HELP


Below you will find information about several topics on the site, including the Web API.


We have also put together a walkthrough to guide you through the basic features of IT-GED.


Browser

Please use the most recent version of your browser. It's safer and faster, and it ensures that you see websites properly (not just this one). The use of Microsoft Internet Explorer prior to version 9 is highly discouraged.

Note: If you would like to use Network Analysis tools but would not like to install Adobe Flash on your computer, consider using Google Chrome, which has a built-in Flash viewer.


The site was inaccessible

If you couldn't connect to the website or you get an unusable layout or notice some missing features, it's because we're still working out some kinks. In addition, the site goes down every Sunday night at 3am (US Central Time) for backup. Thank you for your understanding.


Downloading a CSV

When you click the "Download CSV" link in the search results, you will get the same data as you do when you view a page in HTML, but formatted as a CSV (comma-separated values) file. All the values are surrounded by double quotes (") and separated by commas (,) with no spaces in between. New lines are UNIX-style (\n).

This data format is not easily readable in a browser (or particularly useful for that matter), so you will need to download the file. This should happen automatically when you click it, but if not, right-click (or option-click in Mac OS) the link and select "Save link as..." (or a variant of this) and save the file. Open the downloaded file in your spreadsheet program of choice (e.g. Microsoft Excel or LibreOffice Calc) or a standard text-editor.


Search: Search Buttons

There are two buttons when searching or analyzing data. The "Submit" button submits the parameters you have selected and performs the search or analysis. The "New Window" button does the same thing as the "Submit" button but opens the search or analysis results in a new window (or tab, depending on your browser settings). This is more convenient if you want to perform several searches quickly and keep all the results open. Please note that JavaScript must be enabled for this to work.


Search: Wildcards

Several wildcards are available when searching for a gene symbol, gene name, or unique ID:


* matches multiple unknown characters (does not include spaces) - eg*1 matches Ega1, Egaa1, Egaaa1, Eg1, but not Eg 1. A search for searchterm is equivalent to *searchterm*.
~ matches one unknown character (including spaces) - eg~1 matches Ega1 but not Eg1 or Egaa1
? matches one or zero unknown characters (including spaces) - eg?1 matches Ega1 and Eg1
^ matches the beginning of the string - ^egr matches Egr1 but not Negr1
$ matches the end of a the string - rab1$ matches Rab1 but not Rab12
" or ' searches for exact phrases - searching for calcium channel will return results matching calcium and channel while searching for "calcium channel" or 'calcium channel' will return results matching calcium channel.


Search: Direction of change

IT-GED entries are marked with either "UP" or "DOWN" for the direction of change. This means:


UP: The gene was upregulated in alcohol-preferring animals, human alcoholics, or after alcohol.
DOWN: The gene was downregulated in alcohol-preferring animals, human alcoholics, or after alcohol.


Network Analysis

The gene analysis tool functions as follows:

- Gene symbols are represented as circles (nodes).
- Gene symbols are converted to human genes according to the species you provide. This allows genes across several datasets to be easily compared.
- The nodes are colored according to the relative number of datasets in which they appear in IT-GED. The more datasets a gene is found in, the darker its color.
- Clicking a node searches for the gene symbol in IT-GED (if you get two windows or tabs opening it's a browser issue; try closing and reopening your browser).
- If two genes are found in the same dataset, they are connected by an edge labeled with that dataset.
- In the settings tab, you can choose your layout (see the Cytoscape documentation for details, but note that the Cytoscape Web layouts are slightly different).
- Recalculating a layout redraws the network according to the visible nodes.
- You can choose what labels you want visible. Note that when edges are merged, edge labels cannot be shown.
- Checking the "Merge edges" box combines all the edges between two nodes into one edge.
- You can also filter the visible nodes according to the number of different connections they make. For example, Acsl1 is found in mul2006WB, kim2007Amy, and mul2011FC. If we make a network with Acsl1, Aadac (mul2006WB), and Aagab (mul2006WB), Acsl1 only has one type of connection: mul2006WB. However, if we make a network with Acsl1, Aadat (mul2006WB), Ambra1 (kim2007Amy), and Add2 (mul2006WB, mul2011FC), Add2 has two different connections (mul2006WB and mul2001FC) and Acsl1 has three different connections (mul2006WB, kim2007Amy, and mul2011FC).
- If there are more than ~1000 nodes or ~6000 edges in the network (having too many edges is much more likely), your network will be automatically filtered due to technical limitations. If that is the case and you need to see all the nodes, please download the XGMML file and use the desktop version of Cytoscape.
- There are multiple export options in the export tab. The best image quality is provided by the pdf file.


Web API

This site was designed using the GET method of input for search and comparison requests. This is to enable programmers to easily download CSVs of whatever query they would like. The following is a list of parameters that can be passed. The general format of a command will be (for UNIX):

wget 'http://inia.icmb.utexas.edu/page?parameter1=value1&parameter2=value2&parameter3=value3'

Either single or double quotes are required when you have more than one parameter, because the ampersand will confuse the shell. In addition, don't include "&output=html" on 'search' or 'boolean' because that will download the HTML of the page. To be safe, always use lowercase letters; though every effort was made to make the parameter values case insensitive there is no guarantee that they are. Finally, note that the easiest way to learn to construct a URL properly is to play with the site a little and keep track of the URL as you perform different actions.


/search


/analysis/boolean


/analysis/booleandataset


/analysis/multisearch, /analysis/dataset, /analysis/network, /analysis/datasetnetwork