No probesets met the high stringency of a false-discovery correction for multiple comparisons.
In T47D cells, the LOF of four genes met the high-stringency criterion 1 (BCR2L1, BCR, ATP5A1, and ACTN4), and six additional genes met the lower-stringency criterion 2 (BIRC2, PDPK1, PIP5K1C, FGFR4, SRC, and RIOK3).
In SKBR3, the LOF of only two genes met the high-stringency criterion (BIRC2 and ACTN4), and the LOF of one additional gene (BCL2L1) met the lower-stringency criterion 2. Overall, this suggests that BCL2L1, BIRC2, and ACTN4 are potentially major regulators of TRAIL-induced caspase-3/7 in breast cancer and that their LOF has the potential to overcome resistance to TRAIL-induced cytotoxicity.
Comparisons of genes based on gene ontology (GO) to examine enrichments in the two datasets (all genes that were two-fold regulated by light and all genes whose light regulation met the q ≤ 0.2 stringency requirement) showed overall similar correspondences in GO terms for the top classes (Table S10), with unclassified genes missing in the q ≤ 0.2 set.
More patients met the individual criterion for the RMDQ (32.4%) showing how a composite measure adds more stringency to sole reliance on disability measures.
Of the suggestive male cis eQTLs that met the LOD>3.0 threshold, 73% met the LOD 4.3 threshold cutoff, while only 13% of the trans eQTLs were maintained at this LOD stringency.
Of the suggestive female cis eQTLs that met the LOD>3.0 threshold, 71% met the LOD 4.3 threshold cutoff, while only 8.6% of the female suggestive trans eQTLs were maintained at this LOD stringency, again indicating the relative strength of the cis eQTLs compared to the trans eQTLs.
All subjects met identical methodological stringency criteria, and the comprehensive clinical details have been described in our previous work [ 12– 14, 29].
Unlike FLNB, HIC1 and ZNF189 did not fully meet our stringency criterion for replication, despite being the top two genes associated with iCP in TRIMM analyses of the Norwegian triads.
The genes for hypermethylated in cancer 1 (HIC1) and zinc finger protein 189 (ZNF189) did not fully meet our stringency criterion for replication (both methods detecting associations in both populations).
