Golden et al 2004, N2 differentially expressed gen, 22 genes

Gene list file name:Golden2004_T2_N2_time.txt
Type of gene identifier:MA primer pair (sjj)
Description:Golden et al 2004, Table 2, N2 genes differentially expressed as a function of time  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

C11E4.7 C11E4.7 P W All gene names: C11E4.7; CE08107; WBGene00007521; WP:CE08107; XK237
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Reinke et al 2004, list of genes in                                 
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster C, Reinke et al 2004, mixed sperm soma, Reinke                             
                                              et al 2004, fem3 enriched genes, ViswanathanM et al                                
                                              2005  S2 daf-16 Resveratrol                                                        

C52E4.1 C52E4.1 P W All gene names: cpr-1; gcp-1; C52E4.1; 5M457; CE31896; CPROT/1; NM_073601; WBGene00000781; WP:CE31896 WormBase description: cpr-1 encodes a cysteine protease of the cathepsin B-like cysteine protease family; cpr-1 appears to be required for embryogenesis; cpr-1 is specifically expressed in the gut of all stages except the embryo and around developing embryos in the gonad; expression of cpr-1 is regulated by three promoter GATA motifs. WormBase CDS description: cathepsin-like cysteine protease
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Murphy et al 2003  Fig2 Class1 elongate                             
                                              lifespan, ViswanathanM et al 2005  S2 sir-2.1                                      
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

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                                      

F20D1.5 F20D1.5 P W All gene names: arl-7; F20D1.5; NM_078087; WBGene00000191; XP600
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Reinke et al 2004, list of genes in                                 
                                              cluster order, Reinke et al 2004, mixed sperm soma,                                
                                              Reinke et al 2004, wt herm vs wt herm enriched gen,                                
                                              Reinke et al 2004, list of genes in cluster D, Reinke                              
                                              et al 2004, fem3 enriched genes                                                    

F21F8.4 F21F8.4 P W All gene names: F21F8.4; F21F8.4.1; F21F8.4.2; 5I751; CE09540; WBGene00017678; WP:CE09540 WormBase description: protease
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen                                                                      

F28D1.5 F28D1.5 P W All gene names: thn-2; F28D1.5; 4N149; CE05745; NM_069961; WBGene00009215; WP:CE05745 WormBase description: Arabidopsis pathogenesis-related protein 5 like
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Golden et al 2004, daf-2 differentially                             
                                              expressed , Golden et al 2004, N2 vs daf-2 age                                     
                                              different gene, Jones et al 2001  Non dauer genes                                  
                                              P<0.05, Jones et al 2001  T3 20 most abundant                                      
                                              Mixed-stage, Murphy et al 2003  Fig2 Class1 elongate                               
                                              lifespan, ReichertK et al 2005  T3 xenobiotic                                      
                                              downregulated, ViswanathanM et al 2005  S2 sir-2.1                                 
                                              regulated                                                                          

F36D3.9 F36D3.9 P W All gene names: cpr-2; F36D3.9; 5R14; CE30347; CPROT/2; NM_074785; WBGene00000782; WP:CE30347 WormBase description: cysteine protease
                                              
Member of lists (Publications lists):
                                              Bishop et al 2004  T4 57 vhl-1 depend                             
                                              hif-1 indep, Golden et al 2004, N2 vs daf-2 different                              
                                              genes at , Golden et al 2004, N2 vs daf-2 age different                            
                                              gene, Golden et al 2004, N2 differentially expressed                               
                                              gen, Jones et al 2001  T3 20 most abundant Dauer, Lund                             
                                              et al 2002  Fig1 aging-regulated genes, Murphy et al                               
                                              2003  Fig2 Class1 elongate lifespan, ViswanathanM et al                            
                                              2005  S2 daf-16 Resveratrol, ViswanathanM et al 2005                               
                                              S2 sir-2.1 regulated, Wang et al 2003  S8 SAGE genes in                            
                                              the dauer exit                                                                     

