Baugh et al 2003, subclass SE_186min, 50 genes

Gene list file name:Baugh2003_classSEpi_186min.txt
Type of gene identifier:Affymetrix custom chip
Description:Baugh et al 2005, Supplymental Dataset, subclass SE_186min  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

AFF_T08G5.7 Aff_T08G5.7 P W
B0272.1 Aff_B0272.1 P W All gene names: tbb-4; B0272.1; CE00850; NM_077184; WBGene00006538; WP:CE00850; XK54 WormBase description: tubulin beta chain
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, McCarroll et al 2004  SFig1-4 conserved w/                               
                                              Drosoph, Portman et al 2004  T1 newly found ray-genes                              
                                              in25c, Portman et al 2004  T1 25 candidate ray genes,                              
                                              Reinke et al 2004, IVb male soma enriched genes,                                   
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

B0303.2 Aff_B0303.2 P W All gene names: B0303.2; 3J775; CE00536; WBGene00015124; WP:CE00536
                                              
Member of lists (Publications lists):
                                              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                                                         

C01F1.3 Aff_C01F1.3 P W All gene names: phi-41; C01F1.3; C01F1.3a.1; C01F1.3a.2; 2E587; CE06744; CE39553; WBGene00015298; WP:CE06744; WP:CE39553
                                              
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, Romagnolo et al 2002  Fig3b Metabolism,                                 
                                              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                                                                    

C02F12.1 Aff_C02F12.1 P W All gene names: tsp-17; C02F12.1; CE35213; NM_076233; WBGene00006643; WP:CE35213; XE303 WormBase description: transpanin
C02F12.7 Aff_C02F12.7 P W All gene names: tag-278; C02F12.7; CE03901; WBGene00015356; WP:CE03901; XE304
                                              
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 sir-2.1 regulated                               

C05A9.2 Aff_C05A9.2 P W All gene names: C05A9.2; CE05222; WBGene00007317; WP:CE05222; XL460
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05                                                                             

C05B5.8 Aff_C05B5.6 P W All gene names: C05B5.8; 3L96; CE33967; WBGene00007324; WP:CE33967
C05C8.3 Aff_C05C8.3 P W All gene names: dao-1; fkb-3; C05C8.3; 5H707; CE07921; NM_072434; WBGene00001428; WP:CE07921 WormBase description: fkb-3 encodes a peptidylprolyl cis/trans isomerase homologous to mammalian FK506 immunosuppressant-binding protein 9; FKB-3 expression is positively regulated by signaling through the DAF-2 insulin receptor-like pathway and the activity of the DAF-16 fork-head transcription factor suggesting that FKB-3 could play a role in metabolism and longevity; however, as loss of FKB-3 function via RNA-mediated interference (RNAi) does not result in any abnormalities, the precise role of FKB-3 in C. elegans development and/or behavior is not yet known; FKB-3 contains a predicted endoplasmic reticulum (ER) retention sequence and is thus proposed to localize to the ER. WormBase CDS description: FKBP-binding protein
                                              
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, 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                                                         

C10A4.3 Aff_C10A4.3 P W All gene names: C10A4.3; CE02471; WBGene00015664; WP:CE02471; XI19
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

C14A4.6 Aff_C14A4.6 P W All gene names: C14A4.6; C14A4.6.1; C14A4.6.2; 2K884; CE02147; WBGene00007557; WP:CE02147
C14F11.6 Aff_C14F11.6 P W All gene names: C14F11.6; CE02482; WBGene00015781; WP:CE02482; XG856 WormBase description: DTDP-4-dehydrorhamnose 3,5-epimerase (RFBC gene)
                                              
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 sir-2.1 regulated,                              
                                              Wang et al 2003  S5 genes common to feeding ANOVA, Wang                            
                                              et al 2003  S3  genes pass one-way ANOVA                                           

C17C3.12 Aff_C17C3.12 P W All gene names: acdh-2; C17C3.12; C17C3.12c.1; C17C3.12c.2; CE29175; CE29176; CE34697; NM_062665; NM_062666; NM_062667; WBGene00015894; WP:CE29175; WP:CE29176; WP:CE34697 WormBase description: acyl-CoA dehydrogenase
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

