This tool makes comparisons between an input pattern of interest (including expression of a gene or microRNA, activity of a drug, or any pattern of interest) and i) gene expression, ii) microRNA expression, iii) and drug activity levels. Start by selecting the "Pattern comparison" tool shown, and one of the six possible types of input, "Gene transcript", "microRNA", "Drug NSC#", "Protein RPPA", "Protein SWATH" or "60-element pattern". Input your identifier(s) in "Step 2", using a gene, microRNA, drug or pattern. The first three of these are the same gene expression levels, drugs activity levels, and microRNA expression levels, described above. The forth option is to input any pattern across the NCI-60 that is of interest to the user. A "Pattern comparison template file" for this option is accessible for download in the Step 1 footnotes.
The output is returned as a single Excel spreadsheet file that includes three pages. The first page contains the "Significant" results where the outputs are based on statistical significance (p <0.05) in the absence of multiple comparisons correction. The second page contains "All" the results and the third page contains the pattern of the input identifier. The footnotes are in a seperate spreadsheet. The "Significant" and "All" pages contain the same 10 blocks of results; "Drug activities", "Genetic variants: Amino acid changing", "Genetic variants: Protein function affecting", "DNA Methylation", "DNA gene copy number", "Gene transcript levels (microarrays)", "mircoRNA levels", "Protein: RPPA levels", "Protein: SWATH levels" and "Miscellaneous phenotypic parameters". Only three of the blocks of data and a few of the top rows for an input of CNBP transcript expression are shown. The data used for the correlation calculations for the is the same as what you see in more detail in the "Cell line signatures" tools. Details are provided in as a separate Excel "footnotes" output.
| Table 1: Significant correlations between the selected input pattern and several parameters a | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Drug activities | Gene transcript levels (microarray) | Protein: RPPA levels | ||||||||||||
| Correlations | P-value | NSC number | Name | Mechanism | FDA Status | Correlations | P-value | Gene Symbol | Correlations | P-value | Gene symbol | Antibody | ||
| 0.555 | 0.000005 | 658145 | 2-(2-(dimethylamino)ethylamino)naphthazarin | - | - | 1 | 0.000000 | CNBP | 0.417 | 0.000927 | TIGAR | TIGAR:TIGAR | ||
| 0.566 | 0.000076 | 156215 | streptovaricin b | - | - | 0.815 | 0.000000 | MRPL3 | 0.407 | 0.001255 | GSK3B | GSK3B | ||
| 0.467 | 0.000167 | 355063 | granatomycin a | - | - | 0.784 | 0.000000 | PIK3R4 | 0.38 | 0.002784 | COPS5 | JAB1:COPS5 | ||
| 0.468 | 0.000189 | 109874 | Benzimate | Tu | Clinical trial | 0.774 | 0.000000 | QTRTD1 | 0.378 | 0.002925 | SRSF1 | SF2:SRSF1 | ||
| 0.467 | 0.000193 | 658274 | - | - | - | 0.762 | 0.000000 | NAA50 | 0.377 | 0.002951 | BECN1 | BECLIN:BECN1 | ||
| 0.456 | 0.000253 | 658870 | 1,8-naphthyridin-4(1h)-one, 2-phenyl- | - | - | 0.747 | 0.000000 | CCDC58 | 0.366 | 0.003976 | RAB11A | RAB11:RAB11A | ||
| 0.478 | 0.000258 | 756765 | ;(trans-1,2-Cyclohexanediamine)(dihydrogen pyrophosphato... | - | - | 0.728 | 0.000000 | ZNF330 | 0.36 | 0.004670 | PIK3R1 | PI3KP85:PIK3R1 | ||
| ... | ... | ... | ||||||||||||