F42A10.7 F42A10.7 P W All gene names: F42A10.7; F42A10.7.1; F42A10.7.2; 3H268; CE01298; WBGene00018343; WP:CE01298
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Golden et al 2004, N2 vs daf-2 age                                  
                                              different gene, Reinke et al 2004, wt herm vs wt herm                              
                                              enriched gen, ViswanathanM et al 2005  S2 sir-2.1                                  
                                              regulated                                                                          

F44C4.3 F44C4.3 P W All gene names: cpr-4; F44C4.3; F44C4.3.1; F44C4.3.2; 5H95; CE07251; NM_072281; WBGene00000784; WP:CE07251 WormBase description: cpr-4 encodes a cathepsin B-like cysteine protease expressed at all life stages. WormBase CDS description: cathepsin B-like cysteine proteinase 4 precursor
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Reinke et al 2004, list of genes in                                 
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster C, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated                                                                          

F49A5.6 F49A5.6 P W All gene names: thn-4; F49A5.6; 5R346; CE16069; NM_074862; WBGene00009858; WP:CE16069 WormBase description: Thaumatin family
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Golden et al 2004, N2 vs daf-2 different                            
                                              genes at , Golden et al 2004, N2 vs daf-2 age different                            
                                              gene, Murphy et al 2003  Fig2 Class1 elongate lifespan                             

H22K11.1 H22K11.1 P W All gene names: asp-3; H22K11.1; CE19495; NM_076741; WBGene00000216; WP:CE19495; XH411 WormBase description: asp-3 encodes an aspartyl protease homolog that is required, in parallel with ASP-4 but downstream of CLP-1 and TRA-3, for degenerative (necrotic-like) cell death in neurons induced by mutations such as mec-4(d), deg-3(d), or gsa-1(gf). WormBase CDS description: aspartyl protease
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Murphy et al 2003  Fig2 Class1 elongate                             
                                              lifespan, ViswanathanM et al 2005  S2 sir-2.1 regulated                            

K07G5.2 K07G5.2 P W All gene names: xpa-1; K07G5.2; 1H737; CE06130; NM_059624; WBGene00006963; WP:CE06130 WormBase description: xpa-1 encodes an ortholog of human XPA, the xeroderma pigmentosum complementation group A protein (OMIM:278700, mutations are associated with sensitivity to ultraviolet light and carcinomata at an early age); by homology, XPA-1 is predicted to function as a DNA-binding protein that is required for nucleotide excision repair of damaged DNA; in C. elegans, loss of xpa-1 activity via mutation or RNA-mediated interference (RNAi) results in increased sensitivity to UV irradiation at all stages of development; xpa-1 mRNA is detected in eggs and mixed stage populations. WormBase CDS description: DNA-repair protein XP-A homolog like
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 vs daf-2 age                                
                                              different gene, Golden et al 2004, N2 differentially                               
                                              expressed gen, McCarroll et al 2004  SFig1-4 conserved                             
                                              w/ Drosoph, Reinke et al 2004, list of genes in cluster                            
                                              order, Reinke et al 2004, intrinsic, Reinke et al 2004,                            
                                              wt vs glp-4 enriched genes, Reinke et al 2004, wt herm                             
                                              vs wt male enriched gen, Reinke et al 2004, GO                                     
                                              categories, Reinke et al 2004, list of genes in cluster                            
                                              E, ViswanathanM et al 2005  S2 sir-2.1 regulated                                   

M60.2 M60.1 P W All gene names: M60.2; M60.2.1; M60.2.2; CE28630; WBGene00019779; WP:CE28630; XI865
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 vs daf-2                                    
                                              different genes at , Golden et al 2004, N2 vs daf-2 age                            
                                              different gene, Golden et al 2004, N2 differentially                               
                                              expressed gen, Reinke et al 2004, wt herm vs wt male                               
                                              enriched gen, Reinke et al 2004, herm soma enriched                                
                                              genes, Wang et al 2003  S3  genes pass one-way ANOVA,                              
                                              Wang et al 2003  S4 Early genes, Wang et al 2003  S4                               
                                              genes pass two-wayANOVA P0                                                         

