Fig. 1
From: GeneSCF: a real-time based functional enrichment tool with support for multiple organisms
Summary of methodology used in GeneSCF. a The bar graphs shows the increase in information (yearly) stored on KEGG database such as number of genes covered (left panel), number of supported organisms (right panel) and number of functional pathways (bottom-left panel). b The workflow starts with the input gene list from the user in the form of gene symbols or Entrez GeneID’s as plain text format and searches the remote database based on the preferred choice of database. The gene hits in the database are clustered based on matching functions and followed by ranking of enriched functions using different statistical methods. The final output from GeneSCF will be plain text and tab-separated list of enriched functions and an optional enrichment plot. c The contingency table represents the matrix to perform Fisher’s exact test for calculating significance level (P-values). The equation below the table is used by GeneSCF to calculate P-values. The contingency table is explained in detail in article sub-section Enrichment analysis under Implementation and usage main section