C23F12.1 Aff_B0272.5 P W All gene names: C23F12.1; CE32133; CE32134; WBGene00016006; WP:CE32133; WP:CE32134; XK45
                                              
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                                                                          

C26G2.1 Aff_C26G2.1 P W All gene names: syg-2; C26G2.1; CE19703; NM_078034; WBGene00007750; WP:CE19703; XP281 WormBase description: syg-2 encodes a transmembrane protein that is a member of the immunoglobulin superfamily of proteins; during larval development, SYG-2 activity is required in vulval epithelial cells for proper synaptic specificity of the HSNL neuron; in regulating synapse formation, SYG-2 acts as a guidepost protein for the SYG-1 receptor that interacts with SYG-2 and acts within HSNL to regulate synaptic specificity; a SYG-2::GFP fusion protein is expressed in the primary vulval cell lineages beginning at the L3 larval stage, with expression increasing during the L4 stage and finally disappearing by adulthood; in embryos, SYG-2::GFP expression is detected in some head neurons and body wall muscles, the latter of which also express the reporter during the L1 and L2 larval stages. WormBase CDS description: Immunoglobulin domain ; Fibronectin type III domain
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph                                                               

C27C12.6 Aff_C27C12.6 P W All gene names: dmd-4; C27C12.6; CE23560; WBGene00007776; WP:CE23560; XP476 WormBase description: doublesex protein like
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph                                                               

C33D12.7 Aff_C33D12.7 P W All gene names: ceh-30; C33D12.7; CE06909; NM_076123; WBGene00000451; WP:CE06909; XD683 WormBase description: ceh-30 encodes a homeodomain protein most similar to Drosophila and mammalian BarH1 (OMIM:605211) which function in neuronal cell fate determination; the precise biological role of CEH-30 in C. elegans development and/or behavior is not yet known. WormBase CDS description: homeobox protien
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, ViswanathanM et al 2005  S2                                  
                                              sir-2.1 regulated                                                                  

C33F10.7 Aff_C33F10.7 P W All gene names: C33F10.7; C33F10.7b.1; C33F10.7b.2; 2F108; CE04140; CE37751; WBGene00016355; WP:CE04140; WP:CE37751 WormBase description: esterase and beta-lactamase
                                              
Member of lists (Publications lists):
                                              Kwon et al 2004 T1 late-induction                                 
                                              Ethanol-response, Reinke et al 2004, list of genes in                              
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster B, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

C54D1.4 Aff_C54D1.4 P W All gene names: alh-10; C54D1.4; C54D1.4.1; C54D1.4.2; CE06980; NM_076802; WBGene00000116; WP:CE06980; XH760 WormBase description: aldehyde dehydrogenase
                                              
Member of lists (Publications lists):
                                              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                                                         

D1005.2 Aff_D1005.2 P W All gene names: D1005.2; CE29741; WBGene00016996; WP:CE29741; XC81
                                              
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, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol, Wang et al 2003  S3  genes pass one-way                               
                                              ANOVA, Wang et al 2003  S4 LateList, Wang et al 2003                               
                                              S4 genes pass two-wayANOVA P0                                                      

DY3.3 Aff_DY3.3 P W All gene names: hlh-16; DY3.3; 1J342; CE15747; NM_059971; WBGene00001960; WP:CE15747 WormBase description: Helix-loop-helix DNA-binding domain
F14B4.1 Aff_F14B4.1 P W All gene names: F14B4.1; 1J842; CE38950; WBGene00008779; WP:CE38950 WormBase description: LDL receptor-related protein
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster order                                                                      

F21D5.9 Aff_F21D5.9 P W All gene names: F21D5.9; 4J485; CE03251; WBGene00009014; WP:CE03251 WormBase description: Zinc finger, C2H2 type
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

F35G2.4 Aff_F35G2.4 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                                  

F37C4.4 Aff_F37C4.4 P W All gene names: F37C4.4; F37C4.4b.1; F37C4.4b.2; 4E635; CE17047; CE31505; WBGene00018144; WP:CE17047; WP:CE31505
                                              
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, Wang et al 2003  S3  genes pass one-way                                 
                                              ANOVA, Wang et al 2003  S4 LateList, Wang et al 2003                               
                                              S4 genes pass two-wayANOVA P0                                                      

