"Combined effective significances (CES)" are calculated by weighting, normalizing, transforming, and combining the element's specific p-values into one single element significance using a Fisher-like transformation (with the Pointillist option called "power") and by finally smoothing the distribution of these significances using a smoothed Gaussian kernel density function.
"Combined effective significances" are calculated for each elements by weighting, normalizing, transforming, and combining the element's specific p-values into one single element significance using a Fisher-like transformation and by finally smoothing the distribution of these significances using a smoothed Gaussian kernel density function.
Therefore, GraP offers users GSEA and cis-element significance analysis tools for relevant analysis of their gene batches.
Moreover, gene set enrichment analysis and cis-element significance analysis tools are also provided for gene batch analysis of high-throughput data sets.
We then built some function toolboxes: e.g. gene co-expression network, cis-element significance analysis tool, expression pattern search module and some other functions.
The resulting web pages for both 'Expression pattern search' and 'Tissue/time specific search' also include links to 'agriGO' [ 73] for GO enrichment analysis and 'motif scan' function for cis-element significance analysis as described above.
Users can also do cis-element significance analysis, and a job ID is produced by the server the results are stored in the server for several weeks so that they can be traced back.
There are some other function modules, e.g. a cis-element significance analysis toolbox for gene promoter sequences, an expression pattern search for microarray expression data so users can compare gene expression differences in various growth periods or under diverse stresses.
The SFGD also provides some key analysis tools, i.e. BLAST search, expression pattern search and cis-element significance analysis, as well as gene ontology information search and single nucleotide polymorphism display.
We have also developed a soybean gene co-expression regulatory network web service, a graphical display of acyl-lipid metabolic pathways, a cis-element significance analysis toolbox, an expression pattern for positive/negative search function modules and other general tools in the database.
We have also developed a series of functional analysis tools such as cotton gene family analysis, PPI prediction, co-expression network web service, GSEA analysis, cis-element significance analysis toolbox, genome synteny analysis among relative species and other general tools in the database.
