Online program
Rice 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 list | Allow only alphanumeric characters, white spaces, underscores and hyphens | ||||
| Gene list | example: Os01g0501800 Os01g0773700 Os01g0938100 Os02g0578400 Os02g0631100 Os02g0764500 Os03g0333400 Os03g0343900 Os03g0592500 Os03g0667201 Os03g0731100 Os03g0747700 Os03g0778100 Os04g0236400 Os04g0414700 Os04g0457000 Os04g0473150 Os04g0519975 Os04g0522800 Os04g0523000 Os05g0242400 Os05g0313100 Os05g0560000 | or | LOC_Os01g31690.1 LOC_Os01g56680.1 LOC_Os01g71190.1 LOC_Os02g36850.1 LOC_Os02g42000.1 LOC_Os02g52650.1 LOC_Os03g21560.1 LOC_Os03g22370.1 LOC_Os03g39610.1 LOC_Os03g52130.1 LOC_Os03g53640.1 LOC_Os03g56670.1 LOC_Os04g33830.1 LOC_Os04g38410.1 LOC_Os04g44190.1 LOC_Os04g44200.1 LOC_Os05g15280.1 LOC_Os05g24810.1 LOC_Os05g48630.1 | ||
| pdf color background | Black White | ||||
| Keep terms occurring in at least | 2 genes 3 genes | ||||
| FDR threshold (α) | 1‰ 1% 5% | ||||
| p.adjust method | Bonferroni 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. | |||||