Computational and Mathematical Methods in Medicine

Research Article

Systematic Analysis of Time-Series Gene Expression Data on Tumor Cell-Selective Apoptotic Responses to HDAC Inhibitors

Table 3

Gene functional enrichment of GO terms in profile pairs ().
Profile pair (number of genes)GO terms value Count GO terms valueCount
“Invariant”      
#0-#0
(232)		Cellular macromolecule metabolic process 128RNA metabolic process nucleic acid binding 90
GO:0034645GO:0016070
Nucleic acid metabolic process98Nucleic acid binding83
GO:0090304 GO:0003676
Nucleus
GO:0005634		111RNA metabolic process
GO:0016070		130
#2-#2
(689)		Protein binding
GO:0005515		461Intracellular membrane-bounded organelle
GO:0043231		371
Intracellular part
GO:0044424		464 Single-organism cellular process
GO:0044763		74
Membrane-bounded organelle
GO:0043227		401Intracellular organelle
GO:0043229 		419
Response to stress
GO:0006950		167
#12-#12
(731)		Cytoplasm
GO:0005737		397Oxidoreductase activity
GO:0016491		404
Carboxylic acid metabolic process
GO:0019752		71Cofactor metabolic process
GO:0051186		29
Small molecule metabolic process
GO:0044281		158 Carboxylic acid catabolic process
GO:0046395		24
Oxoacid metabolic process
GO:0043436		74 Intraciliary transport particle
GO:0030990		7
#14-#14
(275)		Ribonucleoside triphosphate metabolic process24Ribonucleoside triphosphate catabolic process22
GO:0009199GO:0009203
Nucleoside triphosphate metabolic process
GO:0009141		24 Ribonucleoside metabolic process
GO:0009119		25
“Minitrim”      
#2-#0
(103)		Negative regulation of RNA metabolic process
GO:0051253		25Regulation of RNA metabolic process
GO:0051252		45
Negative regulation of gene expression
GO:0010629		25Gene expression
GO:0010467		60
Negative regulation of biosynthetic process
GO:0009890		26Regulation of transcription, DNA-templated
GO:0006355		42
#0-#2
(141)		DNA-dependent DNA replication
GO:0006261		7DNA replication
GO:0006260		9
DNA metabolic
GO:0006259		17Cellular response to DNA damage stimulus
GO:0000278		13
Replication fork
GO:0005657		5DNA repair
GO:0006281		10
“Reversion”      
#9-#2
(59)		Spindle organization
GO:0007051		7Mitotic cell cycle
GO:0000278		13
Cell division
GO:0051301		14Cell cycle
GO:0007049		16
Nuclear division
GO:0000280		12Regulation of nuclear division
GO:0051783		5
Mitosis
GO:0007067		10Regulation of cell cycle
GO:0051726		10
Cell cycle process
GO:0022402		15Regulation of mitotic cell cycle
GO:0007346		7
#12-#5
(135)		Mitochondrion
GO:0005739		24   
The number of overlapped genes of each “invariant,” “minitrim,” and “reversion” profile pairs is listed in the bracket below the name of each profile pairs in this table.