Baugh et al 2003, subclass SE_41min, 61 genes Gene list file name: Baugh2003_classSEpi_41min.txt Type of gene identifier: Affymetrix custom chip Description: Baugh et al 2005, Supplymental Dataset, subclass SE_41min 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_F40F12.2 Aff_F40F12.2 AFF_T08B6.1 Aff_T08B6.1 AFF_Y47D3A.O Aff_Y47D3A.O AFF_Y54C5B.1 Aff_Y54C5B.1 B0213.6 Aff_B0213.6 nlp-31; B0213.6; 5E459; CE16777; NM_071706; WBGene00003769; WP:CE16777 nlp-31 encodes five predicted neuropeptide-like proteins; in C. elegans, nlp-31 is part of the YGGWamide neuropeptide family that also contains nlp-24, nlp-25, and nlp-27-32; nlp-31 is expressed in the hypodermis, suggesting that the peptides it encodes may have a non-neuronal function; nlp-31 expression is also detected in precomma-stage embryos; as loss of nlp-31 activity via large-scale RNAi screens does not result in any obvious abnormalities, the precise role of the nlp-31-encoded peptides in development and/or behavior is not yet known. Lund et al 2002 Fig4 Mount 15, Reinke et al 2004, IVb male soma enriched genes B0310.4 Aff_B0310.4 B0310.4; CE03877; WBGene00015140; WP:CE03877; XB132 repetitive proline-rich cell wall protein B0563.8 Aff_B0563.8 B0563.8; CE39467; WBGene00015265; WP:CE39467; XJ788 C08F1.3 Aff_C08F1.3 fbxb-13; C08F1.3; 2C79; CE08018; WBGene00015607; WP:CE08018 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins; its encoded protein also contains a Pfam-B45 motif of presently unknown function. C08F1.6 Aff_C08F1.6 C08F1.6; 2C78; CE08021; WBGene00015610; WP:CE08021 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 C28C12.7 Aff_C28C12.7 spp-10; C28C12.7; C28C12.7a.1; C28C12.7a.2; 4J243; CE29486; CE31323; NM_171399; NM_171400; WBGene00004995; WP:CE29486; WP:CE31323 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. 7TM chemoreceptor, spp family 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 C32B5.14 Aff_C32B5.14 C32B5.14; 2B254; CE08522; WBGene00016307; WP:CE08522 Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, mixed oogenesis soma, ViswanathanM et al 2005 S2 sir-2.1 regulated C32B5.16 Aff_C32B5.16 sdz-4; C32B5.16; 2B251; CE08524; WBGene00016309; WP:CE08524 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 sir-2.1 regulated C38C6.4 Aff_C38C6.4 sre-13; C38C6.4; 2O918; CE38042; NM_064641; WBGene00007997; WP:CE38042 7TM receptor, sre family C47D12.4 Aff_C47D12.4 C47D12.4; 2L969; CE20568; WBGene00008138; WP:CE20568 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins. Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, mixed oogenesis soma, ViswanathanM et al 2005 S2 daf-16 Resveratrol C51E3.2 Aff_C51E3.2 srsx-27; C51E3.2; 5K627; CE33986; NM_073208; WBGene00008248; WP:CE33986 opoid receptor C52E2.1 Aff_C52E2.I fbxb-95; C52E2.1; C52E2.I; 2C127; CE25826; WBGene00016880; WP:CE25826 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins; this gene's encoded protein also contains an FTH/DUF38 motif, which may also mediate protein-protein interaction. Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, mixed oogenesis soma F08D12.11 Aff_F08D12.11 fbxb-111; F08D12.11; 2D64; CE09244; WBGene00017254; WP:CE09244 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins; its encoded protein also contains a Pfam-B45 motif of presently unknown function. F14B6.3 Aff_F14B6.3 F14B6.3; 1M823; CE17665; WBGene00008784; WP:CE17665 Murphy et al 2003 Fig2 Class2 shorten lifespan, 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 F19F10.5 Aff_F19F10.5 F19F10.5; 5I36; CE09485; WBGene00017601; WP:CE09485 DNA-binding protein ViswanathanM et al 2005 S2 sir-2.1 regulated F23A7.1 Aff_F23A7.1 