Tutorial 1

Anni 2 .0 Tutoria l: Analyzing a mi croarrray da tasetVersion 1.0The in put f ileIn this exampl e, we will u se a set of genes that are significantl y up or down regulated following agonistic sti mulation of the androgen receptor in a prostate cancer cell line. The androgen receptor is a transcription factor, activated by the androgens testosterone and dihy drotestosterone. The androgen receptor is responsible for developm ent and main tenance of the function of the norma l prostate and for growth of earl y stage pro state cancer. Illustration 1 s hows the input file in a s preadsheet program. In this case, the input file contains three columns, with various infor mation about the genes. Please note that this format is not compulsory! You can specif y any columns y ou want, a s long as at least one colu mn contains identifiers, s uch as names, or in this case Entrez-Gene identif iers, that can be u sed to identif y the concepts (in this case all concepts are genes). The file is saved as a tab- delimited text file, and Illustration 1: The input file, shown in a s preadsheet is availab le on the Bioseman tics.org website. program.Importing t he file i nto An niClick the import concepts button as shown in Illustration 2 to open the import dialog.Illustration 2: Click the import button to load the file in AnniNext, click the load button, select the file and click open. The file is now loaded into the table. Anni now needs to know which concepts belong ...