Table 3.
Association of functionally important variants and likely oncogenic variants with response to Indian natural products
| NSC number | Gene | Variant | p-value | t-statistic | # of cell lines with variant | # of cell lines without variant | Mean logGI50 with variant | Mean logGI50 without variant | Prevalence in 1000 Genomes | SNP Type | OncoKB level | OncoKB annotation | FDR adjusted p-value | INP name |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 112166 | MET | T992I | 0.0000368 | -4.782802 | 3 | 47 | -5.806500 | -5.703000 | 0.01 | Missense | NA | Likely Oncogenic | 0.0027367 | Cucurbitacin K |
| 112167 | MET | T992I | 0.0006802 | -3.743424 | 3 | 47 | -6.801167 | -6.709511 | 0.01 | Missense | NA | Likely Oncogenic | 0.0243927 | Elatericin B |
| 308606 | BRAF | V600E | 0.0000006 | -6.134195 | 9 | 41 | -7.159667 | -6.693878 | 0.00 | Missense | 1 | Oncogenic | 0.0000742 | Cucurbitacin D |
| 328426 | KDR | C482R | 0.0019152 | -3.308867 | 3 | 56 | -8.222667 | -7.909268 | 0.01 | Missense | NA | Likely Oncogenic | 0.0414968 | Phyllanthoside |
| 643160 | MET | T992I | 0.0001938 | 4.076171 | 3 | 44 | -4.000000 | -4.145977 | 0.01 | Missense | NA | Likely Oncogenic | 0.0089764 | 3-Bromo-4-dimethylamino-alpha-benzoyl cinnamonitrite |
| 710351 | KDR | C482R | 0.0017855 | 3.286695 | 3 | 55 | -4.000000 | -4.137891 | 0.01 | Missense | NA | Likely Oncogenic | 0.0406327 | Achilleol A |
| 710351 | MET | T992I | 0.0017855 | 3.286695 | 3 | 55 | -4.000000 | -4.137891 | 0.01 | Missense | NA | Likely Oncogenic | 0.0406327 | Achilleol A |
| 717335 | MET | T992I | 0.0000616 | -4.338376 | 3 | 55 | -7.993333 | -7.741146 | 0.01 | Missense | NA | Likely Oncogenic | 0.0042724 | Tylophorin |
| 717335 | KNSTRN | A40E | 0.0017579 | -3.300053 | 7 | 51 | -7.954286 | -7.726725 | 0.06 | Missense | NA | Likely Oncogenic | 0.0406327 | Tylophorin |
| 731920 | KNSTRN | A40E | 0.0007237 | -3.790673 | 7 | 42 | -4.671286 | -4.511429 | 0.06 | Missense | NA | Likely Oncogenic | 0.0250871 | Calendulaglycoside B-6'-O-butyl ester |
| 731921 | KDR | C482R | 0.0014349 | -3.902824 | 3 | 48 | -5.905667 | -5.644375 | 0.01 | Missense | NA | Likely Oncogenic | 0.0406327 | Calendulaglycoside D2 |
| 731922 | KDR | C482R | 0.0017287 | -3.535183 | 3 | 47 | -5.191333 | -5.088383 | 0.01 | Missense | NA | Likely Oncogenic | 0.0406327 | Calendulaglycoside D-6'-O-methyl ester |
| 731922 | KNSTRN | A40E | 0.0010801 | -3.482230 | 7 | 43 | -5.183857 | -5.080023 | 0.06 | Missense | NA | Likely Oncogenic | 0.0351046 | Calendulaglycoside D-6'-O-methyl ester |
NSC INP NSC number, Gene Gene name, Variant Sequence variant, p-value original p-value (prior to adjustment for multiple testing) from the Student’s t-test comparing the mean logGI50 values in those cell lines that had each variant to those that were not reported to have the variant, t-statistic value from the Student’s t-test comparing the mean logGI50 values in those cell lines that had each variant to those that were not reported to have the variant, # of cell lines with variant Number of NCI-60 cell lines which had that variant according to information from CellMiner, # of cell lines without variant number of NCI-60 cell lines which were not reported to have that variant according to data from CellMiner, Mean logGI50 with variant Average logGI50 value in NCI-60 cell lines that had the variant, Mean logGI50 without variant average logGI50 value in NCI-60 cell lines not reported to have the variant, Prevalence in 1000 Genomes Frequency of the variant in the 1000 Genomes dataset, according to CellMiner, OncoKB level Highest level of evidence for the variant across tissues according to the OncoKB annotation; OncoKB annotation, OncoKB classification as oncogenic or likely oncogenic, FDR adjusted p-value, p-value (adjusted for multiple testing) from the Student’s t-test comparing the mean logGI50 values in those cell lines that had each variant to those that were not reported to have the variant; INP name, name of the Indian natural product