ReichertK et al 2005 T2 xenobiotic induced Collag, 23 genes

Gene list file name:ReichertK2005.T2_xenobiotic_induced_Collagene.txt
Type of gene identifier:MA primer pair (sjj)
Description:ReichertK et al 2005 Table2: xenobiotic induced Collagene  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

B0222.6 B0222.6 P W All gene names: col-144; B0222.6; 5J640; CE30585; NM_072973; WBGene00000717; WP:CE30585
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, Reinke et al 2004, wt herm vs wt herm                               
                                              enriched gen, Reinke et al 2004, list of genes in                                  
                                              cluster B, 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                                                      

B0222.8 B0222.8 P W All gene names: col-10; B0222.8; 5J644; CE06699; NM_072975; WBGene00000599; WP:CE06699 WormBase description: col-10 encodes a collagen protein; expressed exclusively in hypodermal cells
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, Reinke et al 2004, wt herm vs wt herm                               
                                              enriched gen, Reinke et al 2004, list of genes in                                  
                                              cluster B, 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                                                      

B0491.2 B0491.2 P W All gene names: rol-5; sqt-1; B0491.2; B0491.2.1; B0491.2.2; 2L626; CE02104; NM_064020; Rol; WBGene00005016; WP:CE02104 WormBase description: sqt-1 encodes a cuticle collagen; during larval and adult development, sqt-1 activity is required, likely redundantly, for normal cuticle, and hence organismal, morphology; sqt-1 mRNA abundance oscillates during larval development, peaking at one point during each larval stage and peaking again in adults; sqt-1 transcripts are also detected in animals at the L1-L2d molt; in the temporally distinct waves of collagen gene expression that occur during larval development, sqt-1 mRNA appears to be synthesized during the second, or intermediate, stage, just very slightly earlier than sqt-3/col-1 and dpy-13; SQT-1 protein is detected in cuticle extracts from L2, L3, and L4 larvae, and from adults, but is not detected in extracts from L1 or dauer larvae; sqt-1 interacts genetically with a number of genes also required for normal cuticle and organismal morphology, e.g., rol-6 and lon-3, which also encode cuticular collagens. WormBase CDS description: cuticle collagen SQT-1
                                              
Member of lists (Publications lists):
                                              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 sir-2.1                                     
                                              regulated, 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                                                      

C09G5.6 C09G5.6 P W All gene names: bli-1; C09G5.6; 2L1; CE35827; NM_063910; WBGene00000251; WP:CE35827 WormBase description: The bli-1 gene encodes an unusual cuticular collagen that is required for proper strut formation within the unique medial layer of the adult cuticle; bli-1 interacts genetically with other cuticular collagens such as bli-2 and rol-1, and may be processed for secretion by BLI-4, a Kex2/subtilisin serine endoproteinase; consistent with its role in adult cuticle formation, bli-1 mRNA is highly expressed only during the L4 larval stage. WormBase CDS description: collagen
                                              
Member of lists (Publications lists):
                                              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 C, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

C35B8.1 C35B8.1 P W All gene names: col-175; C35B8.1; CE02534; NM_077154; WBGene00000748; WP:CE02534; XJ852 WormBase description: Cuticle collagen
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05, 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 C,                              
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated,                                     
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

C46A5.3 C46A5.3 P W All gene names: col-14; C46A5.3; 4I519; CE08753; CE29723; NM_068872; WBGene00000603; WP:CE08753; WP:CE29723; col14 WormBase description: col-14 encodes a collagen protein that affects vulval morphology in a large-scale RNAi screen; mRNA expressed in embryos and transcript levels peak during each larval stage.
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05, Jones et al 2001  T3 20 most abundant                                      
                                              Mixed-stage, ReichertK et al 2005  T2 xenobiotic                                   
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, Reinke et al 2004, wt herm vs wt herm                               
                                              enriched gen, Reinke et al 2004, list of genes in                                  
                                              cluster C, 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                                                       

C52D10.13 C52D10.13 P W All gene names: col-138; C52D10.13; 4S124; CE17596; NM_070647; WBGene00000711; WP:CE17596 WormBase description: cuticular collagen
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05, 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 C,                              
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated,                                     
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

