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Table 1 Comparison of GOTM with related software*

From: GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

  FatiGO Onto-Express GOSurfer GoMiner GOTM
Interface/OS Web Web Windows Windows/Mac Web
Input Identifier Unigene ID, Gene symbol, Swiss-Prot ID, Ensembl ID, GenBank ID GenBank ID, Affymetrix probe set ID, Unigene ID Affymetrix probe set ID, LocusID, Unigene ID HUGO gene names LocusID, Gene symbol, Affymetrix probe set ID, UnigeneID, Swiss-Prot ID, Ensembl ID
Multi-level analysis No Yes Yes Yes Yes
Visualization of classification Bar chart, Table, Fixed tree Bar chart, Table Fixed tree Expandable tree, DAG Expandable tree, Bar chart, Fixed tree
Statistical Analysis Fisher's exact test Binomial test, χ2 test, Fisher's exact test χ2 test Fisher's exact test Hypergeometric test
Correction for multiple tests Yes Yes No No No
Visualization of enriched GO categories Bar chart, Table Bar chart, Table Highlight in the full GOTree Highlight in the full DAG Sub-tree and DAG of enriched GO categories; Highlight in the full GOTree and bar chart
Availability Free Partially free Free Free Free
  1. * The comparison was based on the information available from individual website as of August, 2003
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