Roy et al 2002 S2 positivecontrol L1 muscle, 18 genes

Gene list file name:Roy2002.S2_16positivecontrol_L1muscle.txt
Type of gene identifier:MA primer pair (sjj)
Description:Roy et al 2002 Supplement2: positivecontrol L1 muscle  
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                                                   

C09D1.1 C09D1.1 P W All gene names: phm-1; unc-89; C09D1.1; 1E657; CE30426; CE34251; CE34252; CE37701; CE37702; CE37703; CE37704; WBGene00006820; WP:CE30426; WP:CE34251; WP:CE34252; WP:CE37701; WP:CE37702; WP:CE37703; WP:CE37704 WormBase description: protein kinase
                                              
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, Roy et al 2002  S2 positivecontrol L1                                   
                                              muscle, ViswanathanM et al 2005  S2 sir-2.1 regulated                              

C29F9.7 C29F9.7 P W All gene names: pat-4; C29F9.7; C29F9.7.1; C29F9.7.2; 3A708; CE19706; NM_064738; WBGene00003931; WP:CE19706 WormBase description: The pat-4 gene encodes a serine/threonine kinase orthologous to human integrin-linked kinase (ILK, OMIM:602366) and is required for formation of integrin-mediated muscle cell attachments during embryogenesis; PAT-4 probably functions as an adaptor molecule and localizes to dense bodies and M lines; PAT-4 forms a ternary complex with PAT-6/actopaxin and UNC-112, and requires UNC-112, UNC-52/perlecan, PAT-2/alpha integrin, and PAT-3/beta integrin for proper localization to newly forming integrin adhesion complexes. WormBase CDS description: integrin-linked kinase
                                              
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, Roy et al 2002  S2 positivecontrol L1 muscle                            

C36E6.3 C36E6.F P W All gene names: mlc-1; C36E6.3; C36E6.F; CE34269; NM_078428; WBGene00003369; WP:CE34269; XS73 WormBase description: encodes a muscle regulatory myosin light chain that is nearly identical to MLC-2 and functions redundantly with MLC-2 in the body-wall and in pharyngeal muscle to affect L1 larval viability, elongation, and pharyngeal and body-wall muscle development, and also affects locomotion and growth; expressed in the body-wall muscles, pharyngeal muscles, and vulval muscles.
                                              
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, Roy et al 2002  S2 positivecontrol L1 muscle                            

C36E6.5 C36E6.B P W All gene names: mlc-2; C36E6.5; C36E6.5.1; C36E6.5.2; C36E6.B; CE20542; NM_078427; WBGene00003370; WP:CE20542; XS70
                                              
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, Roy et al 2002  S2 positivecontrol L1 muscle                                

C38C3.5 C38C3.5 P W All gene names: UNC-60A; unc-60; unc-66; C38C3.5; C38C3.5c.1; C38C3.5c.2; C38C3.5c.3; 5B957; CE20547; CE20549; CE31893; NM_071026; WBGene00006794; WP:CE20547; WP:CE20549; WP:CE31893 WormBase description: unc-60 encodes orthologs of actin depolymerizing factor/cofilin, actin-binding proteins that regulate actin filament dynamics; one UNC-60 isoform, UNC-60A, primarily binds G-actin, depolymerizes actin filaments, and inhibits actin polymerization; UNC-60A is essential during early embryonic development for polar body extrusion, cytokinesis, and embryonic patterning; UNC-60B, which does not inhibit actin polymerization, binds F- and G-actin and influences the rate of actin polymerization by the UNC-60B:actin ratio; UNC-60B is required for actin filament organization in body wall muscle, locomotion, and for efficient actin filament disassembly by UNC-78, an actin interactin protein 1 (AIP1) ortholog; UNC-60A and UNC-60B are differentially expressed: UNC-60A is found in oocytes, embryos, and the adult gonad and intestine, while UNC-60B is found in body wall muscle, the vulva, and spermatheca.
                                              
Member of lists (Publications lists):
                                              Roy et al 2002  S2 positivecontrol L1                             
                                              muscle, ViswanathanM et al 2005  S2 sir-2.1 regulated,                             
                                              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                                                               

C44B12.2 C44B12.2 P W All gene names: ost-1; C44B12.2; 4B863; CE08703; NM_067638; SPARC; SPARC/1; WBGene00003893; WP:CE08703 WormBase description: osteonectin
                                              
