Baugh et al 2003, subclass SE_186min, 50 genes Gene list file name: Baugh2003_classSEpi_186min.txt Type of gene identifier: Affymetrix custom chip Description: Baugh et al 2005, Supplymental Dataset, subclass SE_186min 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 AFF_T08G5.7 Aff_T08G5.7 B0272.1 Aff_B0272.1 tbb-4; B0272.1; CE00850; NM_077184; WBGene00006538; WP:CE00850; XK54 tubulin beta chain McCarroll et al 2004 SFig5 conserved w/ yeast, McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, Portman et al 2004 T1 newly found ray-genes in25c, Portman et al 2004 T1 25 candidate ray genes, Reinke et al 2004, IVb male soma enriched genes, ViswanathanM et al 2005 S2 sir-2.1 regulated B0303.2 Aff_B0303.2 B0303.2; 3J775; CE00536; WBGene00015124; WP:CE00536 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 C01F1.3 Aff_C01F1.3 phi-41; C01F1.3; C01F1.3a.1; C01F1.3a.2; 2E587; CE06744; CE39553; WBGene00015298; WP:CE06744; WP:CE39553 Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, list of genes in cluster B, Romagnolo et al 2002 Fig3b Metabolism, 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 C02F12.1 Aff_C02F12.1 tsp-17; C02F12.1; CE35213; NM_076233; WBGene00006643; WP:CE35213; XE303 transpanin C02F12.7 Aff_C02F12.7 tag-278; C02F12.7; CE03901; WBGene00015356; WP:CE03901; XE304 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 C05A9.2 Aff_C05A9.2 C05A9.2; CE05222; WBGene00007317; WP:CE05222; XL460 Jones et al 2001 Non dauer genes P<0.05 C05B5.8 Aff_C05B5.6 C05B5.8; 3L96; CE33967; WBGene00007324; WP:CE33967 C05C8.3 Aff_C05C8.3 dao-1; fkb-3; C05C8.3; 5H707; CE07921; NM_072434; WBGene00001428; WP:CE07921 fkb-3 encodes a peptidylprolyl cis/trans isomerase homologous to mammalian FK506 immunosuppressant-binding protein 9; FKB-3 expression is positively regulated by signaling through the DAF-2 insulin receptor-like pathway and the activity of the DAF-16 fork-head transcription factor suggesting that FKB-3 could play a role in metabolism and longevity; however, as loss of FKB-3 function via RNA-mediated interference (RNAi) does not result in any abnormalities, the precise role of FKB-3 in C. elegans development and/or behavior is not yet known; FKB-3 contains a predicted endoplasmic reticulum (ER) retention sequence and is thus proposed to localize to the ER. FKBP-binding protein Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, list of genes in cluster B, 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 C10A4.3 Aff_C10A4.3 C10A4.3; CE02471; WBGene00015664; WP:CE02471; XI19 ViswanathanM et al 2005 S2 sir-2.1 regulated C14A4.6 Aff_C14A4.6 C14A4.6; C14A4.6.1; C14A4.6.2; 2K884; CE02147; WBGene00007557; WP:CE02147 C14F11.6 Aff_C14F11.6 C14F11.6; CE02482; WBGene00015781; WP:CE02482; XG856 DTDP-4-dehydrorhamnose 3,5-epimerase (RFBC gene) 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 S5 genes common to feeding ANOVA, Wang et al 2003 S3 genes pass one-way ANOVA C17C3.12 Aff_C17C3.12 acdh-2; C17C3.12; C17C3.12c.1; C17C3.12c.2; CE29175; CE29176; CE34697; NM_062665; NM_062666; NM_062667; WBGene00015894; WP:CE29175; WP:CE29176; WP:CE34697 acyl-CoA dehydrogenase ViswanathanM et al 2005 S2 sir-2.1 regulated C23F12.1 Aff_B0272.5 C23F12.1; CE32133; CE32134; WBGene00016006; WP:CE32133; WP:CE32134; XK45 Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, list of genes in cluster B C26G2.1 Aff_C26G2.1 syg-2; C26G2.1; CE19703; NM_078034; WBGene00007750; WP:CE19703; XP281 syg-2 encodes a transmembrane protein that is a member of the immunoglobulin superfamily of proteins; during larval development, SYG-2 activity is required in vulval epithelial cells for proper synaptic specificity of the HSNL neuron; in regulating synapse formation, SYG-2 acts as a guidepost protein for the SYG-1 receptor that interacts with SYG-2 and acts within HSNL to regulate synaptic specificity; a SYG-2::GFP fusion protein is expressed in the primary vulval cell lineages beginning at the L3 larval stage, with expression increasing during the L4 stage and finally disappearing by adulthood; in embryos, SYG-2::GFP expression is detected in some head neurons and body wall muscles, the latter of which also express the reporter during the L1 and L2 larval stages. Immunoglobulin