Blurb
   Numerous types of information provided by the Annotate tool can be used to group genes due to their sharing of specific biological characteristics. For example, proteins encoded by a group of genes may all have the same protein domain or may all participate in the same cellular pathway. The question then is whether genes (or their encoded proteins) that share biological characteristics also share similar expression values as determined by microarray analysis. The DragonFamilies tool is being designed to allow for the visualization of groups of genes that are not only biologically related but also share similar gene expression values.
   Presently, DragonFamilies is programmed to analyze two sample ratio data that varies around approximately 2-fold differences (i.e. data collected from Incyte microarrays or glass microarrays simultaneously hybridized with Cy3 and Cy5 labeled probes). For example, data which is within the range of -4 to 4 with the majority of the data between -2 and 2 is optimal. A better description of what DragonFamilies is and how to use it will be coming shortly.
Instructions and Example Data Sets

Before you start...
The first column in your file needs to be your expression values. Also it is highly preferred if the data you use in either the uploaded or pasted form is comma-delimited, not tab-delimited. The easiest way to generate a comma-delimited text file is to save your data as a ".csv" file in MS Excel. The example data sets below will give you an idea of how your data should look.

Example Data Sets
FIRST EXAMPLE DATA SET OR SECOND EXAMPLE DATA SET: Left click on one of the links to the left in order to copy and paste, or right click on it, save it to your computer and then re-upload it with the upload feature below.

Instructions
1) Choose how you want to enter your data.
2a or 2b) Upload or paste your delimited text file in the proper format.
3) Define the parameters of the information you are providing and the colors of the output you would prefer.
4) Specify the columns in which your three types of information are located. (***N.B. Your expression values should be in the first column for DragonFamilies to work properly.Genbank and Type values can be anywhere.)
5) Specify which sorts of delimiters you are using and then press "Analyze Data"
6) Tip: You can save you output page to your computer once it has been generated (even if your browser says that the page may not be saved correctly) so that you don't have to continually refresh the screen while you are analyzing the output. In order to see the little boxes though, you need to be connected to the internet while viewing your downloaded page.
1) Choose how you are going to enter your data.
I am going to upload my data using the file entry field below (Go to 2a).
I am going to paste my data into the textbox below (Go to 2b).
2a) Upload data.
You can submit a file for temporary upload to the DRAGON server.

and then please give your file a name:
2b) Paste your data into the field below.
Or you can paste your data here.
3) Define the parameters of the information you are providing and the colors of the output you would prefer.
Choose your output color scheme:
Red/Green Output | Yellow/Blue Output

Indicate which species is your data from:
Human | Mouse | Rat | Zebrafish

Indicate what sort of information you are using to classify your genes and their expression values:
Pfam Family Numbers | KEGG Pathway Numbers | Swissprot Keywords
4) Specify the columns in which your three types of information are located.
Indicate which columns contain your:
(***N.B. Your expression values should be in the first column for DragonFamilies to work properly. Genbank and Type values can be anywhere.)
Expression values (<-Should be 1.) , Genbank numbers , and Type values
5) Specify which sorts of delimiters you are using.
Text to use as field delimiter (Assumed "," if left blank. Don't use tab-delimited text files.):
Text to use as line delimiter (assumed "newline" if left blank):

Copyright 2001 Kennedy Krieger Institute