PMC:3475486 / 9079-10659 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3475486","sourcedb":"PMC","sourceid":"3475486","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3475486","text":"Cancer gene and pathway annotation workflow\nAfter acquiring user input, CaGe converts various input gene IDs into standard gene symbols, finds known cancer genes and pathways, links various cancer-related annotations to matched genes, and outputs them in the form of tables or text files through the web interface (Fig. 3). Another function of CaGe is to identify over-represented cancer-related or other biological pathways from the input gene list by performing one-tailed Fisher's exact test.\nWhen processing more than one annotation job, users can manage their annotation tasks through the CaGe interface, and access to their results is maintained by the internal job database of CaGe until the jobs are deleted by the user or by a scheduled cleaning process. The IP addresses of client computers are used for secured job management without a logon process. Completed annotation jobs are listed on the job table, and the annotated results can be shown selectively by the user on the annotation result page or can be downloaded as tab-delimited text files for further analyses. The annotation on the results page has many useful links to gene and cancer-related information in the CaGe database or external public databases. In addition to the cancer gene and pathway annotation function, CaGe provides a function to browse cancer genes and pathways so that users can search cancer-related annotations without an input list. The search flows of cancer genes and pathways are connected to each other by crosslinks in the cancer gene information page or pathway information page.","divisions":[{"label":"Title","span":{"begin":0,"end":43}}],"tracks":[]}