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A list of the 38 study factors requested with the data submissions is included in Table 1.
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Genomics data submissions were easier to review when integrated into a standard toxicology report format.
A guidance on Pharmacogenomic Data Submissions was issued by the FDA in March 2005[ 54].
Although this potentially leaves the databases susceptible to accusations of poor coding quality, 24 25 the HES data submissions are regularly cleaned and monitored for data quality and consistency.
Data submissions are accepted from individual researchers, groups and consortia, whereas we also actively gather data sets from various public sources.
All tiers include healthy cell lines as well as cancerous ones, and all data submissions are also subdivided based on the cellular compartments in which measurements were performed.
All accession numbers from external databases such as GEO, SRA and ArrayExpress, referring to the technology platforms used and the data submissions are similarly stored under 'External data source' and 'External data source accession' reserved tags.
While microarray data submissions are encouraged by regulatory agencies and widely accepted in toxicogenomic research [ 2, 13], the third phase of the microarray quality control project (MAQC-III also known as SEQC) recommended further validation using different study designs [ 1, 25].
At the conclusion of our vetting process (i.e. approval by the data submitter), a data submission is considered 'released'released
During the period of this study, while all MTCs submitted data to TARN, data submission is not always complete.
The data submission is then processed by the PRIDE team, and a "PXD identifier" is issued for each dataset.
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