However, variable names would have been manually harmonised either before submitting the datasets to the wizard or in the wizard itself.
We submitted the entire GC dataset of 45,232 proteins (average length 1100 +/− 1134 bp) and the 7782 putative KN sequences to KEGG for annotation, which assigned KO (KEGG orthology group) numbers to 7184 GC and 2657 KN polypeptide sequences, respectively.
In order to assess the benefit of the presented experimental setup, we submitted the mass spectrometric datasets of a previous study conducted in our lab [3] and the present study to the same search and filtering parameters for a comparable amount of MudPIT runs.
In a study of Jacobs, van den Berg and Vosman: Comparison of Chloroplast DNA and AFLP data from Solanum section Petota reveals incongruencies between the datasets, submitted, the incongruencies found between the chloroplast data and the AFLP data suggest that hybridization occurs between species of different series in section Petota.
ML, LMcC and WLC carried out the sequencing reactions, the bioinformatics analyses of the FGAS dataset, and submitted the data to Genbank.
The transcriptome data of T. chinensis cells were submitted in the datasets of Gene Expression Omnibus (GEO) (accession number GSE28539).
Then, a Fisher's exact test was used to check for significant over-representation of GO terms in the submitted dataset against the remaining ones from the Mus musculus genome.
The submitted exemplary dataset represents the first fully functional (independent of vendor software) MS imaging dataset that is publically available and that can be used freely for subsequent reprocessing and interpretation (the original publication [ 14] should be referenced in this case).
Eleven genes from the submitted expression dataset (CD3G, HPSE, TFAP2A, COL1A1, STMN1, CD19, GADD45B, MTA3, TFPI, ATM, EGFR) met the threshold p-value of 0.05 (actual p-values range from 4.64 × 10-4 to 3.30 to 10-2), so are classified in this high-level category by IPA.
By enabling the use of custom software on submitted datasets, the repository becomes more than a passive silo for data, actively enabling depositors and viewers to interact with datasets in a rich, domain-specific way.
