Baugh et al 2005, validated PAL-1 target genes, 22 genes

Gene list file name:Baugh2005_T3_validated_PAL-1_target_genes.txt
Type of gene identifier:MA primer pair (sjj)
Description:Baugh et al 2005, T3 validated PAL-1 target genes  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

B0304.1 B0304.1 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                                                   

C09D4.2 C09D4.2 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 C28C12.7 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                                                                  

C38D4.6 C38D4.6 P W All gene names: ceh-3; nob-2; pal-1; C38D4.6; C38D4.6a.1; C38D4.6a.2; C38D4.6b.1; C38D4.6b.2; 3F896; CE05383; CE27837; NM_065590; WBGene00003912; WP:CE05383; WP:CE27837 WormBase description: pal-1 encodes a homeodomain protein that is the C. elegans Caudal ortholog; PAL-1 is required maternally and embryonically for cell fate specification and posterior patterning during embryogenesis; PAL-1 is also required postembryonically for fate specification of the posterior V6 neuroectoblast during male tail development; PAL-1 is expressed in posterior blastomeres beginning at the four-cell stage of embryogenesis and its expression continues during embryogenesis in posterior-derived tissues and cells undergoing movement or forming midline structures; pal-1 is subject to both transcriptional and translational regulation.
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes,                                
                                              Jones et al 2001  Non dauer genes P<0.05, McCarroll et                             
                                              al 2004  SFig1-4 conserved w/ Drosoph, Reinke et al                                
                                              2004, fem1 enriched genes, Reinke et al 2004, list of                              
                                              genes in cluster order, Reinke et al 2004, oogenesis                               
                                              enriched genes, Reinke et al 2004, wt vs glp-4 enriched                            
                                              genes, Reinke et al 2004, wt herm vs wt male enriched                              
                                              gen, Reinke et al 2004, list of genes in cluster E                                 

C44C10.8 C44C10.8 P W All gene names: hlh-18; hlh-22; hnd-1; C44C10.8; CE05415; NM_077551; WBGene00001981; WP:CE05415; XM301 WormBase description: hnd-1 encodes a Hand bHLH transcription factor required for normal viability, gonadogenesis, and posterior body morphology; HND-1 is required for the formation of both somatic gonadal precursors and primordial germ cells, but not for later gonadogenesis; HND-1 is expressed embryogenesis in embryonic mesodermal precursor cells generating (mostly) body wall muscle, in somatic gonad precursor cells, and in some unidentified head cells; the primary defect in hnd-1 mutants may be, nonautonomously, in mesodermal precursor cells; somatic gonad precursor cells are normally generated in hnd-1 mutants, but not maintained. WormBase CDS description: Helix-loop-helix DNA-binding domain
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes                                 

C46H11.2 C46H11.2 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                                                                    

C54F6.8 C54F6.8 P W All gene names: nhr-171; C54F6.8; 5H991; CE17603; WBGene00016926; WP:CE17603 WormBase description: nuclear hormone receptor
                                              
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 sir-2.1 regulated                                      

C55C2.1 C55C2.1 P W All gene names: C55C2.1; 1D137; CE16948; WBGene00016948; WP:CE16948 WormBase description: zinc-finger transcription factor
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, parrerning involved                                
                                              PAL-1 target, Baugh et al 2005, PAL-1 target genes                                 

D1081.2 D1081.2 P W All gene names: unc-120; D1081.2; 1J37; CE05534; NM_059895; WBGene00006844; WP:CE05534 WormBase description: unc-120 encodes a member of the MADS-box family of transcription factors that contains human and Drosophila serum response factor (SRF) and Saccharomyces cerevisiae MCM1 and ARG80; UNC-120 is required for locomotion and muscle development and for formation of the normal number of muscle A and I bands; UNC-120 is also required for maintaining wild-type expression levels of the muscle components actin and myosin; UNC-120 is first expressed in the early embryo in body wall muscle precursors and later is expressed in both body wall and vulval muscles. WormBase CDS description: MADS domain
                                              
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 A, Reinke                              
                                              et al 2004, list of genes in cluster order                                         