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, Reinke et al 2004, mixed sperm soma, Reinke                             
                                              et al 2004, fem3 enriched genes, Roy et al 2002  S2                                
                                              positivecontrol L1 muscle, ViswanathanM et al 2005  S2                             
                                              sir-2.1 regulated                                                                  

F07A5.7 F07A5.7 P W All gene names: unc-15; F07A5.7; F07A5.7.1; F07A5.7.2; F07A5.7.3; F07A5.7.4; 1H954; CE09197; NM_059684; WBGene00006754; WP:CE09197 WormBase description: The unc-15 gene encodes a paramyosin ortholog; UNC-15 protein physically interacts with MHC A, one isoform of myosin heavy chain (MHC) in striated muscle; UNC-15 accumulation is decreased in the absence of UNC-54 (myosin B), implying that degradation of UNC-15 is inhibited by its binding myosin B; conversely, myosin B (but not MYO-3/myosin A) fails to accumulate in unc-15 mutants. WormBase CDS description: paramyosin
                                              
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, Reinke et al 2004, IVb male soma enriched                               
                                              genes, Roy et al 2002  S2 positivecontrol L1 muscle,                               
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F08B6.4 F08B6.4 P W All gene names: unc-87; F08B6.4; F08B6.4c.1; F08B6.4c.2; F08B6.4c.3; 1H338; CE20658; CE27922; CE36924; WBGene00006819; WP:CE20658; WP:CE27922; WP:CE36924 WormBase description: unc-87 encodes, through alternative splicing, two proteins that are required to maintain the structure of myofilaments in body wall muscle cells; UNC-87 proteins resemble the C-terminal repeat region of calponin but have no obvious orthologs outside of nematodes; in vitro, UNC-87 proteins exist as monomers in solution, associate with thin (F-actin) filaments but not with monomeric G-actin, and bundle F-actin filaments; in vivo, UNC-87 proteins reside in the I-band of bodywall muscle, and GFP-tagged UNC-87 associates with actin stress fibers; unc-87 mutants show degeneration of myofilaments, are profoundly immobile, and have noticeable defects in egg-laying; the unc-87 mutant phenotype is partially suppressed by the unc-54(s95) mutation, which lowers myosin activity but leaves myofilaments intact, indicating that UNC-87 prevents damage by mechanical stress on myofilaments.
                                              
Member of lists (Publications lists):
                                              Lund et al 2002  Aging time course                                
                                              Fig3A muscle, Roy et al 2002  S2 positivecontrol L1                                
                                              muscle, ViswanathanM et al 2005  S2 sir-2.1 regulated,                             
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

F11C3.3 F11C3.3 P W All gene names: myo-4; unc-54; F11C3.3; F11C3.3.1; F11C3.3.2; F11C3.3.3; F11C3.3.4; F11C3.3.5; 1P454; CE09349; NM_061195; WBGene00006789; WP:CE09349 WormBase description: unc-54 encodes a muscle myosin class II heavy chain (MHC B); UNC-54 is the major myosin heavy chain expressed in C. elegans and is required for locomotion and egg-laying; in vivo and in vitro, UNC-54 interacts with ITR-1, an IP3 receptor, and this interaction may provide a link between calcium signaling and the muscle cytoskeleton; UNC-54 is a thick filament component that is expressed in multiple muscle cell classes including body wall, intestinal, anal depressor, and sphincter muscles as well as sex-specific muscles that develop postembryonically. WormBase CDS description: myosin heavy chain
                                              
Member of lists (Publications lists):
                                              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                                                                  

F30H5.1 F30H5.1 P W All gene names: unc-45; F30H5.1; 3B119; CE01925; NM_064804; WBGene00006781; WP:CE01925 WormBase description: P59 protein and TPR domain
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Roy et al 2002  S2                                           
                                              positivecontrol L1 muscle                                                          

F40E10.3 F40E10.3 P W All gene names: csq-1; F40E10.3; F40E10.3.1; F40E10.3.2; CE05839; NM_078037; WBGene00000822; WP:CE05839; XP305 WormBase description: calsequestrin like
                                              
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, Roy et al 2002  S2 positivecontrol L1                                   
                                              muscle, 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                                                               

