| | |
| ||
Source DistributionEverything you need to get a local installation of GONOME up and running.License is MIT. All in one versions: GONOME_All.tar.gz GONOME_All.zip Also, seperated into organisms here |
ExamplesSome examples to give you an idea of what GONOME does.Human CpG Island Results Here we look at the over-represented GO terms from the positions of CpG islands in the human genome. Process terms in the transcribed region of a gene or upstream within 2000 bp The presence of the root GO term 'biological_process' and other general terms here reflects the fact that CpG islands are generally over-represented in the upstream and first exon regions. To find out what GO terms are non-randomly correlated to CpG Islands, we switch the null model to 'Only Scored Regions', which generates the expectations comparing to randoms that hit the region examined in the query as often as the query positions do themselves. Process terms in the transcribed region of a gene or upstream within 2000 bp, Only Scored Regions Further CpG island results, including results for M.musculus and S.cerevisiae can be found here |
| PACE
Here is an example of a promoter seqeunce showing GO terms significantly over-represented. The 190 positions are those of all occurences exact matches to the proteasome associated control element (PACE) upstream activator sequence 3'-GGTGGCAAA-5' in the S.cerevisiae genome. |
|
Promoter Mining in Yeast In a more involved example showing some of the potential of GONOME we extracted all sequences in the cerevisiae genome with lengths 5 to 11 which occurred 5 times or more and ran their positions through GONOME checking for over-represented GO terms, selecting only the 2Kb upstream of genes. Most known function specific promoters are recovered, as well as a number of novel motifs. Further details of method and results are in the paper. Have a peruse of the results here. |
Data SetsThe feature positions used for mouse, human, D. melanogaster and A. thaliana were extracted from their Genbank genomes. The human genome is NCBI build 35, 26 Aug. 2004, the murine genome is NCBI build 33, 2 Sep. 2004, fly is the 13 Apr. 2005 version, and cress the 19 Feb. 2004 version. The S. cerevisiae feature positions were derived from the SGD annotations, 7 Dec. 2004 ( ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/SGD_features.tab). GO annotations for human, mouse and S. cerevisiae were derived from the 200411 version of the main GO database, (5 Nov. 2004).Feature positions (Chromosome contigs, 4 Jul. 2005) and GO annotation table (15 Aug. 2005) for S. pombe came from the Sanger center -ftp://ftp.sanger.ac.uk/pub/yeast/pombe/. C.elegans feature positions were derived from the WS147 build GFF file (22 Aug 2005) and GO table revision 1.52. - ftp://ftp.pub.wormbase.org/pub/wormbase/species/elegans/ D. melanogaster GO annotations came from the revision 1.65 of the FLYBASE GOA table. ftp://flybase.bio.indiana.edu/genomes/Drosophila_melanogaster/ A. thaliana GO annotations were derived from the TAIR GOA table, revision 1.821. http://www.arabidopsis.org LinksGene Ontology ConsortiumSGD NCBI Other GO term inferrence toolsGOStat GO::TermFinder |
