| Blurb |
| The
annotate tool allows you to append multiple types of biological information
to large lists of genes, defined by Genbank accession numbers. The DragonView
suite of tools can then be used to visualize your gene expression data
in light of the information that you derive from the annotate tool.
|
| 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) Choose the types of information you would like DRAGON to
provide.
4) Specify which column of your table contains Genbank accession
numbers.
5) Choose your output method and then press "Submit Gene
List."
|
| 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. |
Submit
a file for upload to the DRAGON server.
If you are running multiple jobs, you may wish to give an identifier here for each individual dataset to distinguish the results from one another:
|
|
2b)
Paste your data into the field below.
|
|
This
is a very simple example data set
you can use to experiment with DRAGON. For more information on how
to use datasets in DRAGON annotate see the tutorial.
NOTE: It should be ok to add a header row to your data. However,
that row may be deleted in the output file. We are currently implementing
a way to specify a header row so that it is retained in the output.
If you are getting strange errors, try deleting the header row in
the file you submit.
N.B.
=> There is a maximum number of characters which this textarea
can handle. After you paste in your data please check to see that
it has not been truncated at the bottom. If you think your data set
is too big and is getting truncated, use the upload feature above.
|
| 3)
Choose the types of information you would like DRAGON to provide.
|
| UniGene
|
|
Unigene Cluster ID |
Example:
Hs.1288 |
|
Cytoband |
Example:
1q42.13-q42.2 |
|
Locuslink |
Example:
58 |
|
Expression Areas |
Example:
Aorta, Blood, Bone, Heart, Kidney, Lung, Muscle, Omentum, Prostate,
Testis, Umbilical cord vein, Whole embryo, adrenal gland, head_normal,
stomach_normal |
|
UniGene Name |
Example:
Actin, alpha 1, skeletal muscle |
| SwissProt |
|
SwissProt ID |
Example:
P02568 |
|
Subcellular Location |
Example:
CYTOPLASMIC |
|
Description |
Example:
ACTIN, ALPHA SKELETAL MUSCLE |
|
Function |
Example:
ACTINS ARE HIGHLY CONSERVED PROTEINS THAT ARE INVOLVED IN VARIOUS TYPES
OF CELL MOTILITY AND ARE UBIQUITOUSLY EXPRESSED IN ALL EUKARYOTIC CELLS |
|
Keywords |
Example:
Multigene family; Structural protein; Methylation; Muscle protein;
Acetylation; 3D-structure |
|
PubMed References |
Example:
11859360 |
|
Amino Acid Sequence |
Example:
MCDEDETTALVCDNGSGLVKAGFAGD |
| Pfam
|
|
PFAM ID |
Example:
PF00022 |
|
Description |
Example:
Actin |
| KEGG
(In order to view pictures
of the KEGG pathways you can go here.)
|
KEGG Pathway Number
|
Example:
00600 |
|
4)
Specify the column in which your Genbank numbers are located.
|
Column
number containing GenBank numbers (with the farthest left column being
1):
(required field)
Text to use as field delimiter (assumed to
be a tab "\t" if left blank):
(optional)
(If possible use a tab-delimited text file, however, if you have another
sort of delimiter in your file, such as a comma (.csv file), then enter
a "," into this text box.)
Text to use as line delimeter (assumed newline if left blank):
(optional)
(This option maybe required
if you are using a Unix-based machine with a file that has Unix line
delimiters.) |
| 5)
Choose the type of output you would prefer.
|
Output as an html table:
(You can copy and paste this type of output into a spreadsheet program
such as MS Excel.)
Output to browser or save as tab-delimited text file:
(If your browser asks you whether you would like open in the browser
or save to disk, you can either open in the browser, select it all and
paste it into a spreadsheet program such as MS Excel or save it to a
folder on your computer and then open it later in a spreadsheet program.)
Output to Email Address:
(You can enter multiple addresses separated by commas. A tab-delimited
text file will be emailed to you when it is ready. This option is good
for large queries such as those that contain more than 1000 genes. Make sure your mail server can handle
messages that may be tens of megabytes in size.)
For certain return fields, keywords for example, there may be mutliple values. You can have every value
reported on one line, or one value per line. Select multiple rows if you will use your output in the DragonView tools. Please choose
one method:
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