F54C1.7 F54C1.7 P W All gene names: pat-10; tnc-1; F54C1.7; F54C1.7.1; F54C1.7.2; F54C1.7.3; 1F588; CE11052; NM_059100; WBGene00003934; WP:CE11052 WormBase description: pat-10 encodes body wall muscle troponin C, the calcium-binding component of the troponin complex of actin thin filaments; PAT-10 is essential for muscle contraction and thus for completion of embryonic morphogenesis and elongation; by homology, PAT-10 likely functions to regulate body wall muscle contraction in response to changes in intracellular calcium; PAT-10 is expressed in body wall muscle but is also detected in vulval and anal muscles; expression in body wall muscle begins during early embryonic morphogenesis, concurrent with expression of other body wall muscle structural components. WormBase CDS description: calcium 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 C, Reinke et al 2004, wt herm vs wt herm                                   
                                              enriched gen, Roy et al 2002  S2 positivecontrol L1                                
                                              muscle, Wang et al 2003  S6 removed genes of                                       
                                              contamination                                                                      

K12F2.1 K12F2.1 P W All gene names: myo-3; sup-3; K12F2.1; 5M708; CE34936; NM_073664; WBGene00003515; WP:CE34936 WormBase description: myo-3 encodes MHC A, the minor isoform of MHC (myosin heavy chain) that is essential for thick filament formation, and for viability, movement, and embryonic elongation; expressed in body muscle, the somatic sheath cell covering the hermaphrodite gonad, and also expressed in enteric muscle, vulval muscles of the hermaphrodite and the diagonal muscles of the male tail. 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, Roy et al 2002  S2 positivecontrol L1                                   
                                              muscle, ViswanathanM et al 2005  S2 sir-2.1 regulated                              

M03F4.2 M03F4.2 P W All gene names: act-4; M03F4.2; M03F4.2a.1; M03F4.2a.2; M03F4.2a.3; M03F4.2b.1; M03F4.2b.2; CE12358; CE28620; CE37134; NM_076440; NM_076441; WBGene00000066; WP:CE12358; WP:CE28620; WP:CE37134; XF583; act4 WormBase description: An actin that is expressed in body wall and vulval muscles and the spermatheca.
                                              
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, wt herm vs wt herm enriched                            
                                              gen, Reinke et al 2004, IVb male soma enriched genes,                              
                                              Roy et al 2002  S2 positivecontrol L1 muscle                                       

T01D1.2 T01D1.2 P W All gene names: etr-1; T01D1.2; T01D1.2a.1; T01D1.2a.2; T01D1.2a.3; 2A459; CE12942; CE28070; CE33441; NM_061272; WBGene00001340; WP:CE12942; WP:CE28070; WP:CE33441 WormBase description: etr-1 encodes a muscle-specific ELAV-type RNA-binding protein, whose homologs include Drosophila ELAV and human CUG-BINDING PROTEIN (CUGBP1; OMIM:601074); etr-1 function is required for embryonic muscle development, which suggests that ETR-1's homology to CUG-BP (implicated in myotonic dystrophy) might reflect conserved roles in development.
                                              
Member of lists (Publications lists):
                                              Roy et al 2002  S2 positivecontrol L1                             
                                              muscle, ViswanathanM et al 2005  S2 sir-2.1 regulated                              

T21C12.1 T21C12.1 P W All gene names: unc-49; unc-49A; unc-49B; unc-49C; T21C12.1; T21C12.1c.1; T21C12.1c.2; 3L621; CE02346; CE28082; CE28083; CE28084; CE28085; CE28086; CE35949; WBGene00006784; WP:CE02346; WP:CE28082; WP:CE28083; WP:CE28084; WP:CE28085; WP:CE28086; WP:CE35949 WormBase description: gamma-aminobutyric-acid receptor
                                              
Member of lists (Publications lists):
                                              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                                                                  

ZC101.2 ZC101.2 P W All gene names: unc-52; ZC101.2; 2O938; CE15028; CE15030; CE15034; CE18424; CE37074; NM_064643; NM_064644; NM_064645; NM_064646; WBGene00006787; WP:CE15028; WP:CE15030; WP:CE15034; WP:CE18424; WP:CE37074 WormBase description: The unc-52 gene encodes perlecan, a protein orthologous to human basement membrane-specific heparan sulfate proteoglycan core protein (HSPG2; OMIM:142461, which when mutated leads to Schwartz-Jampel syndrome or dyssegmental dysplasia); UNC-52 plays essential roles in muscle structure development and regulation of growth factor-like signaling pathways; UNC-52 is synthesized by the hypodermis and localizes to the extracellular matrix between hypodermis and muscle.
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, intrinsic, Reinke                              
                                              et al 2004, wt vs glp-4 enriched genes, Roy et al 2002                             
                                              S2 positivecontrol L1 muscle, 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