Video Tutorial

Watch this short video for a tour of the ESCAPE web interface.

Database design

Relationships between the tables in the database are described by the following entity relations diagram.
Description of the tables is available in the Browse the Download sections.

Networks

This page generates a network from one or several large background networks. It takes a list of genes you provide as seed genes and identify all interacting genes that fall on paths through the background networks between them.
The three background networks used were created from the Interactions from Chip-sep/chip table, the Logof interactions table and from the Protein protein interactions table of ESCAPE database

Instructions

  1. Specify your gene list. This is a list of primary human entrez gene symbols which will be used to find interacting nodes.
  2. Select the background network to use for generating the network.
  3. Select the path length. This is the number of steps to search to find intermediate nodes on paths connecting the seed nodes. A value of 1 will only return connections between seed nodes.
  4. Select filtering options for the background dataset. Remove low quality interactions from the background dataset by removing interactions from high throughput experiments or interactions without enough evidence.

Enrichment analysis

This page does enrichment analysis with list of genes generated from the ESCAPE database. It takes a list of genes you provide and compare it statistically with background generated lists.
The background lists used were created from the Interactions from Chip-sep/chip table, the Logof interactions table of ESCAPE database. The statistical test used is a righ-tailed Fisher test. You can either paste a list of source genes and obtain the most probable targets that these genes regulate or you can paste a list of target genes and obtain the most probable source genes that regulates them. In addition, for the Logof interactions table, you can choose the sign of the interaction: up-regulation, down-regulation or both.

Troubleshooting

Network not showing?

If you don't see the network when using the network generator, make sure that you have flash installed. The Flash plug-in is freely available from Adobe.

Any questions and suggestions

Please, contact us if you have any questions or suggestions.