FAQ

General information
Can I use NetGO with my own experimental data?
Do I have to install a software?
The homepage is very slow, what should I do?

General information

NetGO is a free, on-line software tool to display the complex genomic abnormalities in individual cancers in the biological framework of the Gene Ontology (GO) processes. For visualization, the main network currently contains 1,928 GO biological processes as nodes and 2,565 connections, representing the biological relationships among the nodes. Each node can be further extended to reveal its sub-network.

The current version can take up to 3 different data types (examples used in the paper are DNA mutation, DNA copy number and gene expression data). The user have the options to determine how to map the user defined “abnormal” genes of an individual sample to the GO processes by choosing hyper-geometric statistics to calculate the enrichment significance level or not to use statistics at all. This latter option may be appropriate when only a small number of alterations are loaded and each has experimentally or therapeutically proven functional role. For mutation date we provide three types of mapping options that the user can select, (i) calculate enrichment using hyper geometric p-values (most appropriate for large scale whole exome sequence data); (ii) assign pathway activity if at least one gene in the pathway harbors a known functionally activating mutation (most appropriate for data from targeted sequencing of hot spot mutations) and (iii) the approach used in Boca et al.

A color scheme defines the extent of molecular disturbance in a node. Gray indicates that a node has no significant genomic anomalies in that patient. Blue indicates that only one type of molecular data shows abnormalities. Purple indicates disturbances in two types of data. Red indicates disturbances in all three data types. Users can click on a colored node to reveal actual gene level disturbances details of sub-networks.

Can I use NetGO with my own experimental data?

Yes. On the main page you can upload your data in a tab-delimited text file. The file must contain four columns: Entrez ID of the genes, and 3 columns of genomic data. The first line in the file has to contain the types of the genomic data, and the second line must contain the mapping option to be used. These are:

For the genomic data accepted values are: You can use this template to prepare your own file. An Excel version is also available, but before uploading to the website save it in .txt format. Once uploaded, the new file will be added to the sample dropdown menu, but only you will be able to access it. You will also have an option to dowload the calculated p values in a tab-delimited text file. Your data will be stored for 48 hours.

(Please note: cookies must be enabled for uploading a new sample.)

Do I have to install a software?

No. All necessary software are installed on the server computer. You only need a compatible web browser:

The homepage is very slow, what should I do?

The most probable reason is slow internet connection. Please use the Speedtest application to determine your connection speed. We suggest to use a terminal with a connection speed over 5M.