F14F7.1 F14F7.1 P W All gene names: col-98; F14F7.1; F14F7.1.1; F14F7.1.2; 3O109; CE15821; NM_067302; WBGene00000673; WP:CE15821 WormBase description: collagen
                                              
Member of lists (Publications lists):
                                              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 C, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

F23H12.4 F23H12.4 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                                                                       

F27C1.8 F27C1.8 P W All gene names: dpy-5; F27C1.8; F27C1.8.1; F27C1.8.2; 1G0; CE09720; NM_059194; WBGene00001067; WP:CE09720 WormBase description: dpy-5 encodes a cuticle collagen that affects body length and cuticle structure and specifically affects the formation of annuli and the expression of dpy-7, dpy-13, and col-19; mRNA abundance increases two hours prior to the secretion of each new cuticle, and mRNA levels appear to increase at and after the L2 larval stages. WormBase CDS description: cuticular collagen
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, ViswanathanM et al 2005  S2 sir-2.1                                
                                              regulated, 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                                                      

F30B5.1 F30B5.1 P W All gene names: dpy-13; dpy-16; F30B5.1; 4F1; CE04462; NM_068118; WBGene00001074; WP:CE04462 WormBase description: dpy-13 encodes a member of the collagen superfamily containing 20 copies of the collagen triple helix repeat; transcipt levels oscillate, peaking once during each larval stage. WormBase CDS description: cuticular collagen
                                              
Member of lists (Publications lists):
                                              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 C, Reinke et al 2004, wt herm vs wt herm                                   
                                              enriched gen, ViswanathanM et al 2005  S2 sir-2.1                                  
                                              regulated, 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                                                      

F46C8.6 F46C8.6 P W All gene names: dpy-7; F46C8.6; F46C8.6.1; F46C8.6.2; CE04580; NM_076873; WBGene00001069; WP:CE04580; XI156 WormBase description: dpy-7 encodes a cuticular collagen; DPY-7 functions as a structural constituent of the extracellular cuticle whose activity is required for normal cuticular morphology and hence, proper body form. WormBase CDS description: cuticle collagen
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, Reinke et al 2004, wt herm vs wt herm                               
                                              enriched gen, Reinke et al 2004, IVb male soma enriched                            
                                              genes, Reinke et al 2004, list of genes in cluster B,                              
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated, 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                                                                           

F53F1.5 F53F1.5 P W All gene names: F53F1.5; 5N893; CE10940; NM_073924; WBGene00009983; WP:CE10940 WormBase description: cuticlin
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05, 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 C,                              
                                              Reinke et al 2004, wt herm vs wt herm enriched gen,                                
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

F54C9.4 F54C9.4 P W All gene names: col-38; F54C9.4; 2I858; CE20864; NM_063409; WBGene00000615; WP:CE20864 WormBase description: col-38 encodes a member of the collagen superfamily containing collagen triple helix repeats (20 copies) required for normal body morphology. WormBase CDS description: collagen
                                              
Member of lists (Publications lists):
                                              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 C, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

K09H9.3 K09H9.3 P W All gene names: col-49; K09H9.3; 1D705; CE18038; NM_058705; WBGene00000626; WP:CE18038 WormBase description: cuticular collagen
                                              
Member of lists (Publications lists):
                                              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 C, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

T01B7.7 T01B7.7 P W All gene names: rol-6; T01B7.7; 2J23; CE03591; NM_063457; WBGene00004397; WP:CE03591 WormBase description: The rol-6 gene encodes a cuticle collagen related to human collagen alpha 1 (III) chain precursor (OMIM:120180), and is required for normal cuticular morphology; ROL-6 interacts with SQT-1, a closely related cuticle collagen, and is expressed at all stages from L2 to adult with transcripts detected at each of the molts preceding these stages. WormBase CDS description: cuticle collagen ROL-6
                                              
Member of lists (Publications lists):
                                              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, 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                                                       

T14B4.6 T14B4.6 P W All gene names: dpy-2; rol-2; T14B4.6; 2H5; CE04953; NM_062966; WBGene00001064; WP:CE04953 WormBase description: The dpy-2 gene encodes an unusual cuticular collagen that is required for maintaining the normal body length of the animal in later larval stages; dpy-2 interacts with other cuticular collagens such as dpy-10 and sqt-1, and suppresses mutations in glp-1, mup-1, and emb-5.
                                              
