Shen et al 2005 T1 hif-1 depend hypoxia, 63 genes

Gene list file name:Shen2005.T1_63Hif-1depend_hypoxia.txt
Type of gene identifier:Cosmid name
Description:Shen et al 2005 T1 63 hif-1 dependent hypoxia  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

C01B4.1 str-257 P W All gene names: str-257; C01B4.1; C01B4.J; 5C997; CE38138; NM_071288; WBGene00006283; WP:CE38138 WormBase description: 7TM chemoreceptor, str family
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

C01G6.8 cam-1 P W All gene names: cam-1; kin-8; C01G6.8; 2J586; CE24774; CE32563; CE39126; WBGene00000289; WP:CE24774; WP:CE32563; WP:CE39126 WormBase description: The cam-1 gene encodes a receptor tyrosine kinase of the immunoglobulin superfamily that is orthologous to human ROR1 (OMIM:602336) and ROR2 (OMIM:602337, mutation of which leads to type B brachydactyly) and is required for locomotion, cell migration, asymmetric cell division, axon outgrowth, and dauer formation; CAM-1 is broadly expressed during embryogenesis and larval development with expression first appearing at the 200-cell stage of embryogenesis.
                                              
Member of lists (Publications lists):
                                              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,                                     
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

C01G6.9 C01G6.9 P W All gene names: C01G6.9; 2J584; CE00871; WBGene00007229; WP:CE00871
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster order, Shen et al 2005  T1 hif-1 depend                                    
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

C04A2.1 C04A2.1 P W All gene names: C04A2.1; 2H139; CE36523; WBGene00015410; WP:CE36523
                                              
Member of lists (Publications lists):
                                              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                                     

C24B9.9 C24B9.9 P W All gene names: dod-3; C24B9.9; 5D208; CE17451; NM_071341; WBGene00016052; WP:CE17451
                                              
Member of lists (Publications lists):
                                              Kwon et al 2004  T1 late-repression                               
                                              Ethanol-respon, Murphy et al 2003  Fig2 Class1 elongate                            
                                              lifespan, Reinke et al 2004, IVb male soma enriched                                
                                              genes, Shen et al 2005  T1 hif-1 depend hypoxia, 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                                                                    

C29F9.5 C29F9.5 P W All gene names: C29F9.5; 3A735; CE08453; WBGene00016220; WP:CE08453
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, IVb male soma                                  
                                              enriched genes, Romagnolo et al 2002  Fig3b TF, Shen et                            
                                              al 2005  T1 hif-1 depend hypoxia                                                   

C31G12.2 C31G12.2 P W All gene names: C31G12.2; 5S662; CE15661; WBGene00007851; WP:CE15661 WormBase description: Lectin C-type domain short and long forms
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia                                                                            

C32D5.12 C32D5.12 P W All gene names: phi-45; C32D5.12; 2G648; CE01841; WBGene00016319; WP:CE01841
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster A, Reinke et al 2004, list of genes in cluster                             
                                              order, Shen et al 2005  T1 hif-1 depend hypoxia, 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                                                                    

C34B7.3 C34B7.3 P W All gene names: cyp-36A1; C34B7.3; 1I916; CE08567; NM_059866; WBGene00007913; WP:CE08567 WormBase description: cytochrome P450
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 daf-16 Resveratrol                            

C34D4.14 C34D4.14 P W All gene names: C34D4.14; 4H900; CE17508; WBGene00016405; WP:CE17508
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, McCarroll et al 2004  SFig1-4 conserved w/                               
                                              Drosoph, Shen et al 2005  T1 hif-1 depend hypoxia,                                 
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

C36A4.9 C36A4.9 P W All gene names: C36A4.9; C36A4.9a.1; C36A4.9a.2; C36A4.9a.3; 3E955; CE03076; CE37209; WBGene00007969; WP:CE03076; WP:CE37209 WormBase description: acetyl-coenzyme A synthetase
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, McCarroll et al 2004  SFig1-4 conserved w/                               
                                              Drosoph, Shen et al 2005  T1 hif-1 depend hypoxia,                                 
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

C40D2.4 C40D2.4 P W All gene names: C40D2.4; 2C290; CE19376; WBGene00016557; WP:CE19376
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia                                                                            

C41C4.1 C41C4.1 P W All gene names: C41C4.1; 2I396; CE01516; WBGene00008050; WP:CE01516
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 daf-16 Resveratrol                            

C56E6.2 C56E6.2 P W All gene names: C56E6.2; 2G815; CE30372; WBGene00016970; WP:CE30372 WormBase description: GTP-binding
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