F38B6.6 Aff_F38B6.6 P W All gene names: F38B6.6; CE30976; WBGene00018175; WP:CE30976; XH300
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, ViswanathanM et al 2005  S2                                  
                                              daf-16 Resveratrol                                                                 

F40E10.1 Aff_F40E10.1 P W All gene names: hch-1; nas-34; F40E10.1; CE24964; NM_078039; WBGene00001828; WP:CE24964; XP316 WormBase description: hch-1 encodes a member of the zinc-dependent metalloprotease family that contains an epidermal growth factor-like domain, a CUB domain, and a TSP1 domain and affects hatching and QL neuroblast migration. WormBase CDS description: metalloprotease
                                              
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, Jones et al 2001  Non dauer genes                                  
                                              P<0.05                                                                             

F44E5.3 Aff_F44E5.3 P W All gene names: F44E5.3; 2M52; CE18678; WBGene00009690; WP:CE18678
F52H3.1 Aff_F52H3.1 P W All gene names: let-268; F52H3.1; F52H3.1.1; F52H3.1.2; F52H3.1.3; 2K324; CE03397; NM_063769; WBGene00002497; WP:CE03397 WormBase description: let-268 encodes a procollagen lysyl hydroxylase that processes type IV collagen, a collagen secreted and incorporated into the basement membrane during embryogenesis (and encoded partly by emb-9); LET-268 activity is essential for type IV collagen processing and secretion and for the stability, but not the formation of, the basement membrane that provides mechanical support to body wall muscle once contraction begins; LET-268 also appears to be required for pharyngeal muscle contraction. WormBase CDS description: procollagen-lysine,2-oxoglutarate 5-dioxygenase precusor
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Reinke et al 2004, list of genes                             
                                              in cluster order, Reinke et al 2004, list of genes in                              
                                              cluster B, 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                                                         

F54A5.2 Aff_F54A5.C P W All gene names: F54A5.2; F54A5.C; 1B438; CE20860; WBGene00018787; WP:CE20860
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Reinke et al 2004, wt herm vs wt                             
                                              herm enriched gen                                                                  

F58A6.1 Aff_F58A6.1 P W All gene names: F58A6.1; 2F429; CE04675; WBGene00019022; WP:CE04675
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, ViswanathanM et al 2005  S2                                  
                                              sir-2.1 regulated                                                                  

K07C11.4 Aff_K07C11.4 P W All gene names: K07C11.4; 5I685; CE07347; WBGene00019477; WP:CE07347 WormBase description: esterase
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, GO categories,                                 
                                              Reinke et al 2004, herm soma enriched genes,                                       
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated, Zhang et                            
                                              al 2002, T1 mec-3 dependent genes                                                  

K08A8.2 Aff_K08A8.2 P W All gene names: sox-2; K08A8.2; K08A8.2a.1; K08A8.2a.2; K08A8.2b.1; K08A8.2b.2; K08A8.2b.3; CE28595; CE31200; NM_171725; NM_171726; WBGene00004949; WP:CE28595; WP:CE31200; XI78 WormBase description: The sox-2 gene encodes a homolog of human SRY, which when mutated leads to gonadal dysgenesis (OMIM:306100).
K08B4.2 Aff_K08B4.2 P W All gene names: K08B4.2; 4G840; CE25940; WBGene00019514; WP:CE25940
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, list of genes in                               
                                              cluster order, Reinke et al 2004, list of genes in                                 
                                              cluster E, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

K09E2.4 Aff_K09E2.4 P W All gene names: rig-1; K09E2.4; CE02817; CE34053; WBGene00004369; WP:CE02817; WP:CE34053; XJ289
M01H9.4 Aff_M01H9.4 P W All gene names: M01H9.4; 4F244; CE39601; WBGene00019720; WP:CE39601
                                              
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                                                                              

R09F10.4 Aff_R09F10.4 P W All gene names: inx-5; opu-5; R09F10.4; CE33811; NM_077002; WBGene00002127; WP:CE33811; XI916 WormBase description: inx-5 encodes a predicted member of the innexin family; expressed in the embryonic hypodermis, developing vulva, seam cells, and spermatheca. WormBase CDS description: unc-7-like protein
                                              
