Mining literature for a comprehensive pathway analysis: A case study for retrieval of homocysteine related genes for genetic and epigenetic studies

Sharma, Priyanka; Senthilkumar, RD; Brahmachari, Vani; Sundaramoorthy, Elayanambi; Mahajan, Anubha; Sharma, Amitabh; Sengupta, Shantanu

doi:10.1186/1476-511X-5-1

Lipids in Health and Disease

Table 1 List of genes identified by literature mining that are modulated by elevated level of homocysteine

From: Mining literature for a comprehensive pathway analysis: A case study for retrieval of homocysteine related genes for genetic and epigenetic studies

S.NO	Symbol	Gene Name	Function
1	Adk	Adenosine kinase	Methionine Metabolism
2	Agt1	Angiotensin I	Renin – Angiotensin
3	Ahcyl1	S-adenosylhomocysteine hydrolase – like	Methionine Metabolism
4	Bax	BCL2-associated × protein	Apoptosis
5	Bcl-2	B-cell cll/lymphoma 2	Apoptosis
6	Bhmt2	Betaine-homocysteine methyltransferase2	Methionine Metabolism
7	Calm1	Calmodulin 1	Signaling
8	Proxy1/Cap43	Protein regulated by oxygen 1	Hypoxia
9	Casp12	caspase-12	Apoptosis
10	Casp3	caspase-3	Apoptosis
11	Cav3	Caveolin	Apoptosis
12	Ccr2	Chemokine receptor 2	Atherosclerosis
13	Cdk2	Cyclin-dependent kinase 2	Apoptosis
14	Cetp	Cholesteryl ester transfer protein	Lipid metabolism
15	Cgrp	Calcitonin gene related peptide	Signaling
16	Cck	Cholecystokinin	Insulin secretion
17	Clu	Clusterin	Apoptosis
18	Cmyc	Myc proto-oncogene protein	Apoptosis
19	Cnp	C-type natriuretic peptide	Vasorelaxant activity.
20	Crp	C-AMP receptor protein	Apoptosis/signaling
21	Cubn	Cubilin	Vitamin B12 Transport
22	Cx43	Connexin43	Integral to plasma membrane/Signaling
23	Ccna1	Cyclin A1	Cell cycle
24	clcn	Chloride ion channel gene	Chloride transport
25	Cyc	Cytochrome	Apoptosis
26	Demethylase	Demethylase	Metabolism
27	Dhfr	Dihydrofolate reductase	Metabolism
28	Dnmt1	DNA Methyltransferase 1	Metabolism
29	Dnmt2	DNA Methyltransferase 2	Metabolism
30	Dnmt3a	DNA Methyltransferase 3	Metabolism
31	Erk2	Extracellular Signal-Regulated Kinase 2	Signalling
32	Fak	Focal adhesion kinase	Apoptosis
33	Fbp1/ Folr1	Folate-Binding Protein1	Folate transport
34	Fbp2	Folate-Binding Protein2	Folate transport
35	G6pdh	Glucose-6-phosphate dehydrogenase	Metabolism
36	Gad67	Glutamic acid decarboxylase 67	Apoptosis
37	Gadd153	Glutamic acid decarboxylase 153	Apoptosis
38	Gadd45	Glutamic acid decarboxylase 45	Apoptosis
39	Gata4	GATA-Binding Protein 4	Transcription factor
40	GPX1	Glutathione Peroxidase	Anti-oxidant
41	Gsh1	GS homeobox 1	Transcription Factor
42	Grp78	Glucose related protein 78	Apoptosis
43	Grp94	Glucose related protein 98	Apoptosis
44	H2B	Histone 2B	Histone protein
45	H3	Histone 3	Histone protein
46	HDACs	Histone deacetylases	Histone Deacetylation
47	Hmgcr	Hydroxy-3-Methylglutaryl-Coa Reductase	Lipid metabolism
48	Hmt	Homocysteine-S-methyltransferase	Metabolism
49	Ikβα	Inhibitor Of Kappa Light Chain Gene Enhancer	Signaling
50	IL-1	Interleukin 1	Signaling
51	IL-6	Interleukin 6	Signaling
52	IL-8	Interleukin 8	Signaling
53	Inmt	Indolethylamine N-methyltransferase	Protein methylation
54	iNOS	Inducible Nitric Oxide Synthase	Nitric oxide stress
55	Interferon	Interferon	Signaling
56	Ifg	Ifngamma	Signaling
57	Ldhd	D-Lactate Dehydrogenase	Metabolism
