These credible SNP sets were then annotated for putative function based on transcript location (refseq gene annotation) and localization to ENCODE features (H3K4Me1, H3K4Me3, H3K27Ac, DNase I hypersensitivity and transcription factor ChIP-Seq clusters) using Annovar42.
It is important to note that the exome library used for capture in the ESP study is based on RefSeq transcript annotation.
Cufflinks were used to reconstruct transcript based on genome annotation, and then the transcripts were merged by cuffmerge.
We identified three HMGR transcripts based on KEGG annotation, one of which was more highly expressed in the main root body than in lateral roots, as observed by Kim et al. [ 47].
Based on a larger transcript annotation set (Refseq [15], UCSC [16] and Ensembl genes [17]), among the 185,233 tested RefSeq introns, 13,759 introns contain at least one conditional exon.
The numbers of read tags aligning to each gene were extracted using a custom python script producing a matrix of counts with regions based on the Ensembl transcript annotation (version 66).
However, to ensure the robustness of our results, we also generated two higher confidence sets of promoters: a "high quality" set of 9898 promoters based on FlyBase transcript evidence annotations and a "cap-supported" set of 5389 promoters in which all transcripts have their 5' ends accurately mapped based on cDNA isolation using a 5' cap-dependent method (see Methods).
There was a higher rate redundancy amongst annotated Oases transcripts, although this assembly included representation of over 2000 more unique transcripts (based on the annotation against the Ensembl zebrafish database).
Based on the annotation results, transcripts encoding all of the known enzymes involved in ginsenoside biosynthesis and modification were identified in our dataset.
Based on genome annotation and the transcript profiles of cultures grown in the presence and absence of PAA, the entire homogentisate pathway, which ultimately leads to the formation of fumarate and acetoacetate, could be mapped.
