Jones et al 2001 T2 lifespan and Dauer, 26 genes

Gene list file name:Jones2001.T2_lifespan_Dauer.txt
Type of gene identifier:Cosmid name
Description:Jones et al 2001 Table2: Expression of Genes Implicated Previousl in Lifespan and Dauer  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

B0240.3 B0240.3 P W All gene names: daf-11; B0240.3; 5M200; CE05174; NM_073559; WBGene00000907; WP:CE05174 WormBase description: The daf-11 gene encodes a guanylate cyclase that affects dauer formation, chemotaxis, and axon formation; it is genetically upstream of daf-12 with respect to dauer larvae formation and is expressed in a subset of amphid neurons. WormBase CDS description: guanylate cyclase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer                                                                              

B0334.8 B0334.8 P W All gene names: age-1; daf-23; B0334.8; 2L810; CE23506; NM_064061; WBGene00000090; WP:CE23506 WormBase description: age-1 encodes the C. elegans ortholog of the phosphoinositide 3-kinase (PI3K) p110 catalytic subunit; AGE-1, supplied maternally and embryonically, is a central component of the C. elegans insulin-like signaling pathway, lying downstream of the DAF-2/insulin receptor and upstream of both the PDK-1 and AKT-1/AKT-2 kinases and the DAF-16 forkhead type transcription factor, whose negative regulation is the key output of the insulin signaling pathway; in accordance with its role in insulin signaling, AGE-1 activity is required for regulation of metabolism, life span, dauer formation, stress resistance, fertility, and embryonic development; although the age-1 expression pattern has not yet been reported, ectopic expression studies indicate that pan-neuronal age-1 expression is sufficient to rescue life-span defects, while neuronal, intestinal, or muscle expression can partially rescue dauer formation, and neuronal or muscle expression can rescue metabolic defects. WormBase CDS description: phosphatidylinositol 3-kinase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph, Reinke et al 2004, list of genes in cluster F,                            
                                              Reinke et al 2004, fem1 enriched genes, 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, ViswanathanM et al 2005  S2                               
                                              sir-2.1 regulated                                                                  

B0412.2 B0412.2 P W All gene names: daf-7; B0412.2; 3B431; CE01758; NM_064864; WBGene00000903; WP:CE01758 WormBase description: daf-7 encodes a member of the transforming growth factor beta superfamily that affects dauer larvae formation in a TGF-beta-mediated pathway and also affects egg laying; expressed in the ASI neurons. WormBase CDS description: transforming growth factor beta proteins
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, Reinke et al 2004, list of genes in cluster A,                              
                                              Reinke et al 2004, list of genes in cluster order                                  

C08A9.1 C08A9.1 P W All gene names: sod-3; C08A9.1; CE08002; MnSOD; NM_078363; WBGene00004932; WP:CE08002; XR707 WormBase description: sod-3 encodes a iron/manganese superoxide dismutase, predicted to be mitochondrial, that might defend against oxidative stress and promote normal lifespan; sod-3 mRNA levels are diminished by mutation of daf-16, and heterologously expressed SOD-3 in E. coli protects against methyl viologen-induced oxidative stress. WormBase CDS description: superoxide dismutase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, Lund et al 2002  Fig4 Mount 15, McElwee et al                               
                                              2003  T1 targets of daf-16, McElwee et al 2003  Fig4                               
                                              daf-16 target lifspan, Murphy et al 2003  Fig2 Class1                              
                                              elongate lifespan, Reinke et al 2004, fem1 enriched                                
                                              genes, Reinke et al 2004, mixed oogenesis soma,                                    
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol,                                    
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated, Wang et                             
                                              al 2003  S6 removed genes of contamination                                         

C08H9.5 C08H9.5 P W All gene names: old-1; tkr-1; C08H9.5; 2K154; CE02991; NM_063729; WBGene00003862; WP:CE02991 WormBase description: tyrosine-protein kinase (KIN15/KIN16 subfamily)
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, ViswanathanM et al 2005  S2 sir-2.1 regulated                               

C11E4.1 C11E4.1 P W All gene names: C11E4.1; CE31410; WBGene00007516; WP:CE31410; XK203 WormBase description: glutathione peroxidase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, 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                                                         

