Online program

Arabidopsis GeneCloud/Gene - semantic terms overrepresented in description of a gene list

This script uses a semantic technique to scan over gene descriptions of a particular gene list (that you provide). It returns only semantic terms, on a ‘word cloud’ format, that are significantly more represented in the list of genes compared to the whole genome background. It tends to be very powerful and gives complementary yet similar results with GO term enrichment analysis. Compared to GO analysis, it does not care about categories. Each word in a description is handled on itself. If this word occurs more than randomly it is kept and displayed. For instance if your list of gene is enriched of the term "myb", "hairs", or "endomembrane" it will be displayed.

 Your e-mail 
 Name your listAllow only alphanumeric characters, white spaces, underscores and hyphens
  Gene listexample:

At1g59840
At2g07727
At2g26500
At3g26710
At3g57190
At4g03280
At4g25080
At4g25570
At4g31560
At4g37200
At5g20080
At5g38630
At5g48810
At5g53560
AtCg00570
AtCg00580
AtCg00600
AtCg00720
AtCg00730
AtMg00220
 pdf color backgroundBlack            White
 Keep terms occurring in at least 2 genes         3 genes
 FDR threshold (α)1‰               1%               5%
 p.adjust methodBonferroni    Benjamini & Yekutieli
 
                     
 
Modification of the code (May 20th 2015):
According to user feedback the size of the words displayed in the Cloud is now proportionnal to "occurence x ratio of enrichment".
 

Citation
If you publish these results please cite:
GeneCloud reveals semantic enrichment in lists of gene descriptions
Gabriel Krouk, Clément Carré*, Cécile Fizames*, Alain Gojon, Sandrine Ruffel & Benoît Lacombe
Mol. Plant 8(6):971-3, Jun 2015
 
 This R script was written by Gabriel Krouk, Clément Carré & Cécile Fizames. Interactive use on this web server is free to academic use.
© 2014-2015 M2SB - Legal notice - Publication director: Alain Gojon - R developments: Gabriel Krouk - Conception / Administration: Cécile Fizames