Bishop et al 2004 T1 Upregulated in vhl-1 vs WT, 30 genes

Gene list file name:Bishop2004.T1_30Upregulated_in_vhl-1_vs_WT.txt
Type of gene identifier:Cosmid name
Description:Bishop et al 2004 Table1: 30 genes Upregulated in vhl-1 vs WT  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

C04F6.3 C04F6.3 P W All gene names: cht-1; C04F6.3; C04F6.3.1; C04F6.3.2; CE03923; CHT1; NM_076187; WBGene00000503; WP:CE03923; XE16 WormBase description: cht-1 encodes a chitinase orthologous to human chitinase-1 (OMIM:600031, mutations are associated with chitotriosidase deficiency); CHT-1 is predicted to function as an extracellular O-glycosyl hydrolase that hydrolyzes the glycosidic bond between two or more carbohydrates; in C. elegans, CHT-1 may play a role in embryogenesis, and may also be required for cuticle degradation during molting and degradation of chitin-containing pathogens as part of a host defense mechanism. WormBase CDS description: glycosyl hydrolase (family 18)
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Jones et al 2001  Non dauer genes P<0.05,                             
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              Reinke et al 2004, list of genes in cluster order,                                 
                                              Reinke et al 2004, list of genes in cluster E,                                     
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

C09E8.3 C09E8.3 P W All gene names: mlt-10; C09E8.3; 2A841; CE19349; WBGene00015646; WP:CE19349
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Lund et al 2002  Fig1 aging-regulated                                 
                                              genes, Reinke et al 2004, list of genes in cluster                                 
                                              order, Reinke et al 2004, list of genes in cluster B,                              
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated,                                     
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol, Wang et                            
                                              al 2003  S4 Climbing, Wang et al 2003  S3  genes pass                              
                                              one-way ANOVA, Wang et al 2003  S4 genes pass                                      
                                              two-wayANOVA P0                                                                    

C16C10.3 C16C10.3 P W All gene names: C16C10.3; 3F262; CE01494; WBGene00007624; WP:CE01494
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Reinke et al 2004, fem1 enriched genes,                               
                                              Reinke et al 2004, Fig2b shared gemlines, Reinke et al                             
                                              2004, list of genes in cluster order, Reinke et al                                 
                                              2004, oogenesis enriched genes, Reinke et al 2004, wt                              
                                              vs glp-4 enriched genes, Reinke et al 2004, wt males vs                            
                                              glp4 male enriched , Reinke et al 2004, list of genes                              
                                              in cluster E, ViswanathanM et al 2005  S2 sir-2.1                                  
                                              regulated                                                                          

C31C9.1 C31C9.1 P W All gene names: tag-10; C31C9.1; 2N925; CE32597; CE32598; WBGene00006404; WP:CE32597; WP:CE32598 WormBase description: This gene encodes a protein predicted by Eisenberg and coworkers, with 52% accuracy, to be mitochondrial
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, ViswanathanM et al 2005  S2 daf-16                                    
                                              Resveratrol, Wang et al 2003  S4 Early genes, Wang et                              
                                              al 2003  S3  genes pass one-way ANOVA, Wang et al 2003                             
                                              S4 genes pass two-wayANOVA P0                                                      

C32H11.10 C32H11.10 P W All gene names: dod-21; C32H11.10; 4N699; CE19717; NM_070071; WBGene00007873; WP:CE19717
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Murphy et al 2003  Fig2 Class2 shorten                                
                                              lifespan                                                                           

C32H11.9 C32H11.9 P W All gene names: C32H11.9; 4N698; CE19716; WBGene00007872; WP:CE19716
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Murphy et al 2003  Fig2 Class2 shorten                                
                                              lifespan                                                                           

C55B7.4 C55B7.4 P W All gene names: acdh-1; dod-12; C55B7.4; C55B7.4b.1; C55B7.4b.2; C55B7.4b.3; C55B7.4b.4; 1H75; CE09015; CE32840; NM_059470; NM_181994; WBGene00016943; WP:CE09015; WP:CE32840 WormBase description: acyl-CoA dehydrogenase
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Golden et al 2004, N2 differentially                                  
                                              expressed gen, Golden et al 2004, N2 vs daf-2 different                            
                                              genes at , McCarroll et al 2004  SFig1-4 conserved w/                              
                                              Drosoph, Reinke et al 2004, herm soma enriched genes,                              
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F07C4.7 F07C4.7 P W All gene names: grsp-4; F07C4.7; 5I105; CE09206; WBGene00017201; WP:CE09206
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Reinke et al 2004, list of genes in                                   
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster B, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol, Wang et al 2003  S4 Climbing, Wang et al                              
                                              2003  S3  genes pass one-way ANOVA, Wang et al 2003  S4                            
                                              genes pass two-wayANOVA P0                                                         