T27E4.2 T27E4.2 P W All gene names: hsp-16.11; T27E4.2; 5J571; NM_072956; WBGene00002017 WormBase description: hsp-16.11 encodes a 16-kD heat shock protein (HSP) that is a member of the hsp16/hsp20/alphaB-crystallin (HSP16) family of heat shock proteins, and that is identical to the protein encoded by hsp-16.1; hsp-16.11 expression is induced in response to heat shock or other environmental stresses; HSP-16.11 is likely to function as passive ligand temporarily preventing unfolded proteins from aggregating; HSP-16.11 has been shown to interact with intracellular human beta amyloid peptide, a primary component of the extracellular plaques found in Alzheimer's disease. WormBase CDS description: heat shock protein HSP16-1
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, GuhaThakurta et al 2002  T1 upregu on                               
                                              heat stress, Romagnolo et al 2002  Fig2a heat shock,                               
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated,                                     
                                              ViswanathanM et al 2005  S2 UPR genes, ViswanathanM et                             
                                              al 2005  Fig6A Ethanol HS                                                          

W07B8.4 W07B8.4 P W All gene names: W07B8.4; 5B610; CE14680; WBGene00021072; WP:CE14680 WormBase description: thiol protease
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, ViswanathanM et al 2005  S2 sir-2.1                                 
                                              regulated                                                                          

W07B8.5 W07B8.5 P W All gene names: cpr-5; W07B8.5; 5B612; CE14682; NM_070982; WBGene00000785; WP:CE14682 WormBase description: cpr-5 encodes a cysteine protease. WormBase CDS description: thiol protease
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Reinke et al 2004, fem1 enriched genes,                             
                                              Reinke et al 2004, list of genes in cluster order,                                 
                                              Reinke et al 2004, mixed oogenesis soma, Reinke et al                              
                                              2004, list of genes in cluster C, Reinke et al 2004, GO                            
                                              categories, ViswanathanM et al 2005  S2 daf-16                                     
                                              Resveratrol, ViswanathanM et al 2005  S2 sir-2.1                                   
                                              regulated, Wang et al 2003  S3  genes pass one-way                                 
                                              ANOVA, Wang et al 2003  S4 Early genes, Wang et al 2003                            
                                               S4 genes pass two-wayANOVA P0                                                     

Y38A8.2 Y38A8.2 P W All gene names: pbs-3; Y38A8.2; Y38A8.2.1; Y38A8.2.2; 2F244; CE07571; NM_062512; WBGene00003949; WP:CE07571 WormBase description: pbs-3 encodes a B-type subunit of the 26S proteasome's 20S protease core particle; by homology, PBS-3 is predicted to function in ATP/ubiquitin-dependent nonlysosomal protein degradation; loss of pbs-3 activity via large-scale RNAi screens indicates that, in C. elegans, PBS-3 is required for embryonic and germline development, movement, normal body coloration, and normal body morphology. WormBase CDS description: Peptidase
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 vs daf-2                                    
                                              different genes at , Golden et al 2004, N2 vs daf-2 age                            
                                              different gene, Golden et al 2004, N2 differentially                               
                                              expressed gen, McCarroll et al 2004  SFig5 conserved w/                            
                                              yeast, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph, Reinke et al 2004, intrinsic, Reinke et al                                
                                              2004, wt vs glp-4 enriched genes, ViswanathanM et al                               
                                              2005  S2 sir-2.1 regulated                                                         

