webSAM : online Significance Analysis of Microarrays

1 Choose Species
 2 Choose Study Type
3 Choose Plateform
 4 Healthy or Disease Tissue/Cell?
 Choose Tissue/Cell Type
  Choose Dataset

Dataset:  

Choose the groups of interest

(Group color can be changed by clicking on the corresponding color picker button)
 Group By 
      |     

 Merge sample groups

1 Name of the merged groups
 2 Choose 2 or more groups to merge
 3 Choose a color
 4 Submit

List of merged groups


Name subgroups Color Delete

List of sample names in the dataset

Samples are colored accoording to their groups. To have a description about a given sample, just put mouse over.
  •  Choose Datasets
  •  SAM Result
  •  Expression View

 STEP I - Select a dataset and the subgroups of interest :



 STEP II - Filter and statistical test settings :

  • Probe set filter
  • Statistical test settings
Keep only protein coding genes
Keep only one probe set per gene/ncRNA (with the highest standard deviation (SD))
Number of probe sets with the highest SD: 
Test: 
FDR ≤: 
Fold change ≥: 
Permutation:

Data are: 
Top genes to show in heatmap: 
 webSAM output :






 Export the Gene Set
 Analyze the gene set
 Add Res. to MyGspace
 Heatmap of Top
 Run SAM again


  Expression/Coexpression Report

  •  Expression Profile
  •  Coexpression Analysis
  •  Annotation

Expression of


Dataset:    |   Change dataset
Grouped by:

Legend

Dataset:    |   Change dataset
Plot options
  • Title
  • Axis
Plot title
Show title
Title :
Font : 
X axis
Title
Show title
Title : 
Font : 
Scale
x (min) :     x (max) :
Log scale/Normalize:
Tick mark label
Show tick mark labels
Font : 
Rotation angle: 
Y axis
Title
Show title
Title : 
Font : 
Scale
Y (min) :     Y (max) :
Log scale/Normalize:
Tick mark label
Show tick mark labels
Font : 
Rotation angle: 


Genes/ncRNA coexpressed with


Dataset:    |   Change dataset
Grouped by:

Correlation method:
Correlation coefficient ≥:
P value ≤:
Top correlated genes to draw:

Submit

 Download Coexpression File

 Download The File

 Heatmap Of The Top Correlated Genes/ncRNA

 Download The Heatmap

Legend
 View Coexpression Network
 Change the visual style

Background color:

Line

Nodes

Filter by correlation

Show genes with corr. ≥

Continuous color

 Nodes
 Edges
 
  •  Annotation
  •  Coexpression Plot

 Download The Plot

Legend

 Continuous color

 Color continuously according to the correlation coefficent



High: 

Low: 



Functionnal annotation of



 
 View expression profile

Functionnal Annotation

 Gene Wiki
 Interaction Network
 Coexpr.
 Reagents
 Search
 Search
 Search
 Pathway
 Pathway

Subcellular localisation

 Locate
 Protein

 [See More Plugins...]
 Plugin
Available plugins
GenomicScape Plugin Library
Plugins are 3rd party websites that you can use to learn more about your gene of interest.
Please click on the row of interest, to see more about your genes.
 Heatmap of the top differentially expressed genes

Heatmap of the top10 genes most differentially expressed

 Gscape Tools
 Tools for data analysis
 Please, select a tool to analyze the data...


 Add file
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Your G-space gives you the ability to save online your favorites gene lists and datasets for subsequent analysis.