domain ; Fibronectin type III domain McCarroll et al 2004 SFig1-4 conserved w/ Drosoph C27C12.6 Aff_C27C12.6 dmd-4; C27C12.6; CE23560; WBGene00007776; WP:CE23560; XP476 doublesex protein like McCarroll et al 2004 SFig1-4 conserved w/ Drosoph C33D12.7 Aff_C33D12.7 ceh-30; C33D12.7; CE06909; NM_076123; WBGene00000451; WP:CE06909; XD683 ceh-30 encodes a homeodomain protein most similar to Drosophila and mammalian BarH1 (OMIM:605211) which function in neuronal cell fate determination; the precise biological role of CEH-30 in C. elegans development and/or behavior is not yet known. homeobox protien McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, ViswanathanM et al 2005 S2 sir-2.1 regulated C33F10.7 Aff_C33F10.7 C33F10.7; C33F10.7b.1; C33F10.7b.2; 2F108; CE04140; CE37751; WBGene00016355; WP:CE04140; WP:CE37751 esterase and beta-lactamase Kwon et al 2004 T1 late-induction Ethanol-response, 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, ViswanathanM et al 2005 S2 daf-16 Resveratrol C54D1.4 Aff_C54D1.4 alh-10; C54D1.4; C54D1.4.1; C54D1.4.2; CE06980; NM_076802; WBGene00000116; WP:CE06980; XH760 aldehyde dehydrogenase 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 D1005.2 Aff_D1005.2 D1005.2; CE29741; WBGene00016996; WP:CE29741; XC81 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 LateList, Wang et al 2003 S4 genes pass two-wayANOVA P0 DY3.3 Aff_DY3.3 hlh-16; DY3.3; 1J342; CE15747; NM_059971; WBGene00001960; WP:CE15747 Helix-loop-helix DNA-binding domain F14B4.1 Aff_F14B4.1 F14B4.1; 1J842; CE38950; WBGene00008779; WP:CE38950 LDL receptor-related protein Reinke et al 2004, list of genes in cluster order F21D5.9 Aff_F21D5.9 F21D5.9; 4J485; CE03251; WBGene00009014; WP:CE03251 Zinc finger, C2H2 type ViswanathanM et al 2005 S2 sir-2.1 regulated F35G2.4 Aff_F35G2.4 phy-2; F35G2.4; F35G2.4.1; F35G2.4.2; 4M976; CE05811; NM_069916; WBGene00004025; WP:CE05811 prolyl 4-hydroxylase alpha subunit 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, Romagnolo et al 2002 Fig3b others F37C4.4 Aff_F37C4.4 F37C4.4; F37C4.4b.1; F37C4.4b.2; 4E635; CE17047; CE31505; WBGene00018144; WP:CE17047; WP:CE31505 Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, list of genes in cluster B, 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 F38B6.6 Aff_F38B6.6 F38B6.6; CE30976; WBGene00018175; WP:CE30976; XH300 McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, ViswanathanM et al 2005 S2 daf-16 Resveratrol F40E10.1 Aff_F40E10.1 hch-1; nas-34; F40E10.1; CE24964; NM_078039; WBGene00001828; WP:CE24964; XP316 hch-1 encodes a member of the zinc-dependent metalloprotease family that contains an epidermal growth factor-like domain, a CUB domain, and a TSP1 domain and affects hatching and QL neuroblast migration. metalloprotease Golden et al 2004, N2 vs daf-2 different genes at , Golden et al 2004, N2 vs daf-2 age different gene, Jones et al 2001 Non dauer genes P<0.05 F44E5.3 Aff_F44E5.3 F44E5.3; 2M52; CE18678; WBGene00009690; WP:CE18678 F52H3.1 Aff_F52H3.1 let-268; F52H3.1; F52H3.1.1; F52H3.1.2; F52H3.1.3; 2K324; CE03397; NM_063769; WBGene00002497; WP:CE03397 let-268 encodes a procollagen lysyl hydroxylase that processes type IV collagen, a collagen secreted and incorporated into the basement membrane during embryogenesis (and encoded partly by emb-9); LET-268 activity is essential for type IV collagen processing and secretion and for the stability, but not the formation of, the basement membrane that provides mechanical support to body wall muscle once contraction begins; LET-268 also appears to be required for pharyngeal muscle contraction. procollagen-lysine,2-oxoglutarate 5-dioxygenase precusor 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, 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 F54A5.2 Aff_F54A5.C F54A5.2; F54A5.C; 1B438; CE20860; WBGene00018787; WP:CE20860 McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, Reinke et al 2004, wt herm vs wt herm enriched gen F58A6.1 Aff_F58A6.1 F58A6.1; 2F429; CE04675; WBGene00019022; WP:CE04675 McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, ViswanathanM et al 2005 S2 sir-2.1 regulated K07C11.4 Aff_K07C11.4 K07C11.4; 5I685; CE07347; WBGene00019477; WP:CE07347 esterase Reinke et