Fox et al 2005 S14/T2 Transcription factor Subuni, 154 genes

Gene list file name:Fox2005_S14-T2_unc-4_neuron-transcript_TF
Type of gene identifier:Cosmid name
Description:Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

B0041.7 B0041.7 P W All gene names: slr-8; xnp-1; B0041.7; 1F234; ATRX_CAEEL; CE17314; NM_059022; WBGene00006961; WP:CE17314 WormBase description: xnp-1 encodes an ATP-dependent DNA helicase of the SNF2 family that is orthologous to human XNP/ATR-X, which is associated with a number of X-linked mental retardation syndromes; in C. elegans, xnp-1 activity is required at high temperatures for embryogenesis, somatic gonad development, fertility, and vulval morphogenesis; in addition, animals doubly mutant for xnp-1 and lin-35/Rb, hpl-2/HP1, or nucleosome remodelling and histone deacetylase (NuRD) complex members such as lin-53 and let-418, display larval arrest with growth cessation but continued cell proliferation; xnp-1 is also required, with lin-35/Rb and hpl-2/HP1, for proper regulation of transgene expression; xnp-1 mRNA, detectable in embryos and the germline by in situ hybridization, is expressed at highest levels in embryos with decreasing levels seen in successive larval stages; xnp-1 transcriptional reporter fusions exhibit strong expression beginning at mid-embryogenesis but fading by embryonic morphogenesis; at hatching, expression is observed in all dividing cells including the P lineage, and at later larval stages expression is observed in the vulval precursor cells. WormBase CDS description: helicase
B0336.13 B0336.13 P W All gene names: B0336.13; 3G783; CE26429; WBGene00015150; WP:CE26429; YMYD_CAEEL
B0414.2 B0414.2 P W All gene names: mab-2; rnt-1; run-1; B0414.2; 1G363; CE24772; NM_059278; WBGene00004393; WP:CE24772; run WormBase description: rnt-1 encodes a transcription factor that is the sole C. elegans member of the RUNX family of transcriptional regulators; rnt-1 activity is required for several developmental processes, including regulation of hypodermal seam cell proliferation and proper development of the male tail; RNT-1 can physically interact with SMA-4 and regulates, either directly or indirectly, expression of tlp-1 and cki-1, which encode a C2H2 zinc finger and CDK inhibitor, respectively; RNT-1::GFP reporter fusions are reportedly expressed in the nuclei of hypodermal seam cells, intestinal cells, body wall muscles, and, in males, cells derived from the V5, V6 and T lineages that give rise to the sensory rays.
B0432.2 B0432.2 P W All gene names: B0432.2; 2A581; CE07740; WBGene00015184; WP:CE07740 WormBase description: djr-1.1 encodes an ortholog of DJ-1 (OMIM:602533, mutated in early-onset Parkinson disease); DJR-1.1 is required for resistance to rotenone, a mitochondrial complex I inhibitors that mimics Parkinson disease (PD); djr-1.1(RNAi) animals are partly rescued from PD-like sensitivity by D-beta-hydroxybutyrate or tauroursodeoxycholic acid, and fully rescued by both; by orthology with DJ-1, DJR-1.1 may promote stability of the transcription factors SKN-1 or SKNR-1 (homologs of mammalian NFE2L2).
C06C6.4 C06C6.4 P W All gene names: nhr-63; C06C6.4; 5Q483; CE28202; NM_171557; WBGene00003653; WP:CE28202 WormBase description: Zinc finger, C4 type (two domains)
C08B11.3 C08B11.3 P W All gene names: C08B11.3; 2I314; CE01473; WBGene00007433; WP:CE01473; YP83_CAEEL WormBase description: Zinc finger, C2H2 type
C08C3.3 C08C3.3 P W All gene names: lin-21; mab-5; C08C3.3; 3I868; CE25765; MAB5_CAEEL; NM_066294; WBGene00003102; WP:CE25765 WormBase description: mab-5 encodes a homeodomain transcription factor related to the Antennapedia, Ultrabithorax, and abdominal-A family