Inhibition of Rho Kinase Induces Antioxidative Molecules and Suppresses Reactive Oxidative Species in Trabecular Meshwork Cells

Table 3

Gene ontology of upregulated genes in Y-27632-treated TM cells.

Ontology	Term	Changed genes	Total genes	value
Cellular component	Cell projection	31 (1)	331 (38)	0.0000306
Cellular component	Neuron projection	20 (6)	180 (28)	0.0000901
Cellular component	Cell projection part	17 (0)	142 (0)	0.000135
Biological process	Regulation of neurotransmitter levels	8 (0)	47 (2)	0.00148
Molecular function	Calcium channel regulator activity	4 (3)	11 (9)	0.00225
Cellular component	Presynaptic membrane	5 (5)	20 (20)	0.0024
Cellular component	Plasma membrane part	45 (0)	706 (2)	0.00259
Biological process	Synaptic transmission	16 (10)	170 (66)	0.00374
Molecular function	Channel regulator activity	5 (0)	23 (0)	0.00421
Biological process	Cellular nitrogen compound biosynthetic process	21 (0)	255 (0)	0.00443
Biological process	L-Glutamate import	3 (3)	6 (4)	0.00456
Cellular component	Platelet alpha granule	5 (1)	24 (2)	0.00472
Biological process	Transmission of nerve impulse	17 (0)	189 (3)	0.00563
Molecular function	Anion:cation symporter activity	4 (0)	15 (0)	0.00565
Molecular function	Sodium:dicarboxylate symporter activity	3 (3)	7 (7)	0.00585
Biological process	L-Amino acid import	3 (0)	7 (0)	0.00632
Biological process	Amino acid import	3 (0)	7 (0)	0.00632
Cellular component	Axon part	6 (0)	38 (2)	0.00665
Biological process	Regulation of mitotic cell cycle	8 (1)	62 (6)	0.00683
Molecular function	Anion transmembrane transporter activity	8 (0)	66 (5)	0.00813
Biological process	Cell-cell signaling	21 (4)	268 (74)	0.00841
Molecular function	High-affinity glutamate transmembrane transporter activity	2 (2)	2 (2)	0.00875
Cellular component	Cytoplasmic vesicle part	9 (0)	83 (2)	0.00918
Biological process	Deoxyribonucleoside triphosphate biosynthetic process	2 (0)	2 (0)	0.00923
Biological process	Response to calcium ion	5 (4)	28 (25)	0.00969
Molecular function	Rho guanyl-nucleotide exchange factor activity	5 (5)	29 (29)	0.00984
Biological process	Carboxylic acid transport	9 (0)	81 (1)	0.01005
Molecular function	Phosphatidylinositol binding	3 (3)	9 (9)	0.01012
Molecular function	Dicarboxylic acid transmembrane transporter activity	3 (0)	9 (0)	0.01012
Biological process	Organic acid transport	9 (0)	82 (0)	0.01077
Biological process	Glutamate metabolic process	3 (0)	9 (4)	0.01091
Biological process	Dicarboxylic acid transport	3 (3)	9 (7)	0.01091
Cellular component	Axoneme	4 (2)	19 (5)	0.01104
Molecular function	Structural constituent of cytoskeleton	5 (5)	31 (31)	0.01251
Cellular component	Cytoplasmic membrane-bounded vesicle lumen	4 (0)	20 (0)	0.01285
Cellular component	Platelet alpha granule lumen	4 (4)	20 (20)	0.01285
Cellular component	Dendritic spine	4 (4)	20 (20)	0.01285
Cellular component	Neuron spine	4 (0)	20 (0)	0.01285
Cellular component	Axon	9 (6)	89 (62)	0.01361
Cellular component	Neurofilament	2 (2)	3 (3)	0.01394
Molecular function	Antioxidant activity	5 (2)	32 (12)	0.01401
Biological process	Rho protein signal transduction	7 (1)	57 (15)	0.01403
Molecular function	Phenylalanine 4-monooxygenase activity	2 (2)	3 (3)	0.0142
Biological process	ER to Golgi vesicle-mediated transport	4 (4)	20 (20)	0.01457
Cellular component	Vesicle lumen	4 (0)	21 (1)	0.01484
Biological process	D-Amino acid transport	2 (0)	3 (0)	0.01497
Biological process	D-Aspartate import	2 (2)	3 (3)	0.01497
