GOSEQ: Gene ontology analysis for RNA-seq
Young et al., Gene ontology analysis for RNA-seq: accounting for selection bias Genome Biology 2010, 11:R14
GOSEQ GO term tree
GOSEQ, a new module to MeV 4.7, is a technique for identifying differentially expressed sets of genes, such as GO terms while accounting for the
biases inherent to sequencing data.
After opening the GOSEQ initialization dialog, select the tab indicating the type of analysis you intend to run on your data. Your options are:
1.) GO Analysis: MeV will use GO term annotation to perform a GO analysis.
2.) Cluster Analysis: MeV will run GOSEQ on a cluster of differentially expressed genes. Create a cluster of genes and use the Cluster Browser to select the set.
3.) Differential Expression Analysis: Use one of MeV's RNA-seq specific modules to find a set of differentially expressed genes on which to run GOSEQ.
Probability of differential expression graph
Assign a significance level. Gene sets with a p-value less than alpha will be deemed significant.
Number of permutations: Choose the number of iterations used in significance evaluation. Default is 1000.
Number of genes per transcript length bin: Adjust the size of the bin appropriate for your dataset.
Account for differential expression bias in: Use the drop-down menu to select the type of bias to account for. By default, RNA-seq transcript length is used as the bias.