F11C1.6 F11C1.6 P W All gene names: nhr-25; F11C1.6; F11C1.6a.1; F11C1.6a.2; F11C1.6b.1; F11C1.6b.2; F11C1.6b.3; CE03191; CE35856; NM_077761; WBGene00003623; WP:CE03191; WP:CE35856; XN631 WormBase description: nhr-25 encodes a nuclear hormone receptor orthologous to Drosophila Ftz-F1; NHR-25 is required for embryogenesis, molting, vulval and gonadal development, and hypodermal expression of acn-1; nhr-25 is expressed in gonads and loaded into embryos as a maternal transcript; nhr-25 is zygotically expressed in progeny of the E cell, and then in hypodermis and gut; the role of NHR-25 in molting may be evolutionarily conserved between nematodes and arthopods.
                                              
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,                                
                                              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 Early genes, Wang et al 2003  S4 genes pass                                     
                                              two-wayANOVA P0                                                                    

F35G12.6 F35G12.6 P W All gene names: mab-21; F35G12.6; 3F691; CE32651; NM_065539; WBGene00003112; WP:CE32651 WormBase description: mab-21 encodes a novel protein that is a member of a highly conserved family of proteins with Drosophila and vertebrate orthologs; MAB-21 is cell-autonomously required for specifying the identity of sensory ray 6 in the male tail, and also for backward locomotion, normal body morphology, fecundity, and embryonic morphogenesis; MAB-21 expression begins in embryonic hypodermal cells and continues in larval and adult animals in hypodermis, anterior and ventral cord neurons, some body wall muscles, and ray cells.
                                              
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,                                
                                              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 Early genes, Wang et al 2003  S4 genes pass                                     
                                              two-wayANOVA P0                                                                    

K02B9.4 K02B9.4 P W All gene names: elt-3; K02B9.4; CE23844; NM_077920; WBGene00001251; WP:CE23844; XO559 WormBase description: The elt-3 gene encodes a GATA transcription factor expressed in the embryonic hypodermis; specifically, it is expressed in expressed in all of the major hypodermal cells except the lateral seam cells. WormBase CDS description: GATA-binding transcription factor like
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes                                 

K10B4.6 K10B4.6 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                                 

M142.4 M142.4 P W All gene names: vab-7; M142.4; 3M15; CE12432; NM_067000; WBGene00006873; WP:CE12432 WormBase description: The vab-7 gene encodes an even-skipped-like homeodomain protein that is required for DB motoneuron identity and posterior DB axonal polarity. WormBase CDS description: homeobox protein (even-skipped subfamily)
                                              
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,                                
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

R02D3.1 R02D3.1 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 R07C3.11 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                                     

T07C4.2 T07C4.2 P W All gene names: tbx-8; T07C4.2; 3L437; CE36891; NM_066886; WBGene00006545; WP:CE36891 WormBase description: Brachyury
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes                                 

T07C4.6 T07C4.6 P W All gene names: tbx-9; T07C4.6; T07C4.6.1; T07C4.6.2; 3L430; CE36892; NM_066885; WBGene00006546; WP:CE36892 WormBase description: Brachyury
                                              
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 E                                      

T22B7.3 T22B7.3 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                                                                 

W09C2.1 W09C2.1 P W All gene names: elt-1; W09C2.1; W09C2.1a.1; W09C2.1a.2; 4K383; CE03799; CE39113; NM_069307; WBGene00001249; WP:CE03799; WP:CE39113 WormBase description: The elt-1 gene encodes a GATA transcription factor expressed in the embryonic hypodermis, and is essential for the production of most hypodermal cells. WormBase CDS description: elongation factor ELT
                                              
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, mixed sperm soma, Reinke et al 2004,                            
                                              fem3 enriched genes                                                                

Y75B8A.2 Y75B8A.2 P W All gene names: nob-1; Y75B8A.2; Y75B8A.C; 3N168; CE29009; CE29010; WBGene00003779; WP:CE29009; WP:CE29010 WormBase description: The nob-1 gene encodes one of three C. elegans posterior group homeodomain transcription factors orthologous to Drosophila Abd-B and the vertebrate Hox9-13 proteins; NOB-1, along with an additional posterior Hox ortholog, PHP-3, is required during embryogenesis for proper fate specification and morphogenesis of cells in the posterior region.
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, validated PAL-1                                 
                                              target genes, Baugh et al 2005, PAL-1 target genes                                 

ZK1307.1 ZK1307.1 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