[BioC] Visualization and Interpretation of Go Terms

[Sandy [guest]]

I have performed the Gene Set Enrichment Analysis using the GO Stats package in R and have the Over represented set of genes and their annotated GO terms.

I would like to visualize them as a tree structure to study the relationships.

The number of enriched terms are:
 
     dim(summary(hgOvermatch, pvalue=0.05))
      [1] 214   7


I know there are other packages to create the GO Tree visualization but one needs to perform the analysis within the tool to get the graphs. I also tried using AMIGO to visualize the tree structure but since there are more than 50 terms this is a problem.

I would like to know how to interpret these terms further and also to view them as a tree structure.

Thanks

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: i686-redhat-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] EMA_1.3.2            biomaRt_2.10.0       siggenes_1.32.0      RankProd_2.30.0      GSA_1.03            
 [6] rgl_0.93.928         gcrma_2.30.0         multtest_2.12.0      FactoMineR_1.23      leaps_2.9           
[11] scatterplot3d_0.3-33 ellipse_0.3-7        car_2.0-11           survival_2.36-14     nnet_7.3-5          
[16] MASS_7.3-22          heatmap.plus_1.3     Rgraphviz_2.2.1      GOSim_1.2.7.7        igraph_0.6.5-1      
[21] org.Hs.eg.db_2.8.0   corpcor_1.6.5        Matrix_1.0-9         RBGL_1.34.0          flexmix_2.3-10      
[26] lattice_0.20-13      cluster_1.14.3       topGO_2.10.0         SparseM_0.96         annotate_1.36.0     
[31] RamiGO_1.4.0         gsubfn_0.6-5         proto_0.3-10         BiocInstaller_1.8.3  xtable_1.6-0        
[36] ath1121501.db_2.7.1  org.At.tair.db_2.8.0 GO.db_2.8.0          limma_3.14.4         csSAM_1.2.1         
[41] GOstats_2.24.0       RSQLite_0.10.0       DBI_0.2-5            graph_1.36.2         Category_2.22.0     
[46] AnnotationDbi_1.20.5 affy_1.36.1          Biobase_2.16.0       BiocGenerics_0.4.0   R.utils_1.23.2      
[51] R.oo_1.13.0          R.methodsS3_1.4.2   

loaded via a namespace (and not attached):
 [1] affyio_1.22.0         AnnotationForge_1.0.3 Biostrings_2.22.0     genefilter_1.40.0     GSEABase_1.18.0      
 [6] IRanges_1.16.6        modeltools_0.2-19     parallel_2.15.2       png_0.1-4             preprocessCore_1.18.0
[11] RCurl_1.7-0           RCytoscape_1.8.2      stats4_2.15.2         tcltk_2.15.2          tools_2.15.2         
[16] XML_3.9-4             XMLRPC_0.3-0          zlibbioc_1.4.0     

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