Baugh et al 2005, PAL-1 target_score5-7, 17 genes

Gene list file name:Baugh2005_SDS_PAL-1_target_score5-7.txt
Type of gene identifier:Affymetrix probe set
Description:Baugh et al 2005, Supplymental Dataset, PAL-1 target genes, score 5, 6, 7  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

B0304.1 193759_at P W All gene names: hlh-1; B0304.1; 2E811; CE02423; CE30067; CE31766; MyoD1; WBGene00001948; WP:CE02423; WP:CE30067; WP:CE31766 WormBase description: hlh-1 encodes a basic helix-loop-helix (bHLH) transcription factor that is the sole C. elegans member of the myogenic regulatory factor (MRF) subgroup of bHLH proteins; in C. elegans, HLH-1 activity is required during embryonic development for the proper differentiation and function of body wall muscle cells, indicating that unlike its vertebrate counterparts, hlh-1 is not absolutely required for body wall muscle specification; however, ectopic expression of hlh-1 in the embryo is sufficient to convert nearly all embryonic cell types to a muscle-like fate; in regulating body wall muscle cell development in some cell lineages, hlh-1 likely lies downstream of the PAL-1 homeodomain protein that is required for specification of the C and D founder cell fates; HLH-1 is expressed in nuclei and first appears in body wall muscle precursors beginning at the ~80-cell stage of embryogenesis; expression then continues in these cells and their differentiated descendants throughout embryonic, larval, and adult stages of development. WormBase CDS description: helix-loop-helix transcription factor
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph, Roy                            
                                              et al 2002  S2 positivecontrol L1 muscle, ViswanathanM                             
                                              et al 2005  S2 sir-2.1 regulated                                                   

C01G6.1 171910_x_at P W All gene names: aqp-2; C01G6.1; C01G6.1a.1; C01G6.1a.2; C01G6.1b.1; C01G6.1b.2; 2J550; AQP; CE00863; CE19664; NM_063571; NM_063572; WBGene00000170; WP:CE00863; WP:CE19664 WormBase description: Major intrinsic protein
C09D4.2 180916_at P W All gene names: C09D4.2; 1G59; CE08031; WBGene00015633; WP:CE08031
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              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                                      

C28C12.7 173276_s_at P W All gene names: spp-10; C28C12.7; C28C12.7a.1; C28C12.7a.2; 4J243; CE29486; CE31323; NM_171399; NM_171400; WBGene00004995; WP:CE29486; WP:CE31323 WormBase description: spp-10 encodes two protein isoforms that are orthologous to the human gene PROSAPOSIN (PSAP; OMIM:176801, mutated in Gaucher disease and metachromatic leukodystrophy); SPP-10A and -10B are predicted to have 3 and 4 embedded saposin sequences, that are likely to be split into individual saposin peptides by proteolysis; in mammals, saposins activate the enzymes sphingomyelinphosphodiesterase and beta-glucosylceramidase; spp-10 has no obvious function in mass RNAi assays. WormBase CDS description: 7TM chemoreceptor, spp family
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              Reinke et al 2004, mixed sperm soma, Reinke et al 2004,                            
                                              fem3 enriched genes, ViswanathanM et al 2005  S2                                   
                                              sir-2.1 regulated                                                                  

C46H11.2 184397_s_at P W All gene names: C46H11.2; 1F619; CE08784; WBGene00016728; WP:CE08784 WormBase description: This gene encodes a protein predicted by Eisenberg and coworkers, with 52% accuracy, to be mitochondrial.
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              McCarroll et al 2004  SFig5 conserved w/ yeast,                                    
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              Murphy et al 2003  Fig2 Class1 elongate lifespan,                                  
                                              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  S3  genes pass one-way ANOVA, Wang et al 2003                             
                                              S4 Climbing, Wang et al 2003  S4 genes pass                                        
                                              two-wayANOVA P0                                                                    

F01F1.6 190995_at P W All gene names: alh-9; F01F1.6; F01F1.6.1; F01F1.6.2; F01F1.6.3; 3G947; CE39486; NM_065862; WBGene00000115; WP:CE39486 WormBase description: Aldehyde dehydrogenase
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, PAL-1 target genes,                             
                                              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, 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                                                                    

F23H12.4 174910_at P W All gene names: col-1; dpy-15; sqt-3; F23H12.4; F23H12.4.1; F23H12.4.2; 5M833; CE05707; NM_073694; WBGene00005018; WP:CE05707 WormBase description: collagen
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, PAL-1 target genes,                             
                                              Golden et al 2004, daf-2 differentially expressed ,                                
                                              Golden et al 2004, N2 vs daf-2 different genes at ,                                
                                              ReichertK et al 2005  T2 xenobiotic induced Collag,                                
                                              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,                                    
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated,                                     
                                              ViswanathanM et al 2005 S2 Resveratrol regulate WT,                                
                                              Wang et al 2003  S3  genes pass one-way ANOVA, Wang et                             
                                              al 2003  S4 genes pass two-wayANOVA P0, Wang et al 2003                            
                                               S4 LateList                                                                       

F32H2.5 174796_at P W All gene names: F32H2.5; 1J552; CE09880; WBGene00009342; WP:CE09880 WormBase description: This gene encodes a protein predicted by Eisenberg and coworkers, with 68% accuracy, to be mitochondrial. WormBase CDS description: fatty acid synthase
                                              
