Vlad - Gene List Analysis and Visualization

Version 1.9.0

Input

Run Name:

Provides a title for the output.

The run name appears at the top of the results page.
If this field is blank, a default name will be generated.

Query Set(s):

Specifies set(s) of objects (e.g. genes) to test. Associates a color with each set.

(Optional) Enter a name for the query set to label the output. A default will be provided if not specified.
Upload a file of ids and/or symbols, or enter them into the text area. Ids/symbols should be separated by spaces, commas, newlines, or pipes (vertical bars).
To do a combined analysis of multiple query sets, click "Add query set".
When there is more than one query set, each is assigned a color. You may change the default color by clicking in the colored box.

Annotation Data Set:

Specifies which set of annotations to use for the analysis.

Select one of the data sets listed, or select "Upload your own...".
To upload your own data set:
1. Attach a file in GAF (GO Annotation File) format (version 1.0).
2. Select the ontology that your annotations use. Select one of the listed ontologies, or select "Upload your own...".
3. To upload your own ontology, attach a file in OBO format.

Universe Set:

IDs:
File:

Optional. Constrains the analysis to a subset of the database.

By default, Vlad compares your query set against all the annotated objects (e.g. genes) in the database.
Use this field if you want Vlad to comapare against a subset of the database.
Example scenario: You are analyzing results from a custom microarray containing probes for 5000 genes. You will get better results from Vlad by specifying the 5000 genes as the universe set.
Paste ids and/or symbols into text area, or choose a file.

Analysis

Type of analysis:

Specifies what kind of statistical analysis to perform.

Choose "enrichment" find ontology terms that are overrepresented in the query set relative to the database.
Choose "depletion" to find terms that are underrepresented.
Choose "percentage" to simply characterize your query sets (no analysis).

Evidence Codes
to Exclude:

Specifies evidence codes to exclude from processing.

Annotations with specified evidence codes are removed.
"NOT" annotations (e.g., Gene Abc does NOT have function f) are always removed.

Output

Tabular Output:

HTML:
Excel spreadsheet:
Tab delimited:

Vlad can output your results in tabular form. Check all desired formats.

HTML. If checked, the result page will contain a scrollable table of results.
Excel spreadsheet. If checked, the results are written to an Excel spreadsheet file. This file is available when you "Save" (download) your results. (Warning: this option does not work for very large query sets.)
Tab delimited. If checked, the results are written to a tab-delimited text file. This file is available when you "Save" (download) your results.

Graphical Output:

Enable:
Region(s) of interest:
Limit nodes:	Value:
Cull interior nodes:
Background color:
Node color:
Draw labels on nodes:
Max image size:	(width,height) inches

Vlad can draw a picture of (part of) the ontology with your results "painted on".

Enable. Graphical output is generated only if this is checked.
Region(s) of interest.
- If you only want to see specific regions of the ontology, enter the term id(s) here.
- Any further node limits will be applied within the region.
Limit nodes/Value. Specifies the set of nodes to be drawn:
- ...to top N overall. Draws the top N scoring terms and their ancestors. Enter N (an integer) into Value. Default = 25.
- ...to N local maxima. Draws the top N scoring local maxima (what's this?)) and their ancestors. Enter N (an integer) into Value. Default = 25.
- ...by P-value. Draws terms whose score (minimum P-value) is less than or equal to P. Enter P (a floating point number, e.g., .0001 or 1E-4) into Value. Default = 0.05.
- ...by Q-value. Draws terms whose score (minimum Q-value) is less than or equal to Q. Enter Q (a floating point number, e.g., .0001 or 1E-4) into Value. Default = 0.05.
Cull interior nodes.
- If not checked, the graph includes selected terms and all their ancestors.
- If checked, Vlad applies a heuristic to reduce the number of interior nodes.
Background color / node color.
- By default, graph nodes are light gray, and the graph background color is white.
- You can change either of these by clicking in the corresponding box.
Draw labels on nodes. If checked, term names are drawn on nodes.
Max image size. Graph image will be scaled if necessary so as not to exceed this value.
- Enter width and height, or enter a single number to use for both width and height.
- Values are in inches.
- Leave blank to allow unlimited image size.

Results

Results:

View your results and/or save them to your local disk.

Results are listed in the order generated and labelled with the Run Name.
Each result set is viewable online for a minimum of 24 hours.
At any point during this time, you may save the results to your local disk.
Saved results look and operate the same as results Viewed online. However, your browser may require your explicit permission to load the saved web page the first time.
If you checked "Excel spreadsheet" and/or "Tab delimited" under "Tabular output", those files are included when you Save.