Supplementary Table 2A. Top20HDL_GeneWithTopGO

Document Sample
Supplementary Table 2A. Top20HDL_GeneWithTopGO Powered By Docstoc
					Supplementary Table 6A. The 20 genes with highest similarity scores with HDL, with the selected ontology terms highly contri
the abstracts mentioning about the phenotype. The red color highlighted are for the genes with no previous implicated in lipid m
Gene Id Gene Name
   19   ABCA1
   19   ABCA1
   19   ABCA1
   19   ABCA1
   19   ABCA1
 4023   LPL
 4023   LPL
 4023   LPL
 4023   LPL
 4023   LPL
 1071   CETP
 1071   CETP
 1071   CETP
 1071   CETP
 1071   CETP
 3931   LCAT
 3931   LCAT
 3931   LCAT
 3931   LCAT
 3931   LCAT
 3990   LIPC
 3990   LIPC
 3990   LIPC
 3990   LIPC
 3990   LIPC
 9388   LIPG
 9388   LIPG
 9388   LIPG
 9388   LIPG
 9388   LIPG
 5465   PPARA
 5465   PPARA
 5465   PPARA
 5465   PPARA
 5465   PPARA
23659   LYPLA3
23659   LYPLA3
23659   LYPLA3
23659   LYPLA3
23659   LYPLA3
 6559   SLC12A3
 6559   SLC12A3
 6559   SLC12A3
 7018   TF
 7018   TF
 7018   TF
 7018   TF
 7018   TF
 5371   PML
53353   LRP1B
53353   LRP1B
53353   LRP1B
53353   LRP1B
53353   LRP1B
 6560   SLC12A4
 6560   SLC12A4
 6560   SLC12A4
 5699   PSMB10
 5699   PSMB10
 1506   CTRL
 1506   CTRL
 1506   CTRL
10449   ACAA2
10449   ACAA2
10449   ACAA2
10449   ACAA2
10449   ACAA2
 7520   XRCC5
 7520   XRCC5
 7520   XRCC5
 7520   XRCC5
 7520   XRCC5
 6678   SPARC
 6678   SPARC
 6678   SPARC
 6678   SPARC
 6678   SPARC
 4155   MBP
 4155   MBP
 4155   MBP
 3569   IL6
 3569   IL6
 3569   IL6
 3569   IL6
 3569   IL6
ementary Table 6A. The 20 genes with highest similarity scores with HDL, with the selected ontology terms highly contributing to the scores
stracts mentioning about the phenotype. The red color highlighted are for the genes with no previous implicated in lipid metabolism, but we u
             Annotation
             ATP-binding cassette, sub-family A (ABC1), member 1
             ATP-binding cassette, sub-family A (ABC1), member 1
             ATP-binding cassette, sub-family A (ABC1), member 1
             ATP-binding cassette, sub-family A (ABC1), member 1
             ATP-binding cassette, sub-family A (ABC1), member 1
             lipoprotein lipase
             lipoprotein lipase
             lipoprotein lipase
             lipoprotein lipase
             lipoprotein lipase
             cholesteryl ester transfer protein, plasma
             cholesteryl ester transfer protein, plasma
             cholesteryl ester transfer protein, plasma
             cholesteryl ester transfer protein, plasma
             cholesteryl ester transfer protein, plasma
             lecithin-cholesterol acyltransferase
             lecithin-cholesterol acyltransferase
             lecithin-cholesterol acyltransferase
             lecithin-cholesterol acyltransferase
             lecithin-cholesterol acyltransferase
             lipase, hepatic
             lipase, hepatic
             lipase, hepatic
             lipase, hepatic
             lipase, hepatic
             lipase, endothelial
             lipase, endothelial
             lipase, endothelial
             lipase, endothelial
             lipase, endothelial
             peroxisome proliferative activated receptor, alpha
             peroxisome proliferative activated receptor, alpha
             peroxisome proliferative activated receptor, alpha
             peroxisome proliferative activated receptor, alpha
             peroxisome proliferative activated receptor, alpha
             lysophospholipase 3 (lysosomal phospholipase A2)
             lysophospholipase 3 (lysosomal phospholipase A2)
             lysophospholipase 3 (lysosomal phospholipase A2)
             lysophospholipase 3 (lysosomal phospholipase A2)
             lysophospholipase 3 (lysosomal phospholipase A2)
             solute carrier family 12 (sodium/chloride transporters), member 3
             solute carrier family 12 (sodium/chloride transporters), member 3
             solute carrier family 12 (sodium/chloride transporters), member 3
             transferrin
             transferrin
             transferrin
             transferrin
             transferrin
             promyelocytic leukemia
low density lipoprotein-related protein 1B (deleted in tumors)
low density lipoprotein-related protein 1B (deleted in tumors)
low density lipoprotein-related protein 1B (deleted in tumors)
low density lipoprotein-related protein 1B (deleted in tumors)
low density lipoprotein-related protein 1B (deleted in tumors)
solute carrier family 12 (potassium/chloride transporters), member 4
solute carrier family 12 (potassium/chloride transporters), member 4
solute carrier family 12 (potassium/chloride transporters), member 4
proteasome (prosome, macropain) subunit, beta type, 10
proteasome (prosome, macropain) subunit, beta type, 10
chymotrypsin-like
chymotrypsin-like
chymotrypsin-like
acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)
acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)
acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)
acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)
acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)
X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kDa)
X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kDa)
X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kDa)
X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kDa)
X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kDa)
secreted protein, acidic, cysteine-rich (osteonectin)
secreted protein, acidic, cysteine-rich (osteonectin)
secreted protein, acidic, cysteine-rich (osteonectin)
secreted protein, acidic, cysteine-rich (osteonectin)
secreted protein, acidic, cysteine-rich (osteonectin)
myelin basic protein
myelin basic protein
myelin basic protein
interleukin 6 (interferon, beta 2)
interleukin 6 (interferon, beta 2)
interleukin 6 (interferon, beta 2)
interleukin 6 (interferon, beta 2)
interleukin 6 (interferon, beta 2)
contributing to the scores are shown. All the non-highlighted are genes previously implicated in lipid metabolism. The highlighted ones are g
ipid metabolism, but we used our approach to find lipid-related ontology terms linking the gene and the phenotype, examples of the Pubmed
             Similarity Score Traite     GO Id
                    5084.15   HDL        GO#GO_0030301
                    5084.15   HDL        GO#GO_0005320
                    5084.15   HDL        GO#GO_0005321
                    5084.15   HDL        GO#GO_0006869
                    5084.15   HDL        GO#GO_0005215
                    2267.08   HDL        GO#GO_0004465
                    2267.08   HDL        GO#GO_0004091
                    2267.08   HDL        GO#GO_0005320
                    2267.08   HDL        GO#GO_0003675
                    2267.08   HDL        GO#GO_0005321
                    1473.99   HDL        GO#GO_0005321
                    1473.99   HDL        GO#GO_0005320
                    1473.99   HDL        GO#GO_0030301
                    1473.99   HDL        GO#GO_0006869
                    1473.99   HDL        GO#GO_0005322
                     913.96   HDL        GO#GO_0016747
                     913.96   HDL        GO#GO_0005320
                     913.96   HDL        GO#GO_0030301
                     913.96   HDL        GO#GO_0005321
                     913.96   HDL        GO#GO_0006869
                    885.971   HDL        GO#GO_0004091
                    885.971   HDL        GO#GO_0005321
                    885.971   HDL        GO#GO_0005320
                    885.971   HDL        GO#GO_0030301
                    885.971   HDL        GO#GO_0006869
                    313.241   HDL        GO#GO_0005321
                    313.241   HDL        GO#GO_0005320
                    313.241   HDL        GO#GO_0004091
                    313.241   HDL        GO#GO_0004465
                    313.241   HDL        GO#GO_0005322
                    211.493   HDL        GO#GO_0005320
                    211.493   HDL        GO#GO_0005777
                    211.493   HDL        GO#GO_0006869
                    211.493   HDL        GO#GO_0030301
                    211.493   HDL        GO#GO_0016088
                    105.835   HDL        GO#GO_0005321
                    105.835   HDL        GO#GO_0030301
                    105.835   HDL        GO#GO_0006869
                    105.835   HDL        GO#GO_0004091
                    105.835   HDL        GO#GO_0016747
                    67.2739   HDL        GO#GO_0006810
                    67.2739   HDL        GO#GO_0005215
                    67.2739   HDL        GO#GO_0007588
                    55.7379   HDL        GO#GO_0005320
                    55.7379   HDL        GO#GO_0004888
                    55.7379   HDL        GO#GO_0003675
                    55.7379   HDL        GO#GO_0006810
                    55.7379   HDL        GO#GO_0010324
                    52.5758   HDL        GO#GO_0003675
52.1034   HDL   GO#GO_0005322
52.1034   HDL   GO#GO_0004888
52.1034   HDL   GO#GO_0003675
52.1034   HDL   GO#GO_0010324
52.1034   HDL   GO#GO_0008243
44.1126   HDL   GO#GO_0006810
44.1126   HDL   GO#GO_0005215
44.1126   HDL   GO#GO_0001524
40.1262   HDL   GO#GO_0005320
40.1262   HDL   GO#GO_0016547
39.2387   HDL   GO#GO_0030301
39.2387   HDL   GO#GO_0005320
39.2387   HDL   GO#GO_0030271
39.0624   HDL   GO#GO_0030301
39.0624   HDL   GO#GO_0006869
39.0624   HDL   GO#GO_0005901
39.0624   HDL   GO#GO_0005777
39.0624   HDL   GO#GO_0005886
37.3821   HDL   GO#GO_0003675
37.3821   HDL   GO#GO_0003674
37.3821   HDL   GO#GO_0016899
37.3821   HDL   GO#GO_0019787
37.3821   HDL   GO#GO_0005818
37.3694   HDL   GO#GO_0003675
37.3694   HDL   GO#GO_0032501
37.3694   HDL   GO#GO_0046903
37.3694   HDL   GO#GO_0008001
37.3694   HDL   GO#GO_0005625
37.3539   HDL   GO#GO_0003675