F23A7.1; CE09576; WBGene00009067; WP:CE09576; XQ831 F27E11.3 Aff_F27E11.3 cfz-2; F27E11.3; 5D920; CE39149; CE39150; CFZ2; NM_071563; NM_071564; WBGene00000478; WP:CE39149; WP:CE39150 cfz-2 encodes a member of the Frizzled family of membrane receptors. McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, mixed oogenesis soma, ViswanathanM et al 2005 S2 daf-16 Resveratrol F39F10.4 Aff_F39F10.4 F39F10.4; CE07206; WBGene00018204; WP:CE07206; XR516 Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, mixed oogenesis soma F40F4.1 Aff_F40F4.1 fbxb-71; F40F4.1; CE04531; WBGene00018236; WP:CE04531; XD883 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins; its encoded protein also contains a Pfam-B45 motif of presently unknown function. Murphy et al 2003 Fig2 Class2 shorten lifespan, Romagnolo et al 2002 Fig3b Unkown, Romagnolo et al 2002 Fig5 genes in let-60 timecour, ViswanathanM et al 2005 S2 sir-2.1 regulated F40H6.4 Aff_F40H6.4 CE-TBX-11; tbx-11; F40H6.4; 3H134; CE01281; NM_065916; WBGene00006547; WP:CE01281 tbx-11 encodes a T-box transcription factor that is orthologous to members of the Tbx2 subfamily of T-box transcription factors; by homology, TBX-11 is predicted to function in transcriptional regulation during cellular differentiation, potentially as both an activator and a repressor; however, as loss of tbx-11 function via large-scale RNAi screens does not result in any obvious abnormalities, the precise role of tbx-11 in C. elegans development and/or behavior is not yet known. Reinke et al 2004, list of genes in cluster order F42F12.4 Aff_F42F12.4 F42F12.4; F42F12.4.1; F42F12.4.2; CE16031; WBGene00009636; WP:CE16031; XM970 McCarroll et al 2004 SFig5 conserved w/ yeast, McCarroll et al 2004 SFig1-4 conserved w/ Drosoph, ViswanathanM et al 2005 S2 sir-2.1 regulated F45C12.11 Aff_F45C12.11 bath-32; sdz-18; F45C12.11; 2B994; CE10456; WBGene00018442; WP:CE10456 ViswanathanM et al 2005 S2 sir-2.1 regulated F45C12.13 Aff_F45C12.13 fbxb-48; F45C12.13; 2C6; CE10460; WBGene00018444; WP:CE10460 F45C12.6 Aff_F45C12.6 F45C12.6; 2C13; CE10446; WBGene00018437; WP:CE10446 ViswanathanM et al 2005 S2 sir-2.1 regulated, ViswanathanM et al 2005 S2 daf-16 Resveratrol F55A8.1 Aff_Y48A5B.B egl-18; elt-5; pvl-3; F55A8.1; F55A8.1.1; F55A8.1.2; F55A8.1.3; 4C681; CE28339; NM_067742; WBGene00001186; WP:CE28339 egl-18 encodes a member of the GATA-family of transcription factors that affects cell migration, cell fate specification; expressed in the head, in hypodermal seam cells, VC neurons, and vulval precursor cells. zinc finger protein Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, mixed oogenesis soma, Reinke et al 2004, list of genes in cluster E, ViswanathanM et al 2005 S2 sir-2.1 regulated F56H6.2 Aff_F56H6.2 F56H6.2; 1M871; CE28567; WBGene00010163; WP:CE28567 F58E1.11 Aff_F58E1.11 F58E1.11; 2B982; CE36171; WBGene00019042; WP:CE36171 Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, mixed oogenesis soma, Reinke et al 2004, GO categories, ViswanathanM et al 2005 S2 daf-16 Resveratrol F58E1.14 Aff_F58E1.14 fbxb-47; F58E1.14; 2B992; CE11398; WBGene00019045; WP:CE11398 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins. Reinke et al 2004, list of genes in cluster order, ViswanathanM et al 2005 S2 daf-16 Resveratrol F58E1.3 Aff_F58E1.3 fbxb-26; F58E1.3; 2B971; CE11376; WBGene00019035; WP:CE11376 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins. ViswanathanM et al 2005 S2 sir-2.1 regulated F58E10.2 Aff_F58E10.2 end-1; F58E10.2; 5O467; CE18784; NM_074074; WBGene00001310; WP:CE18784 end-1 encodes a GATA-like transcription factor sufficient to initiate