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 C, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol, Wang et al 2003  S4 Early genes, Wang et                              
                                              al 2003  S3  genes pass one-way ANOVA, Wang et al 2003                             
                                              S4 genes pass two-wayANOVA P0                                                      

K10B4.6 188486_s_at P W All gene names: Wnt-1; cwn-1; K10B4.6; 2A422; CE12072; CE33421; WBGene00000857; WP:CE12072; WP:CE33421 WormBase description: cwn-1 encodes one of five C. elegans Wnt signaling ligands; although the precise developmental role of cwn-1 is not yet known, during embryogenesis cwn-1 likely functions as a downstream target of the PAL-1 homeodomain protein in the regulatory network that specifies cell fates in the C lineage that gives rise to ectodermal and muscle tissue; consistent with this role, loss of cwn-1 activity via RNAi results in rare larval tail defects that may result, in part, from abnormal morphogenesis of C lineage descendants; a cwn-1 reporter is expressed in C and D muscle cells, as well as in two posterior C ectodermal cells; cwn-1 mRNA is detectable at all developmental stages, with highest levels of expression seen in embryonic stages.
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes                                 

R02D3.1 189080_at P W All gene names: R02D3.1; 4B3; CE18095; WBGene00019819; WP:CE18095 WormBase description: The R02D3.1 gene encodes an ortholog of the human gene ALPHA-AMINOADIPATE SEMIALDEHYDE SYNTHASE (AASS; OMIM:605113), which when mutated leads to hyperlysinemia (OMIM:238700). WormBase CDS description: dehydrogenase
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              McCarroll et al 2004  SFig5 conserved w/ yeast,                                    
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              Reinke et al 2004, list of genes in cluster order,                                 
                                              Reinke et al 2004, fem3 enriched genes, Reinke et al                               
                                              2004, mixed sperm soma, Reinke et al 2004, list of                                 
                                              genes in cluster C, ViswanathanM et al 2005  S2 sir-2.1                            
                                              regulated                                                                          

R07C3.11 184902_at P W All gene names: R07C3.11; 2B196; CE12542; WBGene00019927; WP:CE12542
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

T22B7.3 181552_at P W All gene names: T22B7.3; CE31242; WBGene00020672; WP:CE31242; XG273
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              Reinke et al 2004, list of genes in cluster A, Reinke                              
                                              et al 2004, list of genes in cluster order, Reinke et                              
                                              al 2004, IVb male soma enriched genes, Romagnolo et al                             
                                              2002  Fig3b Unkown                                                                 

T27D12.1 191788_at P W All gene names: T27D12.1; T27D12.1.1; T27D12.1.2; T27D12.1.3; 2M135; CE06516; WBGene00012085; WP:CE06516 WormBase description: sodium/phosphate transporter
                                              
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                              

Y71F9AL.17 173371_s_at P W All gene names: Y71F9AL.17; Y71F9AL.D; 1D464; CE29136; WBGene00022119; WP:CE29136 WormBase description: Y71F9AL.17 encodes an alpha subunit of the coatomer (COPI) complex; in mass RNAi assays, Y71F9AL.17 is required for embryonic viability, fertility, normal locomotion, and normally rapid growth. WormBase CDS description: coatomer, alpha chain
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, PAL-1 target genes,                             
                                              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                                      

ZK1307.1 187462_at P W All gene names: ZK1307.1; ZK1307.1b.1; ZK1307.1b.2; 2J946; CE01690; CE35921; WBGene00014244; WP:CE01690; WP:CE35921
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              Reinke et al 2004, list of genes in cluster order,                                 
                                              Reinke et al 2004, list of genes in cluster C,                                     
                                              Romagnolo et al 2002  Fig3b Unkown, ViswanathanM et al                             
                                              2005  S2 sir-2.1 regulated, Wang et al 2003  S3  genes                             
                                              pass one-way ANOVA, Wang et al 2003  S4 Climbing, Wang                             
                                              et al 2003  S4 genes pass two-wayANOVA P0                                          

ZK622.3 181305_s_at P W All gene names: phi-40; ZK622.3; ZK622.3a.1; ZK622.3a.2; ZK622.3a.3; ZK622.3c.1; ZK622.3c.10; ZK622.3c.11; ZK622.3c.2; ZK622.3c.3; ZK622.3c.4; ZK622.3c.5; ZK622.3c.6; ZK622.3c.7; ZK622.3c.8; ZK622.3c.9; ZK622.3d.1; ZK622.3d.2; ZK622.3d.3; ZK622.3d.4; ZK622.3d.5; ZK622.3d.6; ZK622.3d.7; ZK622.3d.8; 2F570; CE29162; CE32290; CE33504; CE33505; WBGene00022781; WP:CE29162; WP:CE32290; WP:CE33504; WP:CE33505
                                              
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  S4 Climbing, Wang et al 2003  S3                                  
                                              genes pass one-way ANOVA, Wang et al 2003  S4 genes                                
                                              pass two-wayANOVA P0                                                               

ZK829.4 172994_at P W All gene names: ZK829.4; ZK829.4.1; ZK829.4.2; ZK829.4.3; ZK829.4.4; 4M719; CE06652; WBGene00014095; WP:CE06652 WormBase description: ZK829.4 is orthologous to the human gene GLYCINE DECARBOXYLASE PRECURSOR (GLUD1; OMIM:238300), which when mutated leads to disease. WormBase CDS description: glutamate dehydrogenase
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, PAL-1 target genes,                             
                                              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