DisGeNET data have been aggregated according to origin and level of curation into CURATED (expert-curated associations obtained from UniProt and CTD human datasets), PREDICTED (containing human GDAs inferred from mouse and rat models, i.e. CTD mouse and CTD rat datasets, and RGD and MGD datasets), and ALL.
We aggregated the data according to their type and level of curation: CURATED (expert-curated associations obtained from UniProt and CTD human datasets), PREDICTED (containing human GDAs inferred from CTD mouse and CTD rat datasets, and from RGD and MGD data), and ALL.
We find that PhosphOrtholog increases the coverage of conserved phosphorylation sites between human-rat MS experiments by 136 % and 148 % in the two example human-rat datasets and maps novel MS-based modification sites seamlessly between target species.
Out of 72 human datasets, only 38 passed non-specific filtering, whereas 24 out of 82 mouse and 18 out of 35 rat datasets passed the filtering and were used for the analysis.
The results of this analysis are given in the Additional files 4, 5 and 6: Differential expression of the BDNF gene in human, mouse and rat datasets.
In summary, 299 subsets were obtained from 38 human, 24 mouse and 18 rat datasets.
The level of differential expression between pre- vs. post- estrogen treatment was calculated for each of the human and OVX rat datasets.
This was suggested by the mouse study, in comparison with Illumina, and the rat kidney comparison with qRT-PCR data, although fold changes of gene expression in the rat datasets were comparable with those from Illumina and Operon arrays.
The 100% of MDEGs (164 genes) are found in mice datasets, the 28.6% (47 genes) are found in human, the 25% (41 genes) in yeast and the 55.5% (91 genes) in rat datasets.
Among 18 rat datasets, 11 datasets were related to neurological diseases (spinal cord injury, addiction, epilepsy, aging, ischemia etc), 5 datasets were with "normal tissue samples" composition and 2 datasets examined heart diseases [see Additional file 2: Microarray datasets].
In the rat datasets, the minimal Illumina-Operon pairwise correlations were all greater than 0.8 for all strain comparisons (Table 1).
