Pattern comparison

A systems biology tool that allows easy comparison of an input pattern to gene expression, microRNA expression, and drug

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 five possible types of input, "Gene transcript", "microRNA", "Drug NSC#", "Protein RPPA", 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 9 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" 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
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