CC8.2 CC8.2 P W All gene names: CC8.2; CC8.2a.1; CC8.2a.2; 4E410; CE20615; CE23615; WBGene00016987; WP:CE20615; WP:CE23615
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, Murphy et al 2003  Fig2 Class1 elongate                                  
                                              lifespan, Shen et al 2005  T1 hif-1 depend hypoxia,                                
                                              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                                                                    

F02E8.6 npc-1 P W All gene names: ncr-1; npc-1; F02E8.6; CE29251; NM_076370; WBGene00003561; WP:CE29251; XF92 WormBase description: ncr-1 encodes a large transmembrane glycoprotein with a patched-like domain that is orthologous to human NPC1 (OMIM:257220, mutated in Niemann-Pick type C disease); NCR-1 and NPC1 are eukaryotic members of the resistance-nodulation-division (RND) family of membrane permeases, and have a putative sterol-sensing domain; by homology, NCR-1 is predicted to function in intracellular cholesterol and glycolipid trafficking; in C. elegans, NCR-1 is required for growth and survival in the absence of cholesterol, newly hatched ncr-1 mutant larvae grow poorly on cholesterol-free medium and die at the L1 or L2 stage; NCR-1 is also involved in negative regulation of dauer formation, being required redundantly with NCR-2, a second C. elegans NPC1-like protein, for preventing constitutive dauer formation; dauer formation in ncr-1; ncr-2 double mutants is suppressed by mutations in daf-12, which encodes a steroid hormone receptor, and by overexpression of daf-9, which encodes a cytochrome P450, suggesting that NCR-1 and NCR-2 may function to transport a sterol precursor that is metabolized by DAF-9 to then serve as the DAF-12 ligand.
                                              
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 daf-16 Resveratrol                            

F08G12.10 inx-2 P W All gene names: inx-2; opu-2; F08G12.10; CE26709; NM_077484; WBGene00002124; WP:CE26709; XL914 WormBase description: innexin
                                              
Member of lists (Publications lists):
                                              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, 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, ViswanathanM et al 2005  S2                            
                                              daf-16 Resveratrol                                                                 

F13H8.4 F13H8.4 P W All gene names: F13H8.4; 2G551; CE35476; WBGene00017437; WP:CE35476
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia                                                                            

F16G10.10 F16G10.10 P W All gene names: F16G10.10; 2C680; CE19399; WBGene00017525; WP:CE19399
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, wt herm vs wt herm                             
                                              enriched gen, Reinke et al 2004, IVb male soma enriched                            
                                              genes, Shen et al 2005  T1 hif-1 depend hypoxia,                                   
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F21D12.3 F21D12.3 P W All gene names: F21D12.3; 2H610; CE32633; WBGene00017663; WP:CE32633
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, 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                                                               

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                                                                        

F22B5.7 zyg-9 P W All gene names: zyg-9; F22B5.7; F22B5.8; 2I753; CE20707; NM_063383; WBGene00006994; WP:CE20707 WormBase description: zyg-9 encodes a predicted microtubule-association protein (MAP) of the XMAP215 family; during early embryonic development, maternal zyg-9 activity is required for microtubule-dependent processes such as meiotic and mitotic spindle organization and pronuclear migration; further, zyg-9 is essential for formation of long astral microtubules; ZYG-9 is required for centrosomal localization of TAC-1, the sole C. elegans TACC family member, with which it interacts, and mutually stabilizes, in vivo; in early embryos, ZYG-9 localizes to the meiotic spindle and spindle poles, as well as to mitotic centrosomes; during metaphase and anaphase ZYG-9 localizes to the central spindle region, and during interphase ZYG-9 is cytoplasmic; proper localization of ZYG-9 to the meiotic spindle is dependent upon wild-type activity of MEI-1, an ATPase essential for meiotic spindle formation, while proper localization of ZYG-9 to centrosomes is dependent, at least in part, upon TAC-1. WormBase CDS description: elongation factor
                                              
Member of lists (Publications lists):
                                              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, list of genes in cluster F, Reinke et al 2004, wt                            
                                              vs glp-4 enriched genes, Reinke et al 2004, list of                                
                                              genes in cluster order                                                             

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                                   

F35D11.10 F35D11.10 P W All gene names: F35D11.10; 2E912; CE39016; WBGene00018050; WP:CE39016
                                              
Member of lists (Publications lists):
                                              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                                     

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                                  

F42A10.4 efk-1 P W All gene names: efk-1; F42A10.4; F42A10.4a.1; F42A10.4a.2; 3H256; CE32415; CE32416; WBGene00001160; WP:CE32415; WP:CE32416; efk1 WormBase description: efk-1 encodes a calcium/calmodulin-dependent protein kinase with homology to human elongation factor-2 kinase; expressed in only a few cells in embryos.
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

