Transcriptome Search: (Transcriptome Search Help Page) The "Transcriptome" for a given patient group is defined as the list of genes that have a P-Value of Detection better than 0.05 in a certain percentage of the samples in that particular patient group. The "Core Transcriptome" for a patient group is the list of genes that have a P-Value of detection better than 0.05 in EVERY one (i.e. 100%) of the patient group's samples. 1.) Retrieve Venn Diagram and Gene List for genes in the: Core Transcriptome (100%) 90% Transcriptome 50% Transcriptome 20% Transcriptome 2.) Select Genes from the different Transcriptomes by Variability Criteria: Restrict Search to the Transcriptome of the following Sample Group: Never Smokers Current Smokers Former Smokers Any Sample Restrict Search to Genes present in % of samples Search Transcriptome Gene Expression by the following parameter: (STD/Mean Expression) x 100% Standard Deviation of Expression Max-Min (Expression Difference) Max/Min (Expression Ratio) Set Threshold: Greater Than Less Than Threshold Value: Restrict Returned Genes by GO Keyword : 3.) Compare the percentage of genes that represent a specified GO Category across the different Transcriptomes generated by the separate smoker classes (Never, Current and Former) Enter GO Category ID to search, e.g. 7155 (cell adhesion): Enter Transcriptome Type to Search: Core 100% Transcriptome 90% Transcriptome 50% Transcriptome The GOMiner Annotation tool (Zeeberg et al.) , analyzes the over/under representation of GO categories in gene lists and generates a graphical display of over- and under-represented GO categories. Download and view the following DAG (Directed Acyclic Graph) files by: Core 100% Transcriptome - DAG file Core 90% Transcriptome - DAG file Core 100% Transcriptome - only Molecular Function - DAG file Core 90% Transcriptome - only Molecular Function - DAG file Core 90% Transcriptome GO Category Summary - only Molecular Function Core 100% Transcriptome GO Category Summary - only Molecular Function Core 90% Transcriptome GO Category Summary Core 100% Transcriptome GO Category Summary To Save Directed Acyclic Graph files follow the following instructions: 1. Right clicking on the Link 2. Selecting the 'Save Target As' option 3. Saving the file to your desktop with an .svg suffix 4. Opening the file by double-clicking the file icon. To view the DAG your browser will need the SVG Viewer plugin. To get the plugin go here.