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, Romagnolo et al 2002  Fig3b Transporters,                               
                                              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                                                               

T06A10.2 Aff_C26C9.2 P W All gene names: T06A10.2; 4R835; CE36609; WBGene00020285; WP:CE36609
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

T22B2.4 Aff_T22B2.4 P W All gene names: sup-12; T22B2.4; CE13934; NM_076273; WBGene00006321; WBGene00020668; WP:CE13934; XE525 WormBase description: RNA-binding protein
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

T22E5.3 Aff_T22E5.3 P W All gene names: T22E5.3; CE37152; WBGene00020691; WP:CE37152; XH5
                                              
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, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol, Wang et al 2003  S4 Climbing, Wang et al                              
                                              2003  S3  genes pass one-way ANOVA, Wang et al 2003  S4                            
                                              genes pass two-wayANOVA P0                                                         

T27A1.5 Aff_T27A1.5 P W All gene names: T27A1.5; T27A1.5a.1; T27A1.5a.2; T27A1.5b.1; T27A1.5b.2; 2A815; CE14213; CE39784; WBGene00020837; WP:CE14213; WP:CE39784
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig5 conserved                             
                                              w/ yeast, Reinke et al 2004, list of genes in cluster                              
                                              order, Reinke et al 2004, list of genes in cluster C,                              
                                              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                                                               

T28B4.3 Aff_T28B4.3 P W All gene names: T28B4.3; CE14325; WBGene00020886; WP:CE14325; XH214
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, mixed sperm soma,                              
                                              Reinke et al 2004, wt herm vs wt herm enriched gen,                                
                                              Reinke et al 2004, GO categories, Reinke et al 2004,                               
                                              fem3 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                                          

T28H10.1 Aff_T28H10.1 P W All gene names: T28H10.1; 5M985; CE06529; WBGene00012142; WP:CE06529 WormBase description: B.subtilis SFP protein like
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated                                                                          

W03A3.1 Aff_W03A3.1 P W All gene names: ceh-10; mig-11; W03A3.1; 3G889; CE07563; NM_065850; WBGene00000435; WP:CE07563 WormBase description: ceh-10 encodes a member of the Paired-like class of homeodomain proteins; the CEH-10 homeodomain is closely related to the homeodomains of two vertebrate retina proteins (Chx10 from mice and Vsx-1 from goldfish); ceh-10 is required for CAN cell fate specification and migration, complete loss of ceh-10 function results in failure of CAN cell migration and loss of expression of CEH-23 and CEH-10 itself in the CAN and AIY interneurons; CEH-10, along with TTX-3 and CEH-23, constitutes a regulatory cascade of transcription factors that controls all sub-type specific features of the AIY interneurons.
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, ViswanathanM et al 2005  S2                                  
                                              daf-16 Resveratrol                                                                 

Y22D7AL.14 Aff_Y119D3_465.U P W All gene names: Y22D7AL.14; 3C742; CE23435; WBGene00021252; WP:CE23435
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 sir-2.1                               
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

Y41D4B.26 Aff_Y41D4B_930.A P W All gene names: nhr-146; Y41D4B.26; 4C397; CE36740; WBGene00021525; WP:CE36740
Y53F4B.14 Aff_Y53F4B.Q P W All gene names: Y53F4B.14; 2P325; CE25395; WBGene00013161; WP:CE25395
Y82E9BR.20 Aff_Y119D3_444.A P W All gene names: Y82E9BR.20; 3C465; CE29934; WBGene00022352; WP:CE29934
ZC8.3 Aff_ZC8.2 P W All gene names: tag-226; ZC8.3; CE33744; WBGene00022499; WP:CE33744; XF621
                                              
Member of lists (Publications lists):
                                              ViswanathanM et al 2005  S2 daf-16                                
                                              Resveratrol                                                                        

ZK75.2 Aff_ZK75.2 P W All gene names: ins-2; ZK75.2; 2G277; CE02101; NM_062793; WBGene00002085; WP:CE02101 WormBase description: 7TM chemoreceptor, ins family
                                              
Member of lists (Publications lists):
                                              Lund et al 2002  Fig1 aging-regulated                             
                                              genes, ViswanathanM et al 2005  S2 sir-2.1 regulated