58	Ldlr	Low Density Lipoprotein Receptor	Lipid metabolism
59	Lpl	Lipoprotein lipase	Lipid metabolism
60	Lox1	Lectin like oxidized LDL receptor-1	Lipid Transport
61	Lpa	Apolipoprotein	Lipid metabolism
62	lyase	Lyase	Lipid metabolism
63	Mcp1	Monocyte Chemoattractant Protein 1	Atherosclerosis
64	Mbd2	Methyl-CpG-Binding Domain Protein 2	Methylation binding protein
65	Mecp2	Methyl-CpG-Binding Protein 2	Methylation binding protein
66	Mapk/Mek	Mitogen-Activated Protein Kinase Kinase	Signalling
67	Mgmt	O6-methylguanine-DNA methyltransferase	Apoptosis
68	Mmp3	Matrix metalloproteinase 3	Remodeling of extracellular matrix
69	Mtap	Methyl Thioadenosine Phosphorylase	Metabolism
70	Mtase	Methyltransferase	Metabolism
71	NF-Kβ	Nuclear Factor Kappa-B	Signaling
72	Nmda	N-methyl-D-aspartate receptors	Alzheimer Disease
73	Nos2	Nitric Oxide Synthase 2	Nitric oxide Synthesis
74	P21 ras	P21 ras	Signaling
75	P38	Serine /threonine protein kinase belong to MAPK subfamily	Apoptosis
76	P53	Tumor protein p53	Apoptosis
77	Pai-1	Plasminogen Activator Inhibitor-1	Blood coagulation
78	Pam	Peptidylglycine alpha-amidating monooxygenase	Neuro peptide amidation
79	Icmt/Pcmt	Isoprenylcysteine Carboxylmethyltransferase	Signaling.
80	Pdgf	Platelet-derived growth factor	Inhibits apoptosis
81	Pemt	Phosphatidylethanolamine (PE) N-Methyltransferase	Methylation of PE
82	Pkc	Protein kinase C	Apoptosis
89	Ppar alpha	Peroxisome Proliferator-Activated Receptor-Alpha	Signaling
84	PPARgamma2	Proliferator-Activated Receptor-Gamma2	Signaling
85	Prmt	Protein Arginine N-Methyltransferase	Protein methylation
86	Ps1	Presenilin 1	Alzheimer Disease
87	S3a	Ribosomal protein S3A	Structural constituent of Ribosome
88	Smap8	smooth muscle-associated protein 8	Signaling
89	Srebp1	sterol regulatory element binding protein-1	Lipid Transport
90	Sst	Somatostatin	Alzheimer Disease
91	Tdag51	T-cell death-associated gene 51	Apoptosis
92	TGFbeta	Transforming growth factor beta	Apoptosis
93	TNFalpha	tumor necrosis factor alpha	Signaling
94	TNFRSF1B	Tumor necrosis factor receptor 2 gene	Signaling
95	Timp1	Tissue Inhibitor Of Metalloproteinase 1	Signaling
96	tPA	Tissue-type plasminogen activator	Blood Coagulation
97	Vcam 1	Vascular Cell Adhesion Molecule 1	Cell adhesion/Signaling
98	Yy1	Yin Yang 1	Transcription factor
99	F2	Coagulation factor II	Blood Coagulation
100	HemK/PrmC	N5-glutamine AdoMet-dependent methyltransferase	Methylation
101	ABCC2	ATP-Binding Cassette subfamily C	Cellular cisplatin transporter.
102	Ace	Angiotensin converting enzyme	Renin – Angiotensin
103	Nat1	arylamine N-acetyltransferase type-1	Detoxification of a plethora of hydrazine and arylamine drugs
104	Gnmt	Glycine N-Methyltransferase	Methylation
105	Apo B	Apolipoproteine B	Lipid metabolism
106	Ins	Insulin	Signalling
107	Sod	Super Oxide Dismutase	Anti-oxidant
108	ApoC3	Apolipoprotein C-III	Lipid metabolism
109	Atf3	Activating transcription factor	Transcription factor
110	Ap1	activating protein-1	Transcription factor
111	Fcmt	Farnesylcysteine methyltransferase	Methylation
112	Hmox	Heme oxygenase	Biliverdin metabolism

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ISSN: 1476-511X

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