C11E4.2 C11E4.2 P W All gene names: C11E4.2; CE08102; WBGene00007517; WP:CE08102; XK205 WormBase description: glutathione peroxidase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, ViswanathanM et al 2005  S2 sir-2.1 regulated,                              
                                              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                                                                    

C15F1.7 C15F1.b P W All gene names: sod-1; C15F1.7; C15F1.7b.1; C15F1.7b.2; C15F1.B; 2H264; CE20508; CE23550; NM_063030; WBGene00004930; WP:CE20508; WP:CE23550 WormBase description: The sod-1 gene encodes an ortholog of human SOD1 (OMIM:147450), which when mutated leads to amyotrophic lateral sclerosis (OMIM:105400).
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, McCarroll et al 2004  SFig1-4 conserved w/                               
                                              Drosoph, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

F25E2.5 F25E2.5 P W All gene names: daf-3; F25E2.5; CE26364; CE28002; CE30963; NM_075760; WBGene00000899; WP:CE26364; WP:CE28002; WP:CE30963; XB438 WormBase description: daf-3 encodes a Smad protein; DAF-3 functions as a transcriptional regulator that is required for formation of the alternative dauer larval stage; DAF-3 activity is antagonized by signaling through the DAF-7/TGF-beta pathway which promotes reproductive growth; in yeast two-hybrid studies, DAF-3 interacts with SMA-3, another Smad protein that does not appear to have a role in dauer formation; a DAF-3::GFP fusion protein is expressed in many tissues that undergo remodeling during dauer development; DAF-3 localizes predominantly to the cytoplasm, but is also found associated with chromosomes in mitotic cells.
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, ViswanathanM et al 2005  S2 daf-16 Resveratrol                              

F26E4.12 F26E4.12 P W All gene names: F26E4.12; 1K359; CE09696; WBGene00009165; WP:CE09696 WormBase description: glutathione peroxidase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig5 conserved w/ yeast,                             
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F29C4.1 F29C4.1 P W All gene names: daf-1; F29C4.1; 4A889; CE17719; CE31492; WBGene00000897; WP:CE17719; WP:CE31492 WormBase description: daf-1 encodes a TGF-beta type I receptor homolog required, in association with the TGF beta-like type II receptor DAF-4, for the regulation of dauer formation by environmental signals through the ASI chemosensory neuron; DAF-1 is bound by BRA-1 and has an intracellular serine-threonine kinase domain; mutations in daf-1 result in constitutive formation of dauer larvae even in abundant food. WormBase CDS description: protein kinase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph, Reinke et al 2004, fem1 enriched genes, Reinke                            
                                              et al 2004, mixed oogenesis soma, ViswanathanM et al                               
                                              2005  S2 sir-2.1 regulated                                                         

F33H1.1 F33H1.1 P W All gene names: daf-19; daf-24; F33H1.1; 2K448; CE17763; CE28019; WBGene00000914; WP:CE17763; WP:CE28019 WormBase description: DNA binding transcription factor
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig5 conserved w/ yeast,                             
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph                                 

F55H2.1 F55H2.1 P W All gene names: SOD4-1; sod-4; F55H2.1; 3K588; CE25009; NM_066690; WBGene00004933; WP:CE25009 WormBase description: Superoxide dismutase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph                                                                            

H42K12.1 H42K12.1 P W All gene names: pdk-1; H33H01.A; H42K12.1; CE28739; CE28740; WBGene00003965; WP:CE28739; WP:CE28740; XB945 WormBase description: The pdk-1 gene encodes an ortholog of the human 3-phosphoinositide dependent kinase 1 (PDK1; OMIM:605213).
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph, Reinke et al 2004, fem1 enriched genes, Reinke                            
                                              et al 2004, mixed oogenesis soma                                                   

R03G5.5 R03G5.5 P W All gene names: R03G5.5; CE07402; WBGene00019846; WP:CE07402; XI416 WormBase description: glutathione peroxidase
                                              
Member of lists (Publications lists):
                                              Custodia et al 2001  T2                                           
                                              Glut-S-transferase, Jones et al 2001  T2 lifespan and                              
                                              Dauer, ViswanathanM et al 2005  S2 sir-2.1 regulated,                              
                                              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                                                               