F16B4.7 F16B4.7 P W All gene names: F16B4.7; 5C65; CE17017; WBGene00017509; WP:CE17017
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, ViswanathanM et al 2005  S2 daf-16                                    
                                              Resveratrol, Wang et al 2003  S3  genes pass one-way                               
                                              ANOVA, Wang et al 2003  S4 Dauer Enriched, Wang et al                              
                                              2003  S4 genes pass two-wayANOVA P0                                                

F22B5.4 F22B5.4 P W All gene names: F22B5.4; 2I741; CE02199; WBGene00009042; WP:CE02199
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T2 Egl-9 hif-1                                 
                                              pathway genes, Bishop et al 2004  T1 Upregulated in                                
                                              vhl-1 vs WT, Reinke et al 2004, mixed sperm soma,                                  
                                              Reinke et al 2004, fem3 enriched genes, Shen et al 2005                            
                                               T1 hif-1 depend hypoxia, ViswanathanM et al 2005  S2                              
                                              sir-2.1 regulated, ViswanathanM et al 2005  S2 daf-16                              
                                              Resveratrol                                                                        

F22E12.4 egl-9 P W All gene names: egl-9; F22E12.4; F22E12.4a.1; F22E12.4a.2; F22E12.4b.1; F22E12.4b.2; 5K955; CE27755; CE31342; CE38327; CE38328; NM_171533; WBGene00001178; WP:CE27755; WP:CE31342; WP:CE38327; WP:CE38328 WormBase description: egl-9 encodes a dioxygenase that negatively regulates hypoxia inducible factor (hif-1) by hydroxylating prolyl residues in HIF-1.
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Dauer specific genes                            
                                              P<0.05, McCarroll et al 2004  SFig1-4 conserved w/                                 
                                              Drosoph, Wang et al 2003  S7 SAGE genes in the dataset,                            
                                              Wang et al 2003  S8 SAGE genes in the dauer exit                                   

F28B4.3 F28B4.3 P W All gene names: F28B4.3; CE07153; WBGene00017892; WP:CE07153; XD846 WormBase description: EGF-like repeat
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Murphy et al 2003  Fig2 Class2 shorten                                
                                              lifespan, Wang et al 2003  S4 Early genes, Wang et al                              
                                              2003  S3  genes pass one-way ANOVA, Wang et al 2003  S4                            
                                              genes pass two-wayANOVA P0                                                         

F35G2.4 phy-2 P W All gene names: phy-2; F35G2.4; F35G2.4.1; F35G2.4.2; 4M976; CE05811; NM_069916; WBGene00004025; WP:CE05811 WormBase description: prolyl 4-hydroxylase alpha subunit
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Reinke et al 2004, list of genes                             
                                              in cluster A, Reinke et al 2004, list of genes in                                  
                                              cluster order, Romagnolo et al 2002  Fig3b others                                  

F37B1.8 F37B1.8 P W All gene names: gst-19; F37B1.8; 2N916; CE09995; NM_064463; WBGene00001767; WP:CE09995 WormBase description: glutathione S-transferase
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Custodia et al 2001  T2                                               
                                              Glut-S-transferase, Wang et al 2003  S6 removed genes                              
                                              of contamination                                                                   

H14N18.4 H14N18.4 P W All gene names: H14N18.4; 5J406; CE17976; CE30811; WBGene00019204; WP:CE17976; WP:CE30811 WormBase description: transpeptidase
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Reinke et al 2004, wt herm vs wt herm                                 
                                              enriched gen, Wang et al 2003  S6 removed genes of                                 
                                              contamination                                                                      

K08C7.5 fmo-12 P W All gene names: fmo-12; fmo-2; K08C7.5; 4L447; CE06138; NM_069571; WBGene00001477; WP:CE06138 WormBase description: flavin-containing monoxygenase
                                              
Member of lists (Publications lists):
                                              Wang et al 2003  S4 Climbing, Wang et                             
                                              al 2003  S3  genes pass one-way ANOVA, Wang et al 2003                             
                                              S4 genes pass two-wayANOVA P0                                                      

K08D8.5 K08D8.5 P W All gene names: K08D8.5; 4N676; CE06144; WBGene00010659; WP:CE06144
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Lund et al 2002  Fig1 aging-regulated                                 
                                              genes, Murphy et al 2003  Fig2 Class2 shorten lifespan,                            
                                              Reinke et al 2004, wt herm vs wt herm enriched gen,                                
                                              Wang et al 2003  S4 Early genes, Wang et al 2003  S3                               
                                              genes pass one-way ANOVA, Wang et al 2003  S4 genes                                
                                              pass two-wayANOVA P0                                                               

K09E4.4 K09E4.4 P W All gene names: K09E4.4; K09E4.4.1; K09E4.4.2; 2O406; CE32692; WBGene00010722; WP:CE32692 WormBase description: K09E4.4 is orthologous to the human gene N-ACETYLGALACTOSAMINIDASE, ALPHA- (NAGLU; OMIM:104170), which when mutated leads to disease.
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Jones et al 2001  Dauer specific genes                                
                                              P<0.05, McCarroll et al 2004  SFig1-4 conserved w/                                 
                                              Drosoph, Wang et al 2003  S3  genes pass one-way ANOVA,                            
                                              Wang et al 2003  S8 SAGE genes in the dauer exit, Wang                             
                                              et al 2003  S7 SAGE genes in the dataset, Wang et al                               
                                              2003  S4 genes pass two-wayANOVA P0, Wang et al 2003                               
                                              S4 Dauer Enriched                                                                  

