Informal documentation on use of VxInsight.

To use VxInsight from the CD that you have, unzip the program. It will install itself in your Program Files. If you do not see all the lists on the left or bottom of the screen, first click the screen enlarge/reduce button in the upper right corner. If this doesn't work, go to Settings in the Start menu. Select Control Panel and in the Control Panel, select Display. In Display, select Settings and decrease the screen area, e.g. to 1280 x 1024.

· Open VxInsight.exe
· go to File (upper left) and select "Open"
· find "dataset" folder where the Vx folder has been placed and select
· select "StanfordAlphaArrest" file in dataset folder and open it
· You should see the screen above
· There are a number of boxes above the topography, these will have descriptors of selected genes, once you have selected them.
· File, Options, Tools, Packages - for the most part, you won't use these - however, if you go into Packages and select Genome, it will open another heading called "Neighbors". When you have selected specific genes, this will allow you to look at the expression for that gene and up to 20 neighbors. You will have a Netscape screen that will show the expression patterns over the 18 experiments. Each gene name will be highlighted on the right and these names, when selected, will connect to the Stanford Genome Database information about that gene.

Description of useful features in VxInsight for reviewers of this manuscript.

Landscape buttons: These allow you to look at the topography in several modes.
In the hill view, individual genes aren't visable, however by moving into the hills or changing the topography to either of the other two modes, it is possible to see individual genes.

Mouse mode:
· magnifying glass - allows you to move into (left mouse click/hold) or out of (right mouse click/hold) the topography
· cross hairs - allows you to select genes. You can then use "Neighbors" above to look at expression and you will also see descriptors about a selected gene in the boxes above the topography
· selection box - this allows you to select groups of genes, e.g. one hill or part of a hill. If you want information about the seleted genes, you can go to the database query box and click on the genes you have selected (by selecting the colored dot that also gives the number of genes you have selected) and then clicking on "Send to Excel". Be patient here, it will take a little time, depending on the number of genes you have selected. This will return an Excel file with the information that is in our database about the genes that were selected.

Peak labels:
· Gene - Name given by Yeast Sequencing project, e.g. YGR236c
· Gene_Name - common name for genes, annotation from Spellman
· Description - annotation again from Spellman

Connections: There are many more here than you need. This is my research dataset and it was just easier to send the whole thing.
· Strong sim - shows links between genes based on strong similarities in expression, R >.887.
· show similar - all similarities (20 for each gene) You may see >20 connections for each gene because similarity scores are not necessarily mirrored between genes.
· show interactions-this is more or less Schwikowski's/Field's dataset, but don't use this one because I think it is missing a few interactions
· Show Ito Interactions Core - these are the smaller set of Ito's reported interactions. It is the set of interactions that was observed three times.
· Show Ito Interactions Full- this is the full dataset, 4549 interactions. Your computer may not show all of the interactions at once.
· Show Fields_nr - this is the Schwikowski dataset that was obtained from two-hybrid and several different databases on interactions identified biochemically or genetically
· Show Ito_exclusive - this is the Ito core data minus the interactions that were also identified in Fields' data
· Show Fields_exclusive
· Show IntersectionItoFullFields - this shows the genes that are in both datasets
· Show ItoFullExclusive - ignore
· ShowFieldsExclusive_Itofull - ignore

Scale range - not operative

Database query:
· Show objects where "area" - you won't use area, but point to it with the mouse and the categories on which you can query become visable.
· Useful queries:

o description - based on description column of Spellman's annotation (use "is like" or "is exactly like")
o essential since 1998 - genes identified as essential by the Yeast Deletion Project that were not known to be essential by other means
o Fields, nr, etc. - these will just highlight genes that are in these datasets
o Fungal only - ignore
o Fungal only essential - ignore
o gene - this is the YDR….c/w name. You can find your favorite genes in the topography
o gene_name - these are for our common names. If you want to know how many of the genes here have common names, you can say where gene_name is like % and it will select all those genes with names.
o inviables - all essential genes (from SGD)
o phenotype - whatever was in Spellman's annotation
o product - again whatever was in Spellman's annotation
o time of max - you can identify genes whose max was in any timepoint -from 1 to 18.

Additional Queries:
· Clear all- when genes are selected and marked by a colored pyramid they are listed to the right of the query box. Clear all removes all these selections.
· Clear entry - this clears selected entries. Entries are selected by clicking on them. This will clear one or more than one entry.
· Advanced query - this allows you to ask more complex questions of the dataset. However, it is not always functional - it depends on how the tables were entered and set up.
· Send to excel -this send a group of selected genes (to the right of the query box) to excel and returns with a file containing information present in the database about the genes.

Additional information can be found at http://www.cs.sandia.gov/projects/VxInsight.html