R10H10.2 R10H10.2 P W All gene names: spe-26; R10H10.2; 4L154; CE06293; NM_069518; WBGene00004972; WP:CE06293 WormBase description: spe-26 encodes a Kelch motif-containing protein similar to the Drosophila proteins kelch and diablo and the Limulus (horseshoe crab) actin-bundling protein scruin; SPE-26 activity is required for several processes including embryogenesis, spermatogenesis, thermotolerance, and regulation of lifespan; SPE-26 mRNA is detected in spermatogonial cells and spermatocytes, but not in spermatids. WormBase CDS description: MIPP repeats
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, Reinke et al 2004, wt vs glp-4 enriched genes,                              
                                              Reinke et al 2004, list of genes in cluster order,                                 
                                              Reinke et al 2004, wt males vs glp4 male enriched ,                                
                                              Reinke et al 2004, spermatogenesis enriched genes,                                 
                                              Reinke et al 2004, list of genes in cluster D, Reinke                              
                                              et al 2004, fem3 enriched genes, Reinke et al 2004,                                
                                              shared sperm                                                                       

R11A8.4 R11A8.4 P W All gene names: sir-2.1; R11A8.4; R11A8.4.1; R11A8.4.2; 4L128; CE06302; NM_069511; WBGene00004800; WP:CE06302 WormBase description: sir-2.1 encodes a homolog of the S. cerevisiae gene SIR2. WormBase CDS description: Yeast regulatory protein SIR2 like
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig5 conserved w/ yeast,                             
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              Reinke et al 2004, wt herm vs wt male enriched gen,                                
                                              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                                                                    

R13H8.1 R13H8.1 P W All gene names: daf-16; daf-17; R13H8.1; R13H8.1e.1; R13H8.1e.2; 1L351; CE28771; CE28772; CE28773; CE33160; CE38722; CE38723; WBGene00000912; WP:CE28771; WP:CE28772; WP:CE28773; WP:CE33160; WP:CE38722; WP:CE38723 WormBase description: daf-16 encodes a transcription factor of the HNF-3/forkhead family (orthologous to mammalian AFX, FKHR, and FKHRL1) that acts in an insulin-mediated pathway to affect dauer formation, and that also affects life span and reproduction; DAF-16 can interact with CBP-1 in vitro, and interacts genetically both with other genes in the insulin signaling and with the nuclear hormone receptor DAF-12; daf-16 is broadly expressed in most if not all cells (though expression in the pharynx and in the somatic gonad differ for the two isoforms); DAF-16 is homologous to human FORKHEAD BOX O1A (FOXO1A), which when mutated leads to rhabdomyosarcoma (OMIM:136533).
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McElwee et al 2003  Fig4 daf-16 target lifspan,                             
                                              Wang et al 2003  S4 TransientList, 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, Wang et al 2003  Fig7 daf-16                                                   

T07A9.6 T07A9.6 P W All gene names: daf-18; T07A9.6; 4B174; CE26385; NM_067525; WBGene00000913; WP:CE26385 WormBase description: daf-18 encodes a lipid phosphatase homologous to the human PTEN tumor suppresor (OMIM:601728, mutated in Cowden disease and several cancers); DAF-18 negatively regulates insulin-like signaling mediated by DAF-2/IR and AGE-1/PI3K and thus plays a role in metabolism, development, and longevity; based on sequence and genetic analysis, DAF-18 is predicted to dephosphorylate AGE-1-generated PIP3 in order to limit activation of the downstream AKT-1 and AKT-2 kinases that negatively regulate DAF-16.
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph, Reinke et al 2004, fem1 enriched genes, 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 herm                             
                                              vs wt male enriched gen, Reinke et al 2004, list of                                
                                              genes in cluster E, ViswanathanM et al 2005  S2 daf-16                             
                                              Resveratrol, ViswanathanM et al 2005  S2 sir-2.1                                   
                                              regulated                                                                          

T24H7.1 T24H7.1 P W All gene names: phb-2; T24H7.1; 2G543; CE02883; NM_062849; WBGene00004015; WP:CE02883 WormBase description: Prohibitin
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig5 conserved w/ yeast,                             
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated, Wang et                             
                                              al 2003  S5 genes common to feeding ANOVA, Wang et al                              
                                              2003  S3  genes pass one-way ANOVA                                                 

