What “omics” technologies can be used with NetDecoder?
NetDecoder was designed to analyze transcriptomic data from platforms such as microarray or RNA-seq. However, any scores derived from “omics” technologies that could be mapped to a gene interaction pair in an interaction network can be used. In the current version of NetDecoder, the human iRefIndex interaction network is available.
Can I use RNA-seq with NetDecoder?
Yes, you can!
What are sources and sinks?
Sources are starting points for searching paths of molecular interactions through the interactome. Sinks are the end point of paths starting at the sources.
Can I define my own sources and sinks?
Yes, you can provide sources as a gene list in a text file. See our NetDecoder tutorial and our paper for detailed instructions. By default, sinks are defined as genes containing transcription-related annotations although it is also possible to upload a list of genes to be used as sinks or define one or more Gene Ontology (GO) categories of your preference. Genes under these GO categories will be defined as sinks. We are currently working to update this feature.
I am having problems running NetDecoder from the web site. What should I do?
Problems analyzing your data are likely to come from:
File containing gene lists are not formatted properly