The datasets were obtained from Oncomine, and eligible datasets were selected as outlined in Figure 2. Two were eliminated for potentially having overlapping data with a previously identified dataset [ 5, 35].
Ingenuity analysis showed that the acute phase response pathway is enriched in the identified dataset with 29 proteins from the pathway seen (see Fig. 5), however only CRP showed the expected difference between outcomes consistent with this pathway taking into account p value alone (Table 2).
However, in absence of a reference homolog, we putatively selected the most prominent contig [GenBank CABF01020060], the longest among the identified dataset (43.7 kb), which significantly covered the length of the other contigs as the putative duplication source locus and utilized it as such for most of the analyses performed in this study.
In order to be included in our study, a dataset was required to (1) be generated from human tumors, (2) compare primary tumors versus distant metastatic tumors, (3) have at least one significant gene with a Q-value < 0.1, and (4) not include samples that overlapped with those of another identified dataset.
The NDI is a fully identified dataset held by the Australian Institute of Health and Welfare (AIHW) which contains mortality records (date, State, and causes of death) collected from each of the State and Territory Births, Deaths and Marriage Registers across Australia.
Using the proteomics workflow described above, over 150,000 peptides were identified (Dataset S1, entire file available at Dryad, Ly et al., 2014), corresponding to 10,929 unique protein groups, over 10,000 of which were detected with two or more peptides.
Use Case II: The DataTank: Once the data of the four pilots was identified and catalogued in Micka or CKAN, it was necessary that some datasets were converted in different formats, as not all identified datasets were geospatial ones.
The first round of data requests, primarily via e-mail, to acquire many of the identified datasets showed significant potential.
The identified datasets were searched for data relevant to the quality of access indicators previously selected.
The breakdown of persons surveyed is displayed in table 4. The three identified datasets were searched for questions related to the use of primary healthcare services.
All relevant experimental literature is critically assessed to identify datasets for testing our model.
