- Enter a name for the analysis run.
- Select the species from the available options based on the genomes in Ensembl.
- Select the format of gene/protein values from the available options based on formats supported by UniProt. This identifier format is later used for comparison with the format of input network.
- Specify the time-course fold change data as a matrix of values or as three groups of genes partitioned by their time of highest fold change and scored as per their fold change values.
- If TimeXNet Web is given a matrix of log fold change values over multiple time points, it first classifies the time points into 3 groups – early, intermediate and late. It then assigns each gene/protein to one of the three groups depending on the time at which it shows the highest fold change value. Each gene/protein is also assigned a score as the ratio of its fold change and the average fold change of all gene at all time points.
- The three groups of genes/proteins and their scores can also be directly given to TimeXNet Web as input in a single file specifying groups 1, 2 or 3, or in 3 separate files, one for each group. Each gene must be present only in one group.
- The user can provide a customized molecular interaction network along with the gene/protein identifier format used. If the identifier format is different from that used in the input gene/protein list, TimeXNet Web converts both the identifier formats to UniProt using the Ensembl BioMart web service.
- The user can also choose to use an in-built protein-protein interaction network provided by HitPredict as input, which is currently available for 12 model organisms. In this case, the user specified identifiers will also be converted to UniProt.
On average, TimeXNet Web requires 3-5 minutes to predict one response network from an input network of approximately 130,000 edges and an input list of approximately 1600 genes/proteins. The run-time increases with the size of the input network and the number of input genes.
- Single gene network: the table on the left lists all the genes from the predicted network, and the graph on the right shows the nodes that connect to the selected gene from the table.
Single gene network can show a maximum of 100 nodes in the graph. If the node limit is not reached, you may click "Add nodes" to display additional nodes, which are linked to the nodes that connect to the selected gene.
- Multi-gene networks: the graph shows the nodes that connect to the genes listed in the select box.
By default, the top two genes with the highest flows from the predicted network are selected. You may add more genes by typing the name of the gene in the select box. You may also remove an unwanted node by clicking the 'x' on the left of the displayed gene. Multi gene network can show a maximum of 500 nodes in the graph.
The enrichment analysis can be performed using the input network or the whole genome as the background. In networks that require conversion from gene names or Ensembl Protein IDs to UniProt IDs, TimeXNet Web may be slow due to the excess time required for format conversion, since the DAVID web service does not allow these two formats as input. Additionally, our testing shows that the DAIVD web service requires a longer time to return enrichment analysis results when a background gene list is provided.
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Genome Research 2003 Nov; 13(11):2498-504.
KEGG: Kyoto Encyclopedia of Genes and Genomes. Kanehisa M, Goto S. Nucleic Acids Res. 2000; 28:27–30.
DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis. Jiao X, Sherman BT, Huang DW, Stephens R, Baseler MW, Lane HC, Lempicki RA. Bioinformatics 2012 doi:10.1093/bioinformatics/bts251.
Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Luo W, Brouwer C. Bioinformatics 2013; 29(14):1830-1831. doi:10.1093/bioinformatics/btt285.