Biological process	D-Aspartate transport	2 (0)	3 (0)	0.01497
Biological process	Glutamate biosynthetic process	2 (2)	3 (3)	0.01497
Biological process	2′-Deoxyribonucleotide biosynthetic process	2 (0)	3 (0)	0.01497
Biological process	Fatty acid transport	4 (1)	21 (6)	0.01681
Molecular function	Ras guanyl-nucleotide exchange factor activity	5 (0)	34 (3)	0.01737
Biological process	Regulation of cell cycle process	6 (0)	47 (0)	0.01912
Biological process	Nucleoside triphosphate biosynthetic process	8 (1)	76 (3)	0.0195
Molecular function	Transporter activity	34 (8)	556 (147)	0.01993
Molecular function	Monocarboxylic acid binding	4 (0)	23 (0)	0.02002
Cellular component	Neurofilament cytoskeleton	2 (0)	4 (1)	0.02037
Biological process	Pyrimidine nucleoside triphosphate biosynthetic process	3 (0)	12 (0)	0.02063
Biological process	Pyrimidine nucleoside triphosphate metabolic process	3 (0)	12 (0)	0.02063
Molecular function	Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen	2 (1)	4 (2)	0.02075
Molecular function	Thioredoxin-disulfide reductase activity	2 (2)	4 (4)	0.02075
Biological process	Regulation of secretion	8 (0)	77 (0)	0.0208
Biological process	Neurotransmitter biosynthetic process	2 (2)	4 (4)	0.02186
Biological process	Tetrahydrobiopterin metabolic process	2 (1)	4 (1)	0.02186
Biological process	Deoxyribonucleoside triphosphate metabolic process	2 (0)	4 (1)	0.02186
Cellular component	Clathrin coat	4 (1)	24 (1)	0.02193
Biological process	Response to metal ion	8 (0)	78 (3)	0.02216
Cellular component	Transport vesicle membrane	3 (0)	13 (0)	0.02236
Biological process	Neurotransmitter metabolic process	3 (1)	13 (3)	0.02465
Biological process	Long-chain fatty acid transport	3 (2)	13 (4)	0.02465
Molecular function	Oxidoreductase activity, acting on sulfur group of donors	4 (0)	25 (0)	0.02549
Molecular function	Organic acid:sodium symporter activity	3 (0)	14 (0)	0.02707
Molecular function	Phosphoinositide binding	6 (2)	53 (30)	0.02738
Molecular function	Carboxylic acid binding	8 (0)	84 (5)	0.02754
Cellular component	MHC protein complex	4 (0)	26 (0)	0.02764
Molecular function	DNA topoisomerase type I activity	2 (2)	5 (5)	0.02831
Molecular function	Solute:sodium symporter activity	4 (0)	26 (0)	0.02853
Cellular component	Synapse	13 (10)	167 (116)	0.0289
Biological process	L-Amino acid transport	3 (0)	14 (1)	0.02906
Biological process	Cilium morphogenesis	3 (1)	14 (3)	0.02906
Cellular component	Secretory granule	8 (3)	86 (27)	0.02929
Biological process	Positive regulation of myeloid leukocyte differentiation	2 (0)	5 (0)	0.0298
Biological process	Glutamate catabolic process	2 (0)	5 (0)	0.0298
Biological process	Sulfate transport	2 (2)	5 (5)	0.0298
Biological process	Deoxyribonucleotide biosynthetic process	2 (0)	5 (2)	0.0298
Cellular component	Endomembrane system	26 (1)	416 (14)	0.03019
Cellular component	External side of plasma membrane	6 (5)	55 (49)	0.03035
Cellular component	Plasma membrane	64 (48)	1224 (935)	0.03044
Cellular component	Endocytic vesicle membrane	3 (3)	15 (12)	0.03078
Cellular component	Clathrin coated vesicle membrane	4 (0)	27 (3)	0.0308
Cellular component	Intrinsic to organelle membrane	8 (0)	87 (0)	0.03095
Biological process	Regulation of rho protein signal transduction	5 (5)	39 (29)	0.03101
Biological process	Neurotransmitter secretion	4 (3)	26 (11)	0.03114
Cellular component	Synapse part	10 (0)	117 (2)	0.03187
Biological process	Vitamin transport	3 (1)	15 (1)	0.03386