endoderm differentiation and binds to the canonical target DNA sequence WGATAR with specificity similar to GATA-1 and D4 transcription factors; its expression bypasses requirement for maternal SKN-1 and the maternal Wnt signaling pathway in endoderm formation and it activates endoderm differentiation in isolated Xenopus ectoderm. GATA family of transcription factors Reinke et al 2004, fem1 enriched genes, Reinke et al 2004, mixed oogenesis soma, 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 F58E10.5 Aff_F58E10.5 end-3; F58E10.5; 5O495; CE18787; NM_074079; WBGene00001311; WP:CE18787 end-3 encodes a GATA zinc finger protein, paralogous to end-1, that helps specify mesoendodermal (as opposed to mesectodermal) lineages derived from the E blastomere. GATA family of transcription factors F58E10.7 Aff_F58E10.7 F58E10.7; 5O473; CE18789; WBGene00010262; WP:CE18789 Reinke et al 2004, IVb male soma enriched genes, Romagnolo et al 2002 Fig3b Unkown, Romagnolo et al 2002 Fig5 genes in let-60 timecour, ViswanathanM et al 2005 S2 sir-2.1 regulated, ViswanathanM et al 2005 S2 daf-16 Resveratrol, 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 K05F6.1 Aff_K05F6.1 fbxb-49; K05F6.1; 2B861; CE17159; WBGene00019412; WP:CE17159 ViswanathanM et al 2005 S2 daf-16 Resveratrol K05F6.9 Aff_K05F6.9 fbxb-46; K05F6.9; 2B858; CE17167; WBGene00019420; WP:CE17167 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins; its encoded protein also contains a Pfam-B45 motif of presently unknown function. ViswanathanM et al 2005 S2 daf-16 Resveratrol M01D1.9 Aff_M01D1.9 fbxb-40; M01D1.9; 2B340; CE12258; WBGene00019704; WP:CE12258 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins; its encoded protein also contains a Pfam-B45 motif of presently unknown function. M151.8 Aff_M151.6 fbxb-33; M151.8; CE38623; WBGene00044314; WP:CE38623 M163.3 Aff_M163.3 his-24; M163.3; CE12450; HH1; NM_078009; WBGene00001898; WP:CE12450; XP109 The his-24 gene encodes a histone H1 isoform (H1.1) that is essential for chromatin silencing and germline development. histone H1 Murphy et al 2003 Fig2 Class2 shorten lifespan, 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 R07C3.11 Aff_R07C3.11 R07C3.11; 2B196; CE12542; WBGene00019927; WP:CE12542 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 R07C3.9 Aff_R07C3.9 R07C3.9; 2B203; CE12538; WBGene00019925; WP:CE12538 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 sir-2.1 regulated R07H5.4 Aff_R07H5.4 sdz-27; R07H5.4; 4L953; CE12556; WBGene00011124; WP:CE12556 Reinke et al 2004, list of genes in cluster order, Reinke et al 2004, mixed sperm soma, Reinke et al 2004, herm soma enriched genes, Reinke et al 2004, fem3 enriched genes, ViswanathanM et al 2005 S2 sir-2.1 regulated, ViswanathanM et al 2005 S2 daf-16 Resveratrol, Wang et al 2003 S6 removed genes of contamination T01C8.5 Aff_T01C8.5 T01C8.5; CE07462; WBGene00020146; WP:CE07462; XR406 aminotransferase 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, 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 T05H10.3 Aff_T05H10.3 T05H10.3; 2I340; CE01640; WBGene00011508; WP:CE01640 T24B8.6 Aff_T24B8.6 hlh-3; T24B8.6; 2J377; CE03714; NM_063537; WBGene00001950; WP:CE03714 hlh-3 encodes a basic helix-loop-helix transcription factor homologous to Drosophila Achaete-scute; in vitro, HLH-3 can heterodimerize, and bind an E-box-containing probe, with HLH-2, the C. elegans E/daughterless ortholog with which it is coexpressed in the nuclei of embryonic neuronal precursors. helix-loop-helix protein T25G12.8 Aff_T25G12.8 T25G12.8; CE07545; WBGene00020814; WP:CE07545; XR852 Wang et al 2003 S4 TransientList, Wang