Y39B6A.20 Y39B6B.g P W All gene names: asp-1; Y39B6A.20; Y39B6A.20.1; Y39B6A.20.2; Y39B6B.G; 5T524; CE21681; NM_171587; WBGene00000214; WP:CE21681 WormBase description: asp-1 encodes a homolog of cathepsin D aspartic protease; it is transcribed exclusively in intestinal cells of the late embryo and early larvae and is not observed in older larvae or adults; ASP-1 is dispensable for neuronal degeneration. WormBase CDS description: peptidase (A1 pepsin family)
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, mixed sperm soma,                              
                                              Reinke et al 2004, fem3 enriched genes, Reinke et al                               
                                              2004, IVb male soma enriched genes                                                 

Y40H7A.10 Y40H7A.10 P W All gene names: Y40H7A.10; 4P968; CE21821; WBGene00012747; WP:CE21821 WormBase description: Cysteine protease
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Golden et al 2004, N2 vs daf-2 different                            
                                              genes at , Jones et al 2001  Non dauer genes P<0.05,                               
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated,                                     
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

Y46H3A.2 Y46H3A.E P W All gene names: hsp-16.41; HSP16-41; Y46H3A.2; Y46H3A.E; 5C283; CE22003; NM_071107; WBGene00002018; WP:CE22003 WormBase description: hsp-16.41 encodes a 16-kD heat shock protein (HSP) that is a member of the hsp16/hsp20/alphaB-crystallin (HSP16) family of heat shock proteins; an hsp-16.41 reporter fusion, expressed broadly but strongest in intestine and pharynx, is induced in response to heat shock or other environmental stresses; expression is detectable in somatic tissues in post-gastrulation embryos, all larval stages, and in adults; HSP-16.41 is likely to function as a passive ligand temporarily preventing unfolded proteins from aggregating. WormBase CDS description: heat shock protein
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Link et al 2003  T3 Abeta highly                                    
                                              induced, Link et al 2003  T2 Abeta induced, 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                                                         

Y46H3A.3 Y46H3A.D P W All gene names: hsp-16.2; Y46H3A.3; Y46H3A.D; 5C282; CE22002; NM_071106; WBGene00002016; WP:CE22002 WormBase description: hsp-16.2 encodes a 16-kD heat shock protein (HSP) that is a member of the hsp16/hsp20/alphaB-crystallin (HSP16) family of heat shock proteins; hsp-16.2 expression, strongest in intestine and pharynx, is induced in response to heat shock or other environmental stresses; HSP-16.2 has been shown to interact with intracellular human beta amyloid peptide, a primary component of the extracellular plaques found in Alzheimer's disease; HSP-16.2 is likely to function as a passive ligand temporarily preventing unfolded proteins from aggregating. WormBase CDS description: heat shock protein
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Golden et al 2004, daf-2 differentially                             
                                              expressed , Link et al 2003  T3 Abeta highly induced,                              
                                              Link et al 2003  T2 Abeta induced, Murphy et al 2003                               
                                              Fig2 Class1 elongate lifespan, Romagnolo et al 2002                                
                                              Fig2a heat shock, ViswanathanM et al 2005  S2 sir-2.1                              
                                              regulated                                                                          

Y47H9C.6 Y47H9C.6 P W All gene names: csp-3; Y47H9C.6; 1M480; CE27635; NM_060610; WBGene00000821; WP:CE27635 WormBase description: csp-3 encodes a protein that is homologous to the C-terminal domain of caspase-like cysteine proteases; unlike other caspases, CSP-3 does not contain a middle or N-terminal domain, and thus may either function in concert with the middle domains of other caspases or may play a regulatory (dominant negative) role in caspase activation; as loss of csp-3 activity via large-scale RNAi does not result in any obvious abnormalities, the precise role of CSP-3 in C. elegans development and/or behavior is not yet known. WormBase CDS description: ICE-like protease (caspase) p10 domain.
                                              
Member of lists (Publications lists):
                                              Golden et al 2004, N2 differentially                              
                                              expressed gen, Reinke et al 2004, mixed sperm soma,                                
                                              Reinke et al 2004, fem3 enriched genes