T28B8.2 T28B8.2 P W All gene names: Ceinsulin-1; igf-1; ins-18; T28B8.2; 1I725; CE27217; NM_059830; WBGene00002101; WP:CE27217 WormBase description: The ins-18 gene encodes an insulin/IGF-like peptide that may act in a common pathway with daf-2 to regulate lifespan. WormBase CDS description: insulin-like growth factor I like
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, Murphy et al 2003  Fig2 Class1 elongate                                     
                                              lifespan, Reinke et al 2004, wt herm vs wt herm                                    
                                              enriched gen, Reinke et al 2004, IVb male soma enriched                            
                                              genes, 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                                                         

Y54G11A.6 Y54G11A.6 P W All gene names: ctl-1; Y54G11A.6; 2O592; CE30713; NM_064578; WBGene00000830; WP:CE30713; cat2 WormBase description: ctl-1 encodes a cytoplasmic catalase. WormBase CDS description: catalase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, Murphy et al 2003  Fig2 Class1 elongate                                     
                                              lifespan, ViswanathanM et al 2005  S2 sir-2.1 regulated                            

Y55D5A.5 Y55D5A.5 P W All gene names: daf-2; Y55D5A.5; Y55D5A_392.A; 3E86; CE27499; NM_065249; WBGene00000898; WP:CE27499 WormBase description: daf-2 encodes a predicted receptor tyrosine kinase that is the C. elegans insulin/IGF receptor ortholog; DAF-2 activity is required for a number of processes in C. elegans, including embryonic and larval development, formation of the developmentally arrested dauer larval stage, adult longevity, reproduction, fat storage, and response to exogenous stressors such as high temperature or bacterial infection; DAF-2 signals through a conserved PI 3-kinase pathway to negatively regulate the activity of DAF-16, a Forkhead-related transcription factor, by inducing its phosphorylation and nuclear exclusion; amongst the 38 predicted insulin-like molecules in C. elegans, genetic and microarray analyses suggest that at least DAF-28, INS-1, and INS-7 are likely DAF-2 ligands; genetic mosaic and tissue-specific promoter studies indicate that daf-2 can function cell nonautonomously and within multiple cell types to influence dauer formation and adult lifespan, likely by regulating the production of secondary signals that coordinate growth and longevity throughout the animal.
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph, Reinke et al 2004, intrinsic, Reinke et al                                
                                              2004, wt vs glp-4 enriched genes, Reinke et al 2004,                               
                                              list of genes in cluster order, Reinke et al 2004, list                            
                                              of genes in cluster E, Roy et al 2002  S3 muscle genes                             

ZC395.2 ZC395.2 P W All gene names: clk-1; coq-1; coq-7; ZC395.2; 3G369; CE01438; NM_065727; WBGene00000536; WP:CE01438 WormBase description: The clk-1 gene partially controls lifespan in vivo; it encodes a homolog of the yeast COQ9 protein, and is necessary for the biosynthesis of ubiquinone (UQ(9)) from demethoxyubiquinone (DMQ(9)).
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig5 conserved w/ yeast,                             
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              Romagnolo et al 2002  Fig3b Oxidation, Roy et al 2002                              
                                              S3 muscle genes, ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

ZC395.6 ZC395.6 P W All gene names: gro-1; ZC395.6; 3G355; CE30119; NM_065721; WBGene00001740; WP:CE30119 WormBase description: This gene encodes a protein predicted by Eisenberg and coworkers, with 52% accuracy, to be mitochondrial. WormBase CDS description: tRNA isopentenyltransferase
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05, Jones et al 2001  T2 lifespan and Dauer,                                   
                                              McCarroll et al 2004  SFig5 conserved w/ yeast, 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, list of genes in                                  
                                              cluster E, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated                                                                          

ZK430.1 ZK430.1 P W All gene names: T12C9.2; ZK430.1; 2E721; CE05078; WBGene00022739; WP:CE05078
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  T2 lifespan and                                 
                                              Dauer, McCarroll et al 2004  SFig1-4 conserved w/                                  
                                              Drosoph, Reinke et al 2004, intrinsic, Reinke et al                                
                                              2004, wt vs glp-4 enriched genes, Reinke et al 2004, GO                            
                                              categories