all tumours diagnosed in England, allowing matching of NSCCG cases diagnosed with multiple cancers to be matched to multiple records.
In addition to these 224 annotated tags, our list of differentially expressed tags also includes 99 tags that could be matched to multiple genes, and 109 tags that were differentially expressed but could not be mapped to any known gene (data not shown).
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For those instances where one RNAi screen was matched to multiple KEGG pathways or GO terms, we considered these pathways or terms as one general function matched to the screen.
If a subset of peptides was matched to multiple proteins, the protein that was supported by the most peptides over the eight mass spectrometric measurements was selected as the representative.
If peptides were matched to multiple members of a protein family, or if a protein appeared under different names and accession numbers, the entry with the highest score was selected.
When the peptides were matched to multiple members of a protein family, or a protein appeared under same names and accession number, the match was considered in terms of a higher Mascot score, the putative function and differential patterns on 2-DE gels.
There were also several cases where a given RefSeq ID was matched to multiple Ensembl IDs.
If at any stage a record was matched to multiple records, these were reviewed to identify the strongest match.
TFs which were matched to multiple canonical motifs were also observed due to multiple DBDs or have DBDs with alternative conformational states.
When the identified peptides were matched to multiple members of a protein family or a protein appeared under the same name and accession number, the match was made in terms of the higher Mascot score, the putative function and the differential patterns of the protein spots on the 2-D DIGE gels.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com