dbERGE II: Database of Experimental Results on Gene Expression
Instructions for query page

What is an "entry" in the database?
Binding assays: In a gel shift, for example, it is the data from 1 column on the gel.

DNA transfer experiment: An entry has only 1 construct, but a construct can be used in more than 1 entry. An entry has only 1 conclusion or result. An entry is one beta-gal measurement that came from one construct.

Selection boxes
For fields with a controlled vocabulary there is a list of terms or expressions which are used to describe the data in the field. These fields can be queried on using the scrolling lists and popup menus. Popup menus allow only 1 item to be selected at a time. Scrolling lists can allow multiple items to be selected, but not all do. On the query page all the scrolling lists except the ones under Feature allow multiple selections. See the FAQ for more help on Feature section. Multiple selections within a box are joined with an "OR".

How to select multiple items varys with the computer platforms.
For Netscape and Internet Explorer:

Even for the boxes where you select only one, the blank space can be used to unselect a previous choice.
Text boxes
The data entered in the fields represented by text boxes are freely typed in by the data enterer. The program searches for what is typed in the box within the entry. For example under DNA fragment, other region name if "neo" is typed it will return entries with names such as "Neo" and "E. coli neo". It looks for exactly what you type with the exception of letter case which is explained later. It is better to type less instead of more if you are unsure of the exact wording used. To continue with the earlier example if "E coli neo" had been typed (notice the missing period) neither entry would have been found.

In most of the text boxes you can look for more than one item by typing an AND or OR between the items you are searching for. For example the name could be queried as "coli OR neo". The case of the words AND and OR does not matter but there must be at least one space before and after the word.

The text boxes for ranges such as the start and stop following an origin are for numbers only. To search for an exact number enter that number under both start and stop. To search for all numbers larger than a given number put that number in the start box. To search for all numbers less than a given number put that number in the stop box.

Options next to submit button
There are some options between the horizontal lines with the submit button which affect the query and how the data is displayed. Select the way the data from different boxes will be joined either with an AND or an OR. Letter case of text typed in text boxes can be ignored or search for exact case only. With the default, ignore case the examples under text boxes above would find all the entries by searching on "neo". With exact case "Neo or neo" would have to be used. This doesn't affect what is selected in a selection box. The display format can be chosen as well.
Display formats
The default display format is a Summary table which lists each reference that has data that meets the criteria of the query. On the summary table there is a button for each reference to view all the data (all data format) that is from that reference and meets the query criteria.

The all data format displays all the fields from the database in an outline format and if many entries are returned can be a rather large page. These pages are divided up with 250 entries per page and buttons to view other pages of data. The detailed display options can be used to limit the fields displayed in this display format.

The last display format is the graphical display. The region to be displayed in the graph must be entered below where the format is chosen. For each entry that meets the query criteria a link is provided to the complete data entry (all data format). This link will open a new browser window so it can viewed at the same time as the graphs. This display has a graph displaying the requested region and the data from outside that region listed on the left side of the graph. At the top of the page there is a graph of the region with the landmarks for this region drawn on it. The boxes for the landmarks are clickable and will bring up the data about that landmark in the same browser window as the links for the entries. Also included in the format are qualitative results for the entry and the medline id which is a link to the PubMed entry. Only 100 entries are displayed per page because of the download time for all the images. If there are more than 100 entries that meet the query criteria there will be buttons at the bottom to view the other pages of graphs.

Detailed display options
These checkboxes and radio buttons allow fields to be removed from the all data display. If the name of the field is checked it will be displayed. Clicking on a checked box will remove the checkmark and prevent that field or fields from being displayed. The radio buttons allow different categories of some fields to be displayed or skipped. For example, under References you can select whether to have all the authors displayed, only the first author or none of the authors. Clicking on one item in a group of radio buttons will unselect the previous selection as well as select the one that was clicked. These options affect the data which is directly viewed in the all data format and the data that is first viewed in the summary table format and then the all data format via a reference's button. Viewing all the data data via the button from the summary page would be an example of a time the reference data is likely not needed. All the data on the page will belong to the one reference in the row with the button that was just clicked.
All regions are described with respect to an origin. When an offset between 2 origins can be calculated the program will search for region using all the origins that the region can be translated to. Entries entered using the "humhbb orig" can be searched for and found with regions using the humhbb, Bulger's humHBB_ORGs_cen, human beta cap, human Agamma cap, and human Ggamma cap origins.

Origins have direction. In the graphical display the genes and other indicated regions may not appear in the customary order if the region is displayed using a reverse origin. Because of this, reverse origins are indicated in the landmarks graphic by red text saying "reverse complement".