37.3539   HDL   GO#GO_0044459
37.3539   HDL   GO#GO_0005625
36.3327   HDL   GO#GO_0051234
36.3327   HDL   GO#GO_0016088
36.3327   HDL   GO#GO_0032501
36.3327   HDL   GO#GO_0042593
36.3327   HDL   GO#GO_0042697
n-highlighted are genes previously implicated in lipid metabolism. The highlighted ones are genes with no obvious previous linkage to lipid m
nd lipid-related ontology terms linking the gene and the phenotype, examples of the Pubmed ID linking the gene and the ontology are shown
             GO Description
             CHOLESTEROL TRANSPORT
             APOLIPOPROTEIN
             HIGH-DENSITY LIPOPROTEIN
             LIPID TRANSPORT
             TRANSPORTER
             LIPOPROTEIN LIPASE
             CARBOXYLESTERASE
             APOLIPOPROTEIN
             PROTEIN
             HIGH-DENSITY LIPOPROTEIN
             HIGH-DENSITY LIPOPROTEIN
             APOLIPOPROTEIN
             CHOLESTEROL TRANSPORT
             LIPID TRANSPORT
             LOW-DENSITY LIPOPROTEIN
             TRANSFERASE ACTIVITY, TRANSFERRING GROUPS OTHER THAN AMINO-ACYL GROUPS
             APOLIPOPROTEIN
             CHOLESTEROL TRANSPORT
             HIGH-DENSITY LIPOPROTEIN
             LIPID TRANSPORT
             CARBOXYLESTERASE
             HIGH-DENSITY LIPOPROTEIN
             APOLIPOPROTEIN
             CHOLESTEROL TRANSPORT
             LIPID TRANSPORT
             HIGH-DENSITY LIPOPROTEIN
             APOLIPOPROTEIN
             CARBOXYLESTERASE
             LIPOPROTEIN LIPASE
             LOW-DENSITY LIPOPROTEIN
             APOLIPOPROTEIN
             PEROXISOME
             LIPID TRANSPORT
             CHOLESTEROL TRANSPORT
             INSULIN
             HIGH-DENSITY LIPOPROTEIN
             CHOLESTEROL TRANSPORT
             LIPID TRANSPORT
             CARBOXYLESTERASE
             TRANSFERASE ACTIVITY, TRANSFERRING GROUPS OTHER THAN AMINO-ACYL GROUPS
             TRANSPORT
             TRANSPORTER
             EXCRETION
             APOLIPOPROTEIN
             TRANSMEMBRANE RECEPTOR
             PROTEIN
             TRANSPORT
             MEMBRANE INVAGINATION
             PROTEIN
LOW-DENSITY LIPOPROTEIN
TRANSMEMBRANE RECEPTOR
PROTEIN
MEMBRANE INVAGINATION
PLASMINOGEN ACTIVATOR
TRANSPORT
TRANSPORTER
GLOBIN
APOLIPOPROTEIN
RNA EDITING
CHOLESTEROL TRANSPORT
APOLIPOPROTEIN
CHYMASE
CHOLESTEROL TRANSPORT
LIPID TRANSPORT
CAVEOLA
PEROXISOME
PLASMA MEMBRANE
PROTEIN
MOLECULAR_FUNCTION
OXIDOREDUCTASE ACTIVITY, ACTING ON THE CH-OH GROUP OF DONORS, OXYGEN AS ACCEPTOR
SMALL CONJUGATING PROTEIN LIGASE
ASTER
PROTEIN
MULTICELLULAR ORGANISMAL PROCESS
SECRETION
FIBRINOGEN
SOLUBLE FRACTION
PROTEIN
PLASMA MEMBRANE PART
SOLUBLE FRACTION
ESTABLISHMENT OF LOCALIZATION
INSULIN
MULTICELLULAR ORGANISMAL PROCESS
GLUCOSE HOMEOSTASIS
MENOPAUSE
 previous linkage to lipid metabolism. We identified ontologies that are highly enriched among the abstracts annotating the gene, and
and the ontology are shown. The strength represents the product between the log adjusted p-values of the gene and the phenotype
             Strength
               144572
               135555
              51296.5
              38118.9
                24401
              84149.7
              79472.8
              37037.3
              10328.7
              8093.12
                60229
              41646.4
              27409.3
              14642.2
              13246.8
                27547
              21752.4
              13735.9
              12045.6
              8888.51
              29160.3
              27329.7
              18482.8
              4875.15
              4432.29
              15050.5
              11967.2
              6040.79
              4225.41
              1768.81
              7673.42
              4361.92
              3419.96
              2279.41
              888.214
              2948.21
              2251.55
              1441.09
              1272.44
              1128.97
              3974.19
              3668.07
              100.602
              3387.05
              1424.78
              1371.09
              904.439
              70.6623
              8517.29
5063.63
990.162
940.339
67.6779
43.5638
3140.96
1582.81
31.2331
6439.93
20.3902
2474.61
1903.48
125.625
2533.35
1634.12
53.9324
33.3901
26.8346
5655.85
 85.784
26.3974
9.71932
8.56907
5601.54
92.1204
38.9946
38.6092
8.06241
5932.83
34.5477
9.25638
3249.64
1188.82
124.103
23.3715
 11.484
linkage to lipid metabolism. We identified ontologies that are highly enriched among the abstracts annotating the gene, and
tology are shown. The strength represents the product between the log adjusted p-values of the gene and the phenotype
             Association with Lipid Metabolism
             Protein responsible for transport of cholesterol out of cell into HDL. The protein responsible for reverse cholesterol transport. Mutations in this gene are
             associated with Tangier's disease