R01E6.3 cah-4 P W All gene names: cah-4; R01E6.3; CE29433; CE29434; NM_077863; NM_077864; WBGene00000282; WP:CE29433; WP:CE29434; XO161 WormBase description: cah-4 encodes a carbonic anhydrase homolog, which is rather divergent from other such homologs in C. elegans (with at most 38% identity to any other carbonic anhydrase, in or out of C. elegans); it is individually dispensable for viability and for grossly normal postembryonic morphology, and thus may have a more subtle biological function than the basic cytoprotective functions expected for carbonic anhydrases. WormBase CDS description: carbonic anhydrase
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, ViswanathanM et al 2005  S2                                  
                                              sir-2.1 regulated                                                                  

R09B5.3 R09B5.3 P W All gene names: cnc-2; R09B5.3; R09B5.3.1; R09B5.3.2; 5B928; CE12622; NM_071017; WBGene00000556; WP:CE12622
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Jones et al 2001  Non dauer genes P<0.05,                             
                                              Jones et al 2001  T3 20 most abundant Mixed-stage                                  

R166.5 R166.5 P W All gene names: mnk-1; R166.5; 2K836; CE03584; CE32920; WBGene00011304; WP:CE03584; WP:CE32920 WormBase description: serine/threonine kinase
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, McCarroll et al 2004  SFig1-4 conserved w/                            
                                              Drosoph, Shen et al 2005  T1 hif-1indepen hypoxia                                  

T03F1.6 T03F1.6 P W All gene names: T03F1.6; 1E408; CE13106; CE28248; WBGene00020188; WP:CE13106; WP:CE28248
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Wang et al 2003  S4 TransientList, Wang et                            
                                              al 2003  S3  genes pass one-way ANOVA, Wang et al 2003                             
                                              S4 genes pass two-wayANOVA P0                                                      

T05B4.2 nhr-57 P W All gene names: nhr-57; T05B4.2; 5E613; CE13195; NM_071752; WBGene00003647; WP:CE13195 WormBase description: zinc finger protein
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Dauer specific genes                            
                                              P<0.05, Wang et al 2003  S7 SAGE genes in the dataset,                             
                                              Wang et al 2003  S8 SAGE genes in the dauer exit                                   

T20F5.4 T20F5.4 P W All gene names: T20F5.4; 1E482; CE13822; WBGene00020626; WP:CE13822
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Reinke et al 2004, list of genes in                                   
                                              cluster A, Reinke et al 2004, list of genes in cluster                             
                                              order                                                                              

W07A12.6 W07A12.6 P W All gene names: W07A12.6; 2J447; CE35050; WBGene00012323; WP:CE35050
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Shen et al 2005  T1 hif-1 depend hypoxia,                             
                                              Wang et al 2003  S6 removed genes of contamination                                 

Y34D9A.1 Y34D9A.1 P W All gene names: Y34D9A.1; 1B494; CE27249; WBGene00021327; WP:CE27249
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, McCarroll et al 2004  SFig1-4 conserved w/                            
                                              Drosoph, ViswanathanM et al 2005  S2 daf-16 Resveratrol                            

Y43F8C.2 Y43F8C.2 P W All gene names: nlp-26; Y43F8C.2; Y43F8C.2.1; Y43F8C.2.2; 5U89; CE21900; NM_075401; WBGene00003764; WP:CE21900 WormBase description: nlp-26 encodes a predicted neuropeptide not found in multigene families within C. elegans and is not clearly related to other well-characterized neuropeptides.
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, ViswanathanM et al 2005  S2 sir-2.1                                   
                                              regulated, Wang et al 2003  S6 removed genes of                                    
                                              contamination                                                                      

Y51A2A.4 Y51A2A.4 P W All gene names: Y51A2A.4; 5S775; CE25360; WBGene00013060; WP:CE25360
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, ViswanathanM et al 2005  S2 sir-2.1                                   
                                              regulated, Wang et al 2003  S3  genes pass one-way                                 
                                              ANOVA, Wang et al 2003  S4 Dauer Enriched, Wang et al                              
                                              2003  S4 genes pass two-wayANOVA P0                                                

Y59A8B.19 Y59A8B.19 P W All gene names: Y59A8B.19; Y59A8C.F; 5S487; CE26209; WBGene00013351; WP:CE26209
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT, Wang et al 2003  S3  genes pass one-way                               
                                              ANOVA, Wang et al 2003  S4 Dauer Enriched, Wang et al                              
                                              2003  S4 genes pass two-wayANOVA P0                                                

ZK896.4 ZK896.4 P W All gene names: ZK896.4; 4N644; CE15455; WBGene00014135; WP:CE15455
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T1 Upregulated in                              
                                              vhl-1 vs WT