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

BMC Genomics

Table 2 Comparison of funcExplorer results of CLEANsmall dataset

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

^*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)

ISSN: 1471-2164