F44B9.1 dpf-6 P W All gene names: dpf-6; F44B9.1; 3J129; CE30989; CE30990; CE30991; NM_171203; NM_171204; NM_171205; WBGene00001059; WP:CE30989; WP:CE30990; WP:CE30991 WormBase description: acylamino-acid-releasing enzyme
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Dauer specific genes                            
                                              P<0.05, Reinke et al 2004, list of genes in cluster A,                             
                                              Reinke et al 2004, list of genes in cluster order,                                 
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated, Wang et                             
                                              al 2003  S7 SAGE genes in the dataset, Wang et al 2003                             
                                              S8 SAGE genes in the dauer exit                                                    

F45D11.1 F45D11.1 P W All gene names: F45D11.1; F45D11.1.1; F45D11.1.2; 2B313; CE32665; WBGene00018448; WP:CE32665
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

F45D11.16 F45D11.16 P W All gene names: F45D11.16; 2B308; WBGene00018461
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

F45D11.2 F45D11.2 P W All gene names: F45D11.2; 2B311; CE23737; WBGene00018449; WP:CE23737 WormBase description: F45D11.2, with F45D11.3 and F45D11.4, encodes a nematode-specific protein that entirely consists of one large (~300-residue) 'domain of unknown function' (DUF684) that is found in several other C. elegans proteins; a transcription unit of either F45D11.2, F45D11.3, or F45D11.4 (genes of essentially identical sequence) has a natural nonsense transcript that is up-regulated in vivo by smg[-] mutations, indicating that at least one of these three genes is a natural substrate for SMG-mediated nonsense suppresssion; F45D11.2 has no obvious function in mass RNAi assays, but, since several other natural mRNA substrates of SMG suppression (e.g., rpl-3, rpl-8, rpl-10a, rpl-12) have protein products that are involved in translation, F45D11.2 protein may may function in translation as well.
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

F53F4.5 fmo-14 P W All gene names: fmo-14; fmo-4; F53F4.5; F53F4.5.1; F53F4.5.2; 5O84; CE30676; NM_073969; WBGene00001479; WP:CE30676 WormBase description: fmo-14 encodes a protein with homology to human hepatic flavin-containing monooxygenase 5. WormBase CDS description: flavin-containing monoxygenase
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster A, Reinke et al 2004, list of genes in cluster                             
                                              order, ViswanathanM et al 2005  S2 daf-16 Resveratrol                              

F54E2.3 pqn-43 P W All gene names: ketn-1; pqn-43; F54E2.3; 5D262; CE28729; CE30807; CE30808; CE38607; KETTIN; NM_071357; WBGene00004130; WP:CE28729; WP:CE30807; WP:CE30808; WP:CE38607 WormBase description: The protein product of this gene is predicted to contain a glutamine/asparagine (Q/N)-rich ('prion') domain, by the algorithm of Michelitsch and Weissman (as of the WS77 release of WormBase, i.e., in wormpep77).
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, ViswanathanM et al 2005  S2                                  
                                              sir-2.1 regulated, ViswanathanM et al 2005  S2 daf-16                              
                                              Resveratrol                                                                        

F56A3.3 npp-6 P W All gene names: npp-6; F56A3.3; F56A3.3a.1; F56A3.3a.2; 1F749; CE11218; CE30281; NM_170857; NM_170858; WBGene00003792; WP:CE11218; WP:CE30281 WormBase description: npp-6 encodes a protein with weak similarity to mouse nuclear pore complex protein Nup160, and affects embryonic and larval viability.
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, fem1 enriched                                  
                                              genes, Reinke et al 2004, wt vs glp-4 enriched genes,                              
                                              Reinke et al 2004, oogenesis enriched genes,                                       
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F57B9.1 F57B9.1 P W All gene names: F57B9.1; 3I53; CE01335; WBGene00018996; WP:CE01335 WormBase description: PNP/PMP oxidase
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, McCarroll et al 2004  SFig1-4 conserved w/                               
                                              Drosoph, Shen et al 2005  T1 hif-1 depend hypoxia,                                 
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F59B10.4 F59B10.4 P W All gene names: F59B10.4; 2K804; CE35885; CE36941; WBGene00010320; WP:CE35885; WP:CE36941
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, IVb male soma                                  
                                              enriched genes, Shen et al 2005  T1 hif-1 depend                                   
                                              hypoxia, 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                                                               