             Enzyme which hydrolyses triglycerides. In the context of HDL, it is necessary for the conversion of Large (HDL2) to small (HDL3) particles




             Neutral lipid transfer protein. Moves chilesteryl ester and triglycerides between lipoprotein classes. Functions to move cholesteryl esters from VLDL to HDL
             during the metabolism of VLDL. Also necessary for HDL2 to HDL3 conversion.




             This gene encodes the extracellular cholesterol esterifying enzyme, lecithin-cholesterol acyltransferase. The esterification of cholesterol is required for
             cholesterol transport. Mutations in this gene have been found to cause fish-eye disease as well as LCAT deficiency. [provided by RefSeq]




             Hormone regulated triglyceride lipase. Increased activity associated with increased coronary artery disease. Involved in conversion of HDL2 to HDL3. Reported
             to enhance binding of lipoproteins to cell surface receptors.




             The protein encoded by this gene has substantial phospholipase activity and may be involved in lipoprotein metabolism and vascular biology. This protein is
             designated a member of the TG lipase family by its sequence and characteristic lid region which provides substrate specificity for enzymes of the TG lipase
             family. [provided by RefSeq]




             Drugs which are PPARα agonists increase HDL levels while lowering VLDL. Select fatty acids are PPAR ligands. Fibrates are agonists. HDL is formed by the
             addition of lipid (cholesterol) to free apoA-I through reverse cholesterol transport mediated by ABCA1. Increased expression of PPArα increases ABCA1
             activity.




             Lysophospholipases are enzymes that act on biological membranes to regulate the multifunctional lysophospholipids. The protein encoded by this gene
             hydrolyzes lysophosphatidylcholine to glycerophosphorylcholine and a free fatty acid. This enzyme is present in the plasma and thought to be associated with
             high-density lipoprotein. A later paper contradicts the function of this gene. It demonstrates that this gene encodes a lysosomal enzyme instead of a
             lysophospholipase and has both calcium-independent phospholipase A2 and transacylase activities. [provided by RefSeq]




             Kozyraki et al showed that Cubilin (CUBN ), an endocytic receptor, can act as a receptor for both transferrin and apolipoprotein.
Related to classical LDL receptor. Related to VLDL receptor. Now linked with Altzheimer's through association with LDL receptor-related protein (LRP).




The encoded protein catalyzes the last step of the mitochondrial fatty acid beta-oxidation spiral. Unlike most mitochondrial matrix proteins, it contains a non-
cleavable amino-terminal targeting signal. [provided by RefSeq]
Example of Abstract Pubmed ID annotating the ontology and the gene (only genes with no obvious association with the phenotype are indicated h
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*




                                                                                                                   11606717
                                                                                                                   11027676


                                                                                                                   11606717
*
*
*
*
*




    12808465

    12231569
    12231569

*
*
*
*
*
he phenotype are indicated here)




               11940510 14645044 14980223 15252009 16300393 9358047 9760232
               11800564 11940510 12044175 12135367 12145410 12210842 12473103 14567694 14580189 14643898


               12951205 15060098 16497717
12808466 14527406 14528300
14980223 15229288 15319290 15924420 6268632 9358047

				
DOCUMENT INFO
Shared By:
Categories:
Stats:
views:4
posted:6/14/2011
language:English
pages:18