Setting up the first analysis
This page introduces you to the various tabs in Evinet and let you get familiar with various tabs and its functionalities available inside EviNet.
- Begin with the project ID and species selection
- Altered Gene sets
- Selecting Network
- Selecting Functional genesets
- Check and Submit
- Interactive Demos
Begin with the project ID and species selection
ALWAYS start from setting your project ID and the organism. Otherwise your analysis might use irrelevant data. Type in project1 to see and try our example files
Altered Gene sets
The whole aim of network enrichment analysis (Alexeyenko et al., 2012) is characterization of certain genes or gene lists.
Hence continue by submitting your altered gene sets (AGS) by either directly pasting gene symbols or by uploading a file with pre-compiled AGS(s) (see below). Finally, the most advanced, dynamic mode of AGS formation is provided via Venn diagrams: see here and here.
Note: uploaded files and text box input can contain the following gene/protein IDs:
Human, mouse, rat:
Gene symbol (HUGO/MGI),
ENSEMBL gene and protein ID,
Swiss-Prot accession number,
TREMBL accession number
These will be converted to standard gene symbols and analyzed against functional gene sets and networks, which are also stored in this format.
Paste gene symbols
Paste your gene symbols in the text box. Currently EviNet only accepts Gene symbols. Examples:TP53, NKX2-2/Nkx2-2, PTCH1/Ptch1.
Upload a file
Once uploaded, a file might remain in your project space
to be re-analyzed later. NOTE: the file should contain at least two columns and you have to specify column roles and the column delimiter. An advantage of using files is that they might contain multiple AGSs (the AGS IDs should then appear in a special column). Our example file contains a few lists of differentially expressed genes "experiment" vs. "control". You can choose desirable AGS and proceed to the next two tabs.Another file in "project1" is CPW_collection.hsa. It is one of the FGS files found in the third tab. Although, we can present any FGS (known pathway etc.) as a novel gene list and explore its functions.
Note: Gene symbols in this particular file are in col. 2, hence leaving the default col. 1 leads to submitting gene IDs in a wrong format (ENSEMBL –currently not supported)
Note: project1 also contains other example files apart from P.matrix.NoModNodiff_wESC.VENN.txt, which were uploaded earlier
Select a network. More detailed networks (FunCoup, STRING) are larger but less precise. Networks from curated resources like KEGG, CORUM, PhosphoSite are confident but much less comprehensive and hence might miss novel genes.You can investigate comparative efficiency of the networks by looking at the ROC curves (below the table). More sensitive and specific options must be higher and shifted to the left.
Note: For each individual analysis one can create unions of networks of different types ("Merged" is a pre-compiled example of such a union). Such merging is often beneficial.
Selecting Functional genesets
Select a collection of functional gene sets, i.e. pathways or GO terms. They should be as close to your angle of view as possible. For example, for cancer it might be our CPW_collection (alternatively, you submit a general collection and then filter the output in the next tab). In most specific and important cases consider submitting your own pathway as a gene list in the text box.
Check and Submit
Check if the three components of the analysis correctly appear at the "Check and submit" tab. NOTE: here you can only see them, but not edit. For editing, return to respective tabs
Finally , click the button
Submit and calculate. It might take time to get the job finished, thus we recommend starting from smaller networks (< 10000 links) and smaller FGS/AGS collections. NOTE: options
Show self-enrichment and
Analyze ...individually can alter the output only if you press
Submit and calculate. As long as you try different options and parameters on your AGS files, executed analyses accumulate in your project directory and can be seen in the
Archive tab. See example analysis output in
Interactive demo buttons helps to go through the various tabs and gives an idea, how to run the EviNet and generate results.