et al 2003 S3 genes pass one-way ANOVA, Wang et al 2003 S4 genes pass two-wayANOVA P0 T26E3.5 Aff_T26E3.5 T26E3.5; 1N254; CE14192; WBGene00012038; WP:CE14192 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins. Reinke et al 2004, intrinsic, Reinke et al 2004, wt vs glp-4 enriched genes T27E4.1 Aff_T27E4.1 T27E4.1; 5J573; CE29357; WBGene00020861; WP:CE29357 Lund et al 2002 Fig1 aging-regulated genes, ViswanathanM et al 2005 S2 sir-2.1 regulated W05H7.4 Aff_W05H7.4 W05H7.4; CE33719; CE35046; CE35047; CE38431; CE38432; WBGene00021047; WP:CE33719; WP:CE35046; WP:CE35047; WP:CE38431; WP:CE38432; XC60 ViswanathanM et al 2005 S2 sir-2.1 regulated W10C8.2 Aff_W10C8.2 pop-1; sys-2; W10C8.2; 1D392; CE26031; NM_058652; WBGene00004077; WP:CE26031 pop-1 encodes an HMG box-containing protein that is the sole C. elegans member of the TCF/LEF family of transcription factors; in C. elegans, POP-1 functions as a component of the canonical and noncanonical Wnt signaling pathways that are required for cell migrations and binary cell fate decisions associated with asymmetric cell division, respectively; in yeast two-hybrid assays, the POP-1 N-terminal beta-catenin binding domain interacts with BAR-1/beta-catenin as well as with the more divergent beta-catenin, SYS-1; when coexpressed with SYS-1, POP-1 is able to activate transcription from a promoter with TCF binding sites; during development, maternally provided POP-1 is first detected in the nuclei of maturing oocytes and then in nearly all cells of the early embryo; in sister blastomeres in the early embryo, POP-1 is detected at lower levels in posterior blastomeres, such as E and P3, than in corresponding anterior blastomeres, MS and C; in later developmental stages, POP-1 is detected in a subset of tissues including hypodermal seam cells, gonadal precursors, and the developing vulva; in the vulva, POP-1 also exhibits an asymmetric staining pattern, with sister cells showing high or low levels of POP-1 depending upon their orientation along the anterior/posterior axis of the vulva. 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 E Y57G11C.8 Aff_Y57G11C.8 Y57G11C.8; 4P547; CE39974; WBGene00013306; WP:CE39974 Reinke et al 2004, herm sperm, Reinke et al 2004, wt vs glp-4 enriched genes, Reinke et al 2004, spermatogenesis enriched genes, Reinke et al 2004, fem3 enriched genes, ViswanathanM et al 2005 S2 sir-2.1 regulated Y57G7A.2 Aff_Y57G7A.2 Y57G7A.2; 2B587; CE19631; WBGene00021966; WP:CE19631 ViswanathanM et al 2005 S2 sir-2.1 regulated, ViswanathanM et al 2005 S2 daf-16 Resveratrol Y60A9.3 Aff_Y60A9.A Y60A9.3; Y60A9B.A; CE22669; WBGene00013370; WP:CE22669; XO997 ViswanathanM et al 2005 S2 sir-2.1 regulated Y61A9LA.3 Aff_Y61A9LA_71.B Y61A9LA.3; 5F63; CE27412; CE31122; CE36964; WBGene00022015; WP:CE27412; WP:CE31122; WP:CE36964 Reinke et al 2004, mixed sperm soma, Reinke et al 2004, fem3 enriched genes, ViswanathanM et al 2005 S2 sir-2.1 regulated, ViswanathanM et al 2005 S2 daf-16 Resveratrol Y71A12B.3 Aff_Y71A12B.M Y71A12B.3; 1O485; WBGene00013501 Y82E9BL.2 Aff_Y119D3_465.D Y82E9BL.2; 3C442; CE23418; WBGene00022319; WP:CE23418 Y82E9BL.5 Aff_Y119D3_465.F Y82E9BL.5; 3C436; CE27547; WBGene00022322; WP:CE27547 ZC204.9 Aff_ZC204.9 fbxb-20; ZC204.9; 2B938; CE15100; WBGene00022559; WP:CE15100 This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein interactions either with homologs of yeast Skp-1p or with other proteins; its encoded protein also contains a Pfam-B45 motif of presently unknown function. ViswanathanM et al 2005 S2 sir-2.1 regulated ZK637.4 Aff_ZK637.4 ZK637.4; 3J983; CE00435; WBGene00014024; WP:CE00435