User manual VIZXLABS GENESIFTER 2005

[. . . ] User's Guide GeneSifter Overview · Login · Upload Tools · Pairwise Analysis · Create Projects For more information about a feature see the corresponding page in the User's Guide noted in the blue circle ( 4 ) . 38 7 63 Scatter Plot Interactive scatter plot provides visualization of the entire array data set and identification of individual genes. Upload Tools Upload microarray data files. Ontology Report Summarize ontology terms for a gene list and assess the biological significance of the genes within the list. 5 33 44 User Login Access your secure account from any computer (PC or Mac) with Internet access. Pairwise Analysis 74 Define two groups and apply normalization, statistical analysis and quality metrics to create lists of differentially expressed genes. One-Click Gene SummaryTM Provides a synopsis of the most current information available for the genes on your array. It includes information from UniGene, LocusLink, Gene Ontology terms and more. 40 Create New Project Create user-defined projects with two or more groups. See next page for project analysis options. Export Results Export data and gene annotation to Excel. GeneSifter Overview · Project Analysis · Filtering · Function Navigation · Pattern Navigation · Clustering 58 Filtering Apply fold change cutoffs, statistical analysis and quality metrics to create lists of differentially expressed genes. 59 63 Ontology Report Summarize ontology terms for a gene list and assess the biological significance of the genes within the list. Clustering Identify patterns of gene expression with unsupervised clustering functions. 62 54 * Cluster Samples Use hierarchical clustering to determine the relationship of samples based on a gene list. 50 Pattern Navigation Define and identify patterns of gene expression with supervised clustering. 52 44 Project Analysis Project analysis functions allow analysis across all conditions in a project. * Function Navigation Rapidly identify and group genes based on function using Gene Ontology terms. Ontology Report, Cluster Samples and the One-Click Gene Summary are available for all types of project analysis. One-Click Gene SummaryTM Includes information from UniGene, LocusLink, Gene Ontology terms and more. GeneSifter Introduction and Login Welcome to GeneSifter, the webbased microarray data management and analysis system, which relies on VizX Labs' BIOMETM bioinformatics software engine. This document gives an overview of some of the features available in Genesifter. [. . . ] Summarizes GO terms for genes in the list (see number 5-8 for additional details). Summarizes the frequency of GO terms listed in summary table (see number 9 for details). 1 3 2 2. 7. Genes link displays the genes in the list that correspond to the current ontology. Ontology Totals: List ­ displays how many genes with the specific ontology term are in the gene list. For pairwise analysis this list is further divided into upregulated (red arrow) and downregulated (green arrow). Array ­ displays how many genes with the specific ontology were measured in the comparison. Typically, this is the number of genes of that specific ontology on the array being analyzed. 5 6 7 8 8. z-score. Indicates whether each GO term occurs more or less frequently than expected. Extreme positive numbers (greater than 2) indicate that the term occurs more frequently than expected, while an extreme negative number (less than -2) indicates that the term occurs less frequently than expected (see number 10 for calculation details). Ontology Report (continued) 9. The pie chart of ontology term distribution is a display of the frequency of GO terms in the summary table. z-score calculation: R = total number of genes meeting selection criteria N = total number of genes measured r = number of genes meeting selection criteria with the specified GO term n = total number of genes measured with the specific GO term 10. 9 10 Z-score Report The Z-score Report is generated from the same data as the Ontology Report. It displays those GO terms that have a z-score greater than 2, or less than -2. In a z-score report generated from a Pairwise analysis, a score is calculated for both up and down-regulated genes. Only one of these scores needs to pass to be included in the cut off. 1 2 1. 2. Click on Z-score Report to list the genes by z-score The default view sorts the terms according to the ontology that is most highly represented within the list. Alternatively, to sort the list by z-score in: a) b) Pairwise - Click on the arrows. Projects - Click on z-score. 3a 3. 3b Pathway Report The Pathway Report is available from any gene list created in GeneSifter by selecting the link for Reports | KEGG. Note: The pathway report is currently available only for human microarrays. The pathway source is from the Kyoto Encyclopaedia of Genes and Genomes (KEGG). The Genes link displays all genes from the list that are associated with the corresponding pathway. The KEGG link displays the corresponding pathway and highlights the appropriate gene(s) from the gene list. Totals: List ­ displays how many genes in the gene list belong to a pathway. For pairwise analysis this list is further divided into up-regulated (red arrow) and down-regulated (green arrow). [. . . ] An additional table will display all data points used in the calculation. In addition to the information in the basic summary, the detailed summary will include the following: · Grp Min - The smallest mean intensity for that condition · Grp Max - The largest mean intensity for that condition · Grp Ave - The mean of all intensities within the condition · Grp Med - The median of all intensities within the condition 5 5a 5b Preferences Analysis Preferences (continued) 6. Row Center Project Data displays data for a selected gene as the intensity for that gene over the mean intensity for that gene across all groups. Quality Cutoff defines whether all groups must pass the selected quality cutoff or just one of the entire set must pass. [. . . ]