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Table 2 Comparison of funcExplorer results of CLEANsmall dataset

From: funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data

CLEAN clusters[21] Corresponding funcExplorer clusters
  Cluster ID (size) Top GO terms BP, CC, MF
1. Nuclear part, RNA processing (126 genes) ID: 117 (250 genes) Cell cycle, macromolecular complex, nucleic acid binding
2. Mitochondrion (125 genes)   
3. Mitosis, Cell cycle (73 genes) ID: 63 (71 genes) Mitotic cell cycle process, nuclear lumen, protein binding
4. DNA replication, Cell cycle (42 genes)   
5. Extracellular region, organ development, cell adhesion (126 genes) ID: 5 (657 genes) Multicellular organismal process, intrinsic component of plasma membrane, receptor activity
6. Extracellular region, organ development, cell adhesion (168 genes) ID: 5 (657 genes) Multicellular organismal process, intrinsic component of plasma membrane, receptor activity
  ID: 91 (77 genes) Extracellular matrix organization, proteinaceous extracellular matrix
7. Immune response, signal transducer activity, receptor activity, response to stress (288 genes) ID: 8 (170 genes) Immune system process, plasma membrane, receptor activity
  ID: 305 (105 genes) Immune system process, plasma membrane part, receptor activity
8. System process, receptor activity, plasma membrane (474 genes) ID: 5 (657 genes) Multicellular organismal process, intrinsic component of plasma membrane, receptor activity
  1. *Note: The best annotation strategy with p-value≤0.001 and no upper limit for term size; cluster IDs ordered by the enrichment score; cluster sizes are given in the brackets; the characteristic functions of CLEAN clusters that also appear significant in the corresponding funcExplorer clusters are highlighted in bold; TOP functions are from GO biological process (BP), cellular component (CC) and molecular function (MF)