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In the refined transcript list, there are 204 gene products with a GO term in the cellular component category.
Indeed since the time of initial probe design on most microarrays, updated genome assemblies and refined transcript structures based on data sources such as full length cDNAs, CAGE (short cap analysis of gene expression sequences) and diTags [ 9] have made updated probeset annotation critically important.
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Importantly, the expression of a number of selected novel or refined transcripts including putative lncRNAs was verified experimentally in bovine skin and in several bovine tissues.
An initial list of codes was then generated and grouped into defined themes and sub-themes, which were then reviewed, refined and transcripts were labelled or 'indexed' [ 26, 27].
The analysis was thus cumulative and iterative, with each focus group building on the discussions of the proceeding group (e.g. focus group interview questions and components of the osteoporosis tool design were modified and refined for transcripts of subsequent focus groups) until themes were saturated.
Furthermore, we were able to detect novel bovine genes and to refine known transcript loci, the structure of which was not completely annotated in the bovine reference genome assembly.
FlyBase plans to refine their transcript confidence to include support from comparative genomics, proteomic analyses, and to potentially provide details on the magnitude and quality of each type of support.
Codes were refined as needed and transcripts were checked to ensure that coded data reflected the refined codes.
During gastrula stages, blastoporal expression is no longer detected, however, Pf-nodal transcripts are refined to an ectodermal domain (Fig. 3L).
As data collection and analysis progressed, a coding frame was devised, tested and adjusted, and once refined applied to the transcripts using qualitative analysis software (NVivo7, 31).
The delimitation of exons available for these genomes was refined by comparison with available transcript sequences.
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