K02E7.6 K02E7.6 P W All gene names: K02E7.6; K02E7.6.1; K02E7.6.2; 2B349; CE33417; WBGene00019311; WP:CE33417
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, IVb male soma                                  
                                              enriched genes, Shen et al 2005  T1 hif-1 depend                                   
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

K04H4.2 K04H4.2 P W All gene names: K04H4.2; K04H4.2a.1; K04H4.2a.2; K04H4.2a.3; K04H4.2c.1; K04H4.2c.2; 3K438; CE32463; CE36653; CE36654; WBGene00010573; WP:CE32463; WP:CE36653; WP:CE36654 WormBase description: Chitin-binding motifs
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

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                                                      

K08E3.1 K08E3.1 P W All gene names: tyr-2; K08E3.1; 3O835; CE18864; NM_067435; WBGene00010661; WP:CE18864 WormBase description: tyrosinase
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster B, Shen et al 2005  T1 hif-1 depend hypoxia                                

K10H10.2 K10H10.2 P W All gene names: K10H10.2; K10H10.2.1; K10H10.2.2; 2O780; CE16252; WBGene00010759; WP:CE16252 WormBase description: This gene encodes a protein predicted by Eisenberg and coworkers, with 68% accuracy, to be mitochondrial. WormBase CDS description: beta-synthase
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T3 xenobiotic                               
                                              downregulated, Reinke et al 2004, GO categories, Reinke                            
                                              et al 2004, herm soma enriched genes, Shen et al 2005                              
                                              T1 hif-1 depend hypoxia, ViswanathanM et al 2005  S2                               
                                              sir-2.1 regulated                                                                  

K10H10.4 K10H10.4 P W All gene names: K10H10.4; 2O787; CE16254; WBGene00010760; WP:CE16254
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster B, Shen et al 2005  T1 hif-1 depend hypoxia,                               
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

M01H9.3 M01H9.3 P W All gene names: M01H9.3; M01H9.3a.1; M01H9.3a.2; 4F234; CE28614; CE28615; CE37722; WBGene00019719; WP:CE28614; WP:CE28615; WP:CE37722
                                              
Member of lists (Publications lists):
                                              Murphy et al 2003  Fig2 Class1                                    
                                              elongate lifespan, Shen et al 2005  T1 hif-1 depend                                
                                              hypoxia, 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                                                               

M02F4.1 M02F4.1 P W All gene names: M02F4.1; CE04762; WBGene00019735; WP:CE04762; XD646
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster C, Shen et al 2005  T1 hif-1 depend hypoxia,                               
                                              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                                                                    

M03A1.1 vab-1 P W All gene names: vab-1; M03A1.1; 2E879; CE25060; CE28617; NM_062405; NM_062406; WBGene00006868; WP:CE25060; WP:CE28617 WormBase description: tyrosine-protein kinase receptor
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Reinke et al 2004, fem1 enriched                             
                                              genes, Reinke et al 2004, wt vs glp-4 enriched genes,                              
                                              Reinke et al 2004, oogenesis enriched genes,                                       
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated,                                     
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

M05D6.5 M05D6.5 P W All gene names: M05D6.5; M05D6.5.1; M05D6.5.2; 2I770; CE03503; WBGene00010878; WP:CE03503
                                              
Member of lists (Publications lists):
                                              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 Unkown, Shen et al                              
                                              2005  T1 hif-1 depend hypoxia, ViswanathanM et al 2005                             
                                              S2 sir-2.1 regulated                                                               

R06C7.10 let-75 P W All gene names: let-75; myo-1; R06C7.10; R06C7.10.1; R06C7.10.2; 1H836; CE06253; NM_059652; WBGene00002348; WP:CE06253; myosin I WormBase description: let-75 encodes a pharynx-specific type II myosin heavy chain (MHC D); LET-75 is required for pharyngeal muscle contraction and thus for normal feeding behavior and post-embryonic development; in vitro, the LET-75 tail domain interacts with ITR-1, an IP3 receptor, and this interaction has been proposed to mediate, in vivo, increased pharnygeal pumping in response to food; LET-75 is expressed exclusively in pharyngeal muscle. WormBase CDS description: myosin heavy chain
                                              
Member of lists (Publications lists):
                                              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                                                                          

R10D12.1 R10D12.1 P W All gene names: R10D12.1; 5O414; CE12672; WBGene00011185; WP:CE12672 WormBase description: sodium/phosphate transporter
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, IVb male soma                                  
                                              enriched genes, Shen et al 2005  T1 hif-1 depend                                   
                                              hypoxia, 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                                                         

