GSEA for prokaryotes

start_g2d_gsea_pro_sh
Functional analysis of Prokaryotes using Gene Set Enrichment Analysis (GSEA). Classes: GO, InterPro, KEGG, COG, PFAM, SMART, Superfamily, KEYWORDS and OPERONS
Use this powerpoint TUTORIAL or this short video the understand the input needed and the interpretation of the results. An example of results can be found here

STEP 1: Select Genome
Select genome from the RefSeq database [typically named ASMxxxx]

Optionally select genome with 'old' locus-tags from the old Genbank database [typically named NC_xxxx]
Genome2D support conversion between old-locus-tags and RefSeq locus-tags here
     Selected Genome = /var/genomes/g2d_mirror/Bacillus_subtilis_subsp_subtilis_str_168/ASM904v1_genomic     

STEP 2: Select Method
GSEA_pro methodDescriptionLoad Example dataParameters
Single Most basic routine to perform a GSEA on a single list of locus tags Example1 / Example2
Experiments GSEA on multiple experiments (see T-REx; DE table of all Contrasts) Example
Clusters/Modules GSEA on Clusters or Modules (see T-REx; k-means clustering) Example Column with header contain IDs

STEP 3: Parameters
ParameterDescriptionValue
Auto detect Cutoff values will be calculated on the basis of GO classification Auto detect ON
Manual Manual setting of cutoff values (only works if Auto detect is OFF) < values >

STEP 4: Upload Data
Upload file:
OR paste data below