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Throughout this paper, the genes containing those intra-gene SNPs are called "S-genes", which means "sequencing-level genes".
DAVID 6.7 [ 82, 83] was used to determine the enriched functional groups, based on GO terms, within the complete list of expressed genes containing those genes with Flybase orthologs.
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From an entirely different angle, [ 21] provided an approach that screened genomic sequences against a database of putative regulatory motifs, evaluating the contribution of the occurrences of the motif on the gene expression by comparing the expression profiles of genes containing this motif against those that do not.
In each random sample, the genes containing the TE insertions, and those metabolites which are synthesized at a reduced rate due to these insertions were determined.
The relevant genes contain the code for proteins that interact with the heart muscle.
Fourty six (46) genes contained the consensus.
However, LANA is recently reported not a general processivity factor, as only those genes containing SRE elements can be activated by LANA [47].
Further we inspected the pattern of intron positions for those genes containing introns.
Only those genes containing more than one PPR repeat were taken into account.
This gene set was finalized by filtering out those genes containing one exon, which were supported only by the transcriptome and EST-derived data.
This can be explained as those genes containing large number of domains are more likely to be grouped into duplicated genes while using lower identity criterion (e.g. >10) compared to genes containing fewer domains.
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