al 2004, GO categories, Reinke et al 2004, herm soma enriched genes, ViswanathanM et al 2005 S2 sir-2.1 regulated, Zhang et al 2002, T1 mec-3 dependent genes K08A8.2 Aff_K08A8.2 sox-2; K08A8.2; K08A8.2a.1; K08A8.2a.2; K08A8.2b.1; K08A8.2b.2; K08A8.2b.3; CE28595; CE31200; NM_171725; NM_171726; WBGene00004949; WP:CE28595; WP:CE31200; XI78 The sox-2 gene encodes a homolog of human SRY, which when mutated leads to gonadal dysgenesis (OMIM:306100). K08B4.2 Aff_K08B4.2 K08B4.2; 4G840; CE25940; WBGene00019514; WP:CE25940 Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, list of genes in cluster E, ViswanathanM et al 2005 S2 daf-16 Resveratrol K09E2.4 Aff_K09E2.4 rig-1; K09E2.4; CE02817; CE34053; WBGene00004369; WP:CE02817; WP:CE34053; XJ289 M01H9.4 Aff_M01H9.4 M01H9.4; 4F244; CE39601; WBGene00019720; WP:CE39601 Reinke et al 2004, list of genes in cluster A, Reinke et al 2004, list of genes in cluster order R09F10.4 Aff_R09F10.4 inx-5; opu-5; R09F10.4; CE33811; NM_077002; WBGene00002127; WP:CE33811; XI916 inx-5 encodes a predicted member of the innexin family; expressed in the embryonic hypodermis, developing vulva, seam cells, and spermatheca. unc-7-like protein Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, list of genes in cluster B, Romagnolo et al 2002 Fig3b Transporters, 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 T06A10.2 Aff_C26C9.2 T06A10.2; 4R835; CE36609; WBGene00020285; WP:CE36609 ViswanathanM et al 2005 S2 sir-2.1 regulated, ViswanathanM et al 2005 S2 daf-16 Resveratrol T22B2.4 Aff_T22B2.4 sup-12; T22B2.4; CE13934; NM_076273; WBGene00006321; WBGene00020668; WP:CE13934; XE525 RNA-binding protein ViswanathanM et al 2005 S2 sir-2.1 regulated T22E5.3 Aff_T22E5.3 T22E5.3; CE37152; WBGene00020691; WP:CE37152; XH5 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, ViswanathanM et al 2005 S2 daf-16 Resveratrol, 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 T27A1.5 Aff_T27A1.5 T27A1.5; T27A1.5a.1; T27A1.5a.2; T27A1.5b.1; T27A1.5b.2; 2A815; CE14213; CE39784; WBGene00020837; WP:CE14213; WP:CE39784 McCarroll et al 2004 SFig5 conserved w/ yeast, Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, list of genes in cluster C, 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 T28B4.3 Aff_T28B4.3 T28B4.3; CE14325; WBGene00020886; WP:CE14325; XH214 Reinke et al 2004, mixed sperm soma, Reinke et al 2004, wt herm vs wt herm enriched gen, Reinke et al 2004, GO categories, Reinke et al 2004, fem3 enriched genes, 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 T28H10.1 Aff_T28H10.1 T28H10.1; 5M985; CE06529; WBGene00012142; WP:CE06529 B.subtilis SFP protein like ViswanathanM et al 2005 S2 sir-2.1 regulated W03A3.1 Aff_W03A3.1 ceh-10; mig-11; W03A3.1; 3G889; CE07563; NM_065850; WBGene00000435; WP:CE07563 ceh-10 encodes a member of the Paired-like class of homeodomain proteins; the CEH-10 homeodomain is closely related to the homeodomains of two vertebrate retina proteins (Chx10 from mice and Vsx-1 from goldfish); ceh-10 is required for CAN cell fate specification and migration, complete loss of ceh-10 function results in failure of CAN cell migration and loss of expression of CEH-23 and CEH-10 itself in the CAN and AIY interneurons; CEH-10, along with TTX-3 and CEH-23, constitutes a regulatory cascade of transcription factors that controls all sub-type specific features of the AIY interneurons. McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, ViswanathanM et al 2005 S2 daf-16 Resveratrol Y22D7AL.14 Aff_Y119D3_465.U Y22D7AL.14; 3C742; CE23435; WBGene00021252; WP:CE23435 ViswanathanM et al 2005 S2 sir-2.1 regulated, ViswanathanM et al 2005 S2 daf-16 Resveratrol Y41D4B.26 Aff_Y41D4B_930.A nhr-146; Y41D4B.26; 4C397; CE36740; WBGene00021525; WP:CE36740 Y53F4B.14 Aff_Y53F4B.Q Y53F4B.14; 2P325; CE25395; WBGene00013161; WP:CE25395 Y82E9BR.20 Aff_Y119D3_444.A Y82E9BR.20; 3C465; CE29934; WBGene00022352; WP:CE29934 ZC8.3 Aff_ZC8.2 tag-226; ZC8.3; CE33744; WBGene00022499; WP:CE33744; XF621 ViswanathanM et al 2005 S2 daf-16 Resveratrol ZK75.2 Aff_ZK75.2 ins-2; ZK75.2; 2G277; CE02101; NM_062793; WBGene00002085; WP:CE02101 7TM chemoreceptor, ins family Lund et al 2002 Fig1 aging-regulated genes, ViswanathanM et al 2005 S2 sir-2.1 regulated