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. [. . . ] If you click on (FASTA) the sequence appears in FASTA format in a new window. RefSeq Prot The ID is from the NCBI Reference Sequence database of comprehensive, non-redundant protein sequences. If you click on (FASTA) the sequence appears in FASTA format in a new window. 3 One-Click Gene SummaryTM (continued) Summary A short paragraph summarizing what is known about the function of the gene (from LocusLink). Gene Ontologies Gene OntologyTM terms for the gene (from LocusLink). Each term is hyperlinked to show the GO hierarchy. KEGG Pathways A link to the Kyoto Encyclopedia of Genes and Genomes (KEGG). It provides pathway information for gene products. PubGene Link to the PubGeneTM Network Browser providing a tool to explore both literature and sequence co-association networks (from PubGeneTM Web database and Tools). Additional Search Features: - Perform Sequence Analysis blastn, blastx and primer design tools - Search PubMed Use either the Gene ID(default) or enter another term to search PubMed. - Search for Homologs Search within other projects for homologous genes. 3 BLAST® Analysis A BLAST search can be performed on any gene sequence within the secure GeneSifter environment. 1. 2. Click on a gene from the results list of either pairwise or project analysis. At the bottom of the One-Click Gene Summary window, click on Perform Sequence Analysis. A new window will open with the selected sequence pasted in a form ready for BLAST analysis. Select the type of BLAST search to perform (blastn or blastx) from the buttons at the bottom left corner of the window. To determine suitable primers for a selected nucleotide sequence, there is a link to primer3, again with the sequence already loaded into the application. 3. 1 4. Note: Use blastn to BLAST the sequence directly against a nucleotide database. Use blastx to BLAST against a protein database. The latter works by translating your nucleotide sequence in all six reading frames (three for each direction) and blasting each result against the protein database. 2 3 4 Ontology Report The Ontology Report is available for any gene list created in GeneSifter. In a gene list from either Pairwise or Project analysis, select the link for Ontology Report in the upper right corner. 1. Gene Ontology (GO) terms are divided into three general categories. The default display will be the Biological Process ontologies. To see the report for either Cellular Component or Molecular Function, select the appropriate link. You can view the data as an Ontology Report or Z-score Report. Summarizes GO terms for genes in the list (see number 5-8 for additional details). [. . . ] Project Gene Title allows the user to select whether gene titles or accession numbers are displayed in the project analysis gene lists. 6 8 7 Preferences Analysis Preferences (continued) Heatmap Figure 9 , 9a Heatmap Figure graphically displays gene regulation in gene lists. The colors are modulated by the Color Scheme under General preferences. · Number Each Row If the option is selected, each row of the Heatmap figure will be consecutively numbered. Open In New Window Upon clicking "View As Image" in the project results page, the Heatmap figure will be opened in a new browser window. [. . . ]