WEBSAGE

Table of contents :

1. How to use WEBSAGE ?

   1. Input of Data

   2. Scatter Plot

   3. Tag's identification

   4. Data Exportation

2. How to obtain file from Kinzler's SAGE software

3. Program

4. References

How to use WEBSAGE ?

a/ Input of data

Click on Input Data link

Enter your file pathname which comes from SAGE 2000 (1)

Enter the legends of X axe and Y axe (first library and second library, respectively) : 20 characters only maximum. These names are displayed on the graph on absisse and coordinate axes (2)

Finally, press submit button for compute a scatter plot... (3)

You can provide Kinzler's file or generic file as :

tag1 number_of_tag1_lib1 number_of_tag1_lib 2

tag2 number_of_tag2_lib1 number_of_tag2_lib 2

...

seprarated by tabulation. The format is automatically detected.

Treatment of 5.000 tags takes approximatively 2'.



b/ Scatter Plot



X and Y axes are normalized and represent the tags of the first and the second library respectively.

The pvalue  is computed according to the formula of Audic and Claverie : p(y | x) = (N2/N1)^y(x + y)!/ x!y!(1+N2/N1)^(x+y+1)

• N1 : size of library 1
• N2 : size of library 2
• x : number of tag in library 1
• y : number of tag in library 2

The number of analysed tags is displayed under the title. On the legend, the number of tags for each class is displayed between bracket.
Each plot corresponds to a tag or a set of tag which have the same apparition's number in libraries and the same p-value.

The color of the plot represents 3 classes of pvalue :

• p <= 0.01 : pvalue significant

• P > 0.01 and P <= 0.05 : Medium significance

• P > 0.05 : pvalue no significant

The plot's size is proportionnal to the number of tags contained in it : 

1

[ 2 , 10 ]

[ 11 , 100 ]

more than 100




The scale is logarithmic and datas are normalized.

c/ Tag's identification

When you click on a plot, a web page is displayed onto tag's informations. The informations are :

• Tag : the tag analysed. When you click on tag link, a new window (NCBI site) gives the chromosom link of the tag



• Number of library legend : the abundance of each tag in each library

• Fold change : the fold increase (Inc) or reduced (Red) gene expression

• GeneBank accession number : accession number in GenBank of the gene corresponding to the tag.

• Unigene accession number : accession number in Unigene of the gene corresponding to the tag.

• P-Value : see above

• Title is the gene name corresponding to the tag,

• KEGG, Biocarta and GO (Gene Ontology) are the informations corresponding to the gene from these databanks.

When you click on one of these links, a new window is displayed on the site respectively



d/ Data exportation

Click into Export local plot button (see above) if you want to export informations corresponding to the plot or click into exportation link if you want to export all your data. In all kind, the exportation is in a csv format, the datas are separated by coma (open by StarOffice, MS Excel or something else)
Attention please ! After global exportation, data of analyse are deleted from temporary tables.