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The quantifications of corresponding M/L ratios showing (Doxo+KSR1)/Control or (Etop+KSR1)/Control from two datasets were evaluated and then compared to provide a complete proteomic repertoire.
We generate a high-confidence dataset for each species, and use it to test whether PPIs are in fact co-located: six publicly available PPI datasets were evaluated and integrated, while SCL information was obtained from Gene Ontology (GO) annotations in UniProt.
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The proposed MBD dataset is evaluated and the MBD-driven ECM process is outlined.
In addition 4 experimental dataset are evaluated and the raw data can be found in Gene Expression Omnibus database [18].
Completeness and accuracy of submitted datasets were evaluated to be 99.0% (1259/1272) and 94.0% (2159/2296) respectively for Hospital A, and 99.3% (1589/1600) and 96.1% (2444/2542) for Hospital B. The majority of accuracy discrepancies pertained to medical history data.
Meta-analysis of tumors from breast cancer patients obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets were evaluated for levels of BST-2 expression and for tumor aggressiveness.
Association between gene expression of the GIPC1 KD signature and each clinical variable in the breast and ovarian cancer datasets were evaluated using globaltest [27].
To our knowledge, the number (32) of real experimental datasets we analyzed is much larger than those analyzed by previous methodological studies: Two experimental datasets were evaluated for the ibmT [ 20] method and one was for the shrinkT [ 23] method.
The interaction datasets were evaluated by co-expression frequency of interacting genes and similarity between gene ontology terms BP (Biological Process) and CC (Cellular component).
Performances for all algorithms with different datasets were evaluated using two worker nodes.
When evaluating the effect of point density, the metrics derived from the thinned datasets were evaluated against the metrics obtained from the original data.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com