Member of lists (Publications lists):
                                              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 sir-2.1                                     
                                              regulated, 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                                                      

T21D12.2 T21D12.2 P W All gene names: col-100; dpy-9; T21D12.2; 4B12; CE35021; NM_067488; WBGene00001071; WP:CE35021 WormBase description: dpy-9 encodes a cuticular collagen family member with similarity to human collagen alpha 5, type IV, and affects body length. WormBase CDS description: cuticular collagen
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, Reinke et al 2004, wt herm vs wt herm                               
                                              enriched gen, Reinke et al 2004, list of genes in                                  
                                              cluster B, ViswanathanM et al 2005  S2 sir-2.1                                     
                                              regulated, 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                                                       

W03G11.1 W03G11.1 P W All gene names: col-181; W03G11.1; CE03781; CE26826; NM_077620; WBGene00000754; WP:CE03781; WP:CE26826; XM725 WormBase description: col-181 is homologous to the human gene PRO ALPHA 1(I) COLLAGEN (COL1A1; OMIM:120150), which when mutated leads to osteogenesis imperfecta. WormBase CDS description: cuticle collagen
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, ViswanathanM et al 2005  S2 sir-2.1                                 
                                              regulated, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol                                                                        

Y41E3.2 Y41E3.2 P W All gene names: col-134; dpy-4; Y41E3.2; 4P750; CE18370; NM_070407; WBGene00001066; WP:CE18370 WormBase description: dpy-4 is an uncloned gene required for normal body length; dpy-4 was first identified with the mutagen ICR. WormBase CDS description: CUTICLE COLLAGEN 1
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, Reinke et al 2004, wt herm vs wt herm                               
                                              enriched gen, Reinke et al 2004, list of genes in                                  
                                              cluster C, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol, ViswanathanM et al 2005  S2 sir-2.1                                   
                                              regulated, Wang et al 2003  S3  genes pass one-way                                 
                                              ANOVA, Wang et al 2003  S4 genes pass two-wayANOVA P0,                             
                                              Wang et al 2003  S4 LateList                                                       

ZK1010.7 ZK1010.7 P W All gene names: col-97; ZK1010.7; 3O82; CE15507; NM_067299; WBGene00000672; WP:CE15507 WormBase description: collagen
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster order, Reinke et al 2004, wt herm vs wt herm                               
                                              enriched gen, Reinke et al 2004, list of genes in                                  
                                              cluster C, ViswanathanM et al 2005  S2 daf-16                                      
                                              Resveratrol, ViswanathanM et al 2005  S2 sir-2.1                                   
                                              regulated, Wang et al 2003  S3  genes pass one-way                                 
                                              ANOVA, Wang et al 2003  S4 genes pass two-wayANOVA P0,                             
                                              Wang et al 2003  S4 LateList                                                       

ZK1290.3 ZK1290.3 P W All gene names: rol-8; ZK1290.3; 2H835; CE29156; CE32085; NM_063181; NM_182112; WBGene00004398; WP:CE29156; WP:CE32085; col6 WormBase description: rol-8 encodes a collagen that is enriched in dauer larvae; mutations cause adults to become left-handed rollers.
                                              
Member of lists (Publications lists):
                                              ReichertK et al 2005  T2 xenobiotic                               
                                              induced Collag, Reinke et al 2004, list of genes in                                
                                              cluster A, Reinke et al 2004, list of genes in cluster                             
                                              order, Reinke et al 2004, wt herm vs wt herm enriched                              
                                              gen, ViswanathanM et al 2005  S2 daf-16 Resveratrol,                               
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated, Wang et                             
                                              al 2003  S3  genes pass one-way ANOVA, Wang et al 2003                             
                                              S4 genes pass two-wayANOVA P0, Wang et al 2003  S4                                 
                                              LateList                                                                           

ZK836.1 ZK836.1 P W All gene names: lon-3; ZK836.1; 5M678; CE15415; WBGene00003057; WP:CE15415 WormBase description: collagen
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05, ReichertK et al 2005  T2 xenobiotic induced                                
                                              Collag, 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