Molecular function	Symporter activity	6 (6)	57 (44)	0.03631
Molecular function	Syntaxin-1 binding	2 (2)	6 (6)	0.03678
Molecular function	Ion channel inhibitor activity	2 (1)	6 (2)	0.03678
Biological process	Cell communication	34 (4)	562 (40)	0.03717
Cellular component	Endocytic vesicle	4 (1)	29 (10)	0.03772
Biological process	Regulation of mitosis	4 (2)	28 (7)	0.03839
Biological process	Regulation of nuclear division	4 (0)	28 (0)	0.03839
Biological process	Response to inorganic substance	10 (1)	118 (8)	0.03843
Biological process	Phosphatidylcholine biosynthetic process	2 (2)	6 (5)	0.03869
Biological process	Interleukin-1 beta secretion	2 (0)	6 (0)	0.03869
Biological process	Interleukin-1 secretion	2 (0)	6 (0)	0.03869
Biological process	Regulation of interleukin-1 beta secretion	2 (0)	6 (0)	0.03869
Biological process	Regulation of interleukin-1 secretion	2 (0)	6 (0)	0.03869
Biological process	Cdc42 protein signal transduction	2 (1)	6 (3)	0.03869
Biological process	L-Phenylalanine catabolic process	2 (2)	6 (6)	0.03869
Biological process	L-Phenylalanine metabolic process	2 (0)	6 (0)	0.03869
Biological process	Tyrosine metabolic process	2 (0)	6 (1)	0.03869
Biological process	Multicellular organismal aging	2 (1)	6 (2)	0.03869
Biological process	Aspartate transport	2 (0)	6 (3)	0.03869
Biological process	Negative regulation of transforming growth factor beta receptor signaling pathway	2 (2)	6 (6)	0.03869
Biological process	Neurofilament cytoskeleton organization	2 (1)	6 (5)	0.03869
Molecular function	Chloride ion binding	4 (4)	29 (29)	0.0389
Biological process	L-Glutamate transport	3 (0)	16 (7)	0.03904
Biological process	Platelet activation	3 (2)	16 (11)	0.03904
Biological process	Positive regulation of secretion	5 (0)	42 (1)	0.03976
Molecular function	Substrate-specific transporter activity	28 (0)	463 (0)	0.04034
Biological process	Nucleotide biosynthetic process	12 (0)	151 (7)	0.04052
Cellular component	Microtubule basal body	3 (3)	17 (17)	0.04062
Molecular function	Calcium-dependent protein binding	3 (3)	17 (17)	0.04164
Biological process	Anion transport	7 (0)	73 (10)	0.04185
Molecular function	Solute:cation symporter activity	5 (0)	44 (0)	0.04201
Biological process	Purine nucleoside triphosphate biosynthetic process	7 (0)	74 (0)	0.0443
Biological process	Acidic amino acid transport	3 (0)	17 (0)	0.04461
Biological process	Pyrimidine nucleoside metabolic process	3 (0)	17 (1)	0.04461
Biological process	Pyrimidine nucleotide biosynthetic process	3 (0)	17 (4)	0.04461
Cellular component	MHC class II protein complex	3 (3)	18 (18)	0.04607
Molecular function	Oxidoreductase activity, acting on sulfur group of donors, NAD, or NADP as acceptor	2 (0)	7 (2)	0.04608
Molecular function	Fatty acid transporter activity	2 (1)	7 (3)	0.04608
Molecular function	Channel inhibitor activity	2 (0)	7 (1)	0.04608
Molecular function	DNA topoisomerase activity	2 (1)	7 (2)	0.04608
Biological process	Regulation of cytokine production	7 (0)	75 (0)	0.04684
Molecular function	NADP or NADPH binding	3 (3)	18 (17)	0.04721
Biological process	Nucleobase, nucleoside, and Nucleotide biosynthetic process	12 (0)	157 (0)	0.04725
Biological process	Nucleobase, nucleoside, nucleotide, and nucleic acid biosynthetic process	12 (0)	157 (0)	0.04725
Biological process	G1 phase	2 (1)	7 (1)	0.04845
Cellular component	Lamellipodium	4 (4)	32 (32)	0.04965
Cellular component	Transport vesicle	4 (1)	32 (11)	0.04965