View - ResearchGate

62 Gonye et al.(http://www.tm4.org) is used for cluster analysis. After clustering is performed,save each cluster table into a separate text file. Copy the gene lists from each fileinto a single column in a spread sheet, one file at a time. Each time, add a clusterlabel (e.g., A, B, C, and so on) in a second column for all the gene identifiers thatare copied from a single cluster table. An example file namedexGeneClusterInfo.txt containing cluster information in the specified formatis available online at http://www.dbi.tju.edu/dbi/publications/MiMBchapter/.3.2.2. Combining Cluster Membership Information With TRNA1. Follow the steps in Subheading 3.1.2. until step 17.2. After step 17, click the Browse button for the parameter Gene cluster informationfile to locate and select the exGeneClusterInfo.txt file.3. Click the Execute Feasnet Analyzer/Viewer button at the end of the form. A newpage will be loaded indicating the status of the analysis.4. Once the analysis and visualization is complete, the highlighted status text at thetop of the page will be replaced by a link to the compressed file containing all theresults including the status page.5. The results from the overrepresentation analysis are under the headings Significanceof TRE occurrence (in clusters compared with a reference) and Significance ofTRE occurrence (in individual clusters compared with the list). Links to thespecific reference used, p-values for overrepresentation, and the Feasnet images areprovided. Under the subheading Hypothesis Gene-TRE network, links are providedto the filtered Feasnet data and images based on the specified p-value threshold(0.10 in step 17). Network image and Graphviz source file are also given. Refer toNotes 4.7 for information on how to interpret the PAINT results.4. Notes4.1. Selection of Gene IdentifiersA key issue that is often underappreciated is that of gene identifiers used inTRNA. Typically, if the gene list is derived from a microarray data set, then themost convenient and proper gene identifiers to use in PAINT are the correspondingClone IDs or Genbank accession numbers. PAINT uses UniGene databaseto map the Clone IDs to the corresponding Entrez gene IDs (used to be namedLocusLink) and then utilize the Ensembl cross-reference annotation informationto obtain the corresponding unique set of Ensembl gene IDs. BecauseUniGene annotation is regularly updated and given that UniGene cluster IDsare not guaranteed to be stable across different UniGene releases, the use ofUniGene IDs as gene identifiers is not permitted in TRNA using PAINT. Incases wherein the gene list is manually derived from previous knowledge ofregulation, for example, all genes implicated in a particular cellular function,then the most convenient and proper gene identifiers to use in PAINT are thecorresponding Entrez gene IDs.