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The confident set of common candidate genes between the two independent studies strongly suggests that they may have essential roles in breast cancer metastasis.
Using several stringent statistical selection criteria and filtering steps on probe sets (exons) and meta-probe sets (transcripts), we obtained a confident set of 2623 candidate genes that undergo isoform or whole gene expression variations specific to metastatic characteristics.
Therefore, it is possible that the segmental dataset represents an even more confident set of relocated retrogenes.
Thus, -fold values >2 represented a reasonable biological threshold to identify a confident set of SUMO-enriched proteins.
In general, ITRAQ values of >2 were taken to indicate significant changes in SUMOylation states, leading to a confident set of 710 proteins.
Table S1 contains processed ITRAQ data with subsections that lists stepwise, process followed to delineate the confident set of 710 proteins.
Similar(44)
This severely limits their utility for use case #2 above, as it strips out one of the key advantages of syntenic analysis, the ability to identify confident sets of "true negatives".
Based on a literature survey of immunity related genes, a significant fraction (∼4.8%) of the confident set could be directly linked to proteins known to be involved in immune function, inclusive of phagocytosis.
Therefore, we first evaluate the subcaptions, which is our most confident set, with the reported number of panel labels.
A small subset of the confident set was validated by in-bacto SUMOylation and shown to be bona-fide SUMO targets.
For the global analyses, the confident set was used.
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