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                                   

T07D1.3 T07D1.3 P W All gene names: T07D1.3; CE04909; WBGene00020302; WP:CE04909; XD60
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated,                            
                                              Zhang et al. 2002, Fig2b overexpressed in mec-3MT                                  

T08G3.6 T08G3.6 P W All gene names: T08G3.6; 5Q927; CE18938; WBGene00011618; WP:CE18938
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia                                                                            

T25E12.4 T25E12.4 P W All gene names: T25E12.4; 5R267; CE18283; CE18967; WBGene00012019; WP:CE18283; WP:CE18967 WormBase description: Phorbol esters/diacylglycerol binding domain (C1 domain) (2 domains), serine/threonine kinase
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia                                                                            

T28F3.1 T28F3.1 P W All gene names: T28F3.1; 4S226; CE09683; CE19806; WBGene00012128; WP:CE09683; WP:CE19806 WormBase description: C2 domain
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, intrinsic, Reinke                              
                                              et al 2004, list of genes in cluster F, 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                              
                                              herm vs wt male enriched gen, Shen et al 2005  T1 hif-1                            
                                              depend hypoxia, ViswanathanM et al 2005  S2 sir-2.1                                
                                              regulated                                                                          

W04E12.4 W04E12.4 P W All gene names: W04E12.4; 5U213; CE34100; WBGene00012249; WP:CE34100
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster order, Reinke et al 2004, spermatogenesis                                  
                                              enriched genes, Reinke et al 2004, wt herm vs wt herm                              
                                              enriched gen, Reinke et al 2004, fem3 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 D, Reinke et al 2004,                            
                                              shared sperm, Shen et al 2005  T1 hif-1 depend hypoxia                             

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                                 

W07A12.7 W07A12.7 P W All gene names: tag-323; W07A12.7; 2J453; CE20163; WBGene00012324; WP:CE20163
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Dauer specific genes                            
                                              P<0.05, Jones et al 2001  T3 20 most abundant Dauer,                               
                                              Shen et al 2005  T1 hif-1 depend hypoxia, Wang et al                               
                                              2003  S6 removed genes of contamination, Wang et al                                
                                              2003  S7 SAGE genes in the dataset, Wang et al 2003  S8                            
                                              SAGE genes in the dauer exit                                                       

Y15E3A.5 Y15E3A.5 P W All gene names: Y15E3A.5; CE31634; WBGene00012444; WP:CE31634; XP963
                                              
Member of lists (Publications lists):
                                              Murphy et al 2003  Fig2 Class1                                    
                                              elongate lifespan, Shen et al 2005  T1 hif-1 depend                                
                                              hypoxia, 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                                                         

Y19D10A.5 Y19D10A.5 P W All gene names: Y19D10A.5; 5C859; WBGene00021220
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, ViswanathanM et al 2005  S2 sir-2.1 regulated                             

Y38E10A.23 Y38E10A.23 P W All gene names: Y38E10A.23; 2M960; CE21604; WBGene00012601; WP:CE21604
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia, 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                                                

Y44A6C.1 Y44A6C.1 P W All gene names: Y44A6C.1; 5V183; CE28852; WBGene00012850; WP:CE28852
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, IVb male soma                                  
                                              enriched genes, Shen et al 2005  T1 hif-1 depend                                   
                                              hypoxia, 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                                                         

Y46G5A.6 Y46G5A.6 P W All gene names: phi-3; Y46G5A.6; 2N32; CE24303; WBGene00012898; WP:CE24303 WormBase description: This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins.
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, intrinsic, Reinke                              
                                              et al 2004, wt vs glp-4 enriched genes, Reinke et al                               
                                              2004, GO categories, Shen et al 2005  T1 hif-1 depend                              
                                              hypoxia, ViswanathanM et al 2005  S2 daf-16 Resveratrol                            

Y48G8AL.6 smg-2 P W All gene names: mab-11; smg-2; Y48G8AL.6; Y48G8A_3304.A; 1B661; CE28367; NM_058428; WBGene00004880; WP:CE28367
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, McCarroll et al 2004  SFig1-4 conserved w/                               
                                              Drosoph                                                                            

Y55F3BR.4 Y55F3BR.4 P W All gene names: Y55F3BR.4; 4B601; CE30056; WBGene00021941; WP:CE30056
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b Unkown,                               
                                              Shen et al 2005  T1 hif-1 depend hypoxia                                           

Y9C9A.12 Y9C9A.12 P W All gene names: fbxa-86; Y9C9A.12; 4F700; CE21348; WBGene00021179; WP:CE21348
                                              
Member of lists (Publications lists):
                                              Shen et al 2005  T1 hif-1 depend                                  
                                              hypoxia