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 All gene names WormBase description WormBase CDS description Proteome description Member of lists (Publications) Other annotations B0222.6 B0222.6 col-144; B0222.6; 5J640; CE30585; NM_072973; WBGene00000717; WP:CE30585 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 col-10; B0222.8; 5J644; CE06699; NM_072975; WBGene00000599; WP:CE06699 col-10 encodes a collagen protein; expressed exclusively in hypodermal cells 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 rol-5; sqt-1; B0491.2; B0491.2.1; B0491.2.2; 2L626; CE02104; NM_064020; Rol; WBGene00005016; WP:CE02104 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. cuticle collagen SQT-1 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 bli-1; C09G5.6; 2L1; CE35827; NM_063910; WBGene00000251; WP:CE35827 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. collagen 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 col-175; C35B8.1; CE02534; NM_077154; WBGene00000748; WP:CE02534; XJ852 Cuticle collagen 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 col-14; C46A5.3; 4I519; CE08753; CE29723; NM_068872; WBGene00000603; WP:CE08753; WP:CE29723; col14 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. 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 col-138; C52D10.13; 4S124; CE17596; NM_070647; WBGene00000711; WP:CE17596 cuticular collagen 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 col-98; F14F7.1; F14F7.1.1; F14F7.1.2; 3O109; CE15821; NM_067302; WBGene00000673; WP:CE15821 collagen 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 col-1; dpy-15; sqt-3; F23H12.4; F23H12.4.1; F23H12.4.2; 5M833; CE05707; NM_073694; WBGene00005018; WP:CE05707 collagen 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 dpy-5; F27C1.8; F27C1.8.1; F27C1.8.2; 1G0; CE09720; NM_059194; WBGene00001067; WP:CE09720 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. cuticular collagen 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 dpy-13; dpy-16; F30B5.1; 4F1; CE04462; NM_068118; WBGene00001074; WP:CE04462 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. cuticular collagen 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 dpy-7; F46C8.6; F46C8.6.1; F46C8.6.2; CE04580; NM_076873; WBGene00001069; WP:CE04580; XI156 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. cuticle collagen 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 F53F1.5; 5N893; CE10940; NM_073924; WBGene00009983; WP:CE10940 cuticlin 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 col-38; F54C9.4; 2I858; CE20864; NM_063409; WBGene00000615; WP:CE20864 col-38 encodes a member of the collagen superfamily containing collagen triple helix repeats (20 copies) required for normal body morphology. collagen 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 col-49; K09H9.3; 1D705; CE18038; NM_058705; WBGene00000626; WP:CE18038 cuticular collagen 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 rol-6; T01B7.7; 2J23; CE03591; NM_063457; WBGene00004397; WP:CE03591 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. cuticle collagen ROL-6 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 dpy-2; rol-2; T14B4.6; 2H5; CE04953; NM_062966; WBGene00001064; WP:CE04953 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. 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 col-100; dpy-9; T21D12.2; 4B12; CE35021; NM_067488; WBGene00001071; WP:CE35021 dpy-9 encodes a cuticular collagen family member with similarity to human collagen alpha 5, type IV, and affects body length. cuticular collagen 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 col-181; W03G11.1; CE03781; CE26826; NM_077620; WBGene00000754; WP:CE03781; WP:CE26826; XM725 col-181 is homologous to the human gene PRO ALPHA 1(I) COLLAGEN (COL1A1; OMIM:120150), which when mutated leads to osteogenesis imperfecta. cuticle collagen 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 col-134; dpy-4; Y41E3.2; 4P750; CE18370; NM_070407; WBGene00001066; WP:CE18370 dpy-4 is an uncloned gene required for normal body length; dpy-4 was first identified with the mutagen ICR. CUTICLE COLLAGEN 1 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 col-97; ZK1010.7; 3O82; CE15507; NM_067299; WBGene00000672; WP:CE15507 collagen 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 rol-8; ZK1290.3; 2H835; CE29156; CE32085; NM_063181; NM_182112; WBGene00004398; WP:CE29156; WP:CE32085; col6 rol-8 encodes a collagen that is enriched in dauer larvae; mutations cause adults to become left-handed rollers. 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 lon-3; ZK836.1; 5M678; CE15415; WBGene00003057; WP:CE15415 collagen 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