SNP-Trait Association

Running this process using the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the SNP-Trait Association process description for more information. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on. that facilitate your analysis.

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Summary Chart: When there are multiple annotation groups (chromosomes or genes, for example), this tab displays the number of significant markers in each annotation group for each test. Separate bar charts are shown for each BY group when any BY variables are specified. This tab is open by default.

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Manhattan Plot: When there are multiple annotation groups (chromosomes or genes, for example), this tab displays a scatter plot of the p-values across all annotation groups.

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Annotation Group Results: When there are multiple annotation groups (chromosomes or genes, for example), a separate Results tab with an overlay plot of p-value by chromosome location is created for each annotation group. If the Calculate trend odds ratios check box was checked, this tab also contains a Volcano Plot of p-value by log odds ratio for all markers.

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All P-Value Plots: When there are multiple annotation groups (chromosomes or genes, for example), the All P-Value Plots tab shows all the p-value plots from the Annotation Group Results tabs in a single display.

Note: When an annotation group variable is not specified or there is only one annotation group, the tab is named P-Value Plot and contains an overlay plot of p-value by chromosome location for all markers.

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All Trends Odds Ratio Plots: : If the Calculate trend odds ratios check box was checked and there are multiple annotation groups (chromosomes or genes, for example), this tab shows all the odds ratio volcano plots.

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Volcano Plot(s): This tab displays a scatter plot of p-value by the Estimate of Minor Allele Genotype Effect for all markers, colored by Annotation Group, when the trend test is performed. When the Output genotype LS means and diffs check box is checked, this tab includes scatter plots of p-value by the LS diffs between genotypes 0 and 1, and genotypes 0 and 2.

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Create Subset Genotype and Annotation Data Sets: Select points from the p-value plots and click Create Subset Genotype and Annotation Data Sets to open the Subset and Reorder Genetic Data process to create the subset data sets.

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GenBank Nucleotide: Select points or rows and click GenBank Nucleotide to opens a browser window directed to a GenBank Nucleotide search for the selected molecular entities.

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UniGene Database: Select points or rows and click UniGene Database to access information from the Unigene database for selected genes or markers

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AceView Database: Select points or rows and click AceView Database to access information from the ACEView database for selected genes or markers.

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dbSNP: Select points or rows and click dbSNP to open a browser window directed to an NCBI dbSNP search for the pair of SNPs associated with the particular instance of this button.

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Plot Trait by Genotype: Select markers from the p-value plots and click Plot Trait by Genotype to view each marker's genotype distribution for each of the Trait Variables values.

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View Venn Diagram of Significant Markers by Trait for the Test Below: Click either Genotype or Trait to view a Venn diagram showing significant association between markers and multiple traits as determined by the specific association test.

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Select Markers in Graphs or Linked Tables, then Click to View Survival Curves: Select the desired points/rows from either a p-value, a Manhattan Plot, or a volcano plot and then click either Genotype or Trend to view the Survival Curves for each of the selected points as determined by the specific association test.

Note: This option is available only when Survival is specified as the Type of Trait and the Output survival function estimates for viewing survival curves check box is checked.

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Genotype Residual Data Set: This data set contains input data set merged with columns of residuals from each genotype test model (each SNP, for example) and is generated when the Genotype test is performed and the Output residuals from every model check box is checked. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _org. Click Open to view the data set.

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Genotype LSMeans and Differences Data Set: This data set contains the LS means and diffs estimates and associated statistics for each regression model and is generated when the Output genotype LS means and diffs check box is checked. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _lsm. Click Open to view the data set.

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Genotype Parameter Estimate Data Set: This data set contains the estimates and test statistics for the fixed effects included in each regression model testing for association, including the marker genotype treated as a categorical variable, and is generated when the Genotype test is performed. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _peg. Click Open to view the data set.

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Genotype Covariance Parameter Estimate Data Set: This data set contains the estimates for the covariance parameters (random effects) included in each regression model testing for association, including the residual. This data set is generated when the Genotype test is performed and random effects are specified. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _cpg. Click Open to view the data set.

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Genotype Survival Function Data Set: This data set contains the survival function estimates for each individual from each model (each SNP, for example). This data set is used for plotting the survival curves with the Genotype action button when one or markers are selected from the p-value or volcano plots. This data set is generated when the Genotype test is performed with a survival trait and the Output survival function estimates for viewing survival curves check box is checked. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _sfg. Click Open to view the data set.

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Trend Residual Data Set: This data set contains input data set merged with columns of residuals from each trend test model (each SNP, for example). This data set is generated when the Trend test is performed. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _ort. Click Open to view the data set.

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Trend Parameter Estimate Data Set: This data set contains the estimates and test statistics for the fixed effects included in each regression model testing for association, including the numeric marker genotype treated as a continuous variable, and is generated when the Trend test is performed. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _pet. Click Open to view the data set.

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Trend Covariance Parameter Estimate Data Set: This data set contains the estimates for the covariance parameters (random effects) included in each regression model testing for association, including the residual. This data set is generated when the Trend test is performed and random effects are specified. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _cpt. Click Open to view the data set.

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Trend Survival Function Data Set: This data set contains the survival function estimates for each individual from each model (each SNP, for example). This data set is used for plotting the survival curves with the Trend action button when one or markers are selected from the p-value or volcano plots. This data set is generated when the Trend test is performed with a survival trait and the Output survival function estimates for viewing survival curves check box is checked. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _sfa. Click Open to view the data set.

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P-value Data Set: This data set contains all the columns from the annotation data set, plus the test statistics and p-values from the tests performed. This data set can be used as the annotation data set for subsequent processes to accumulate results from multiple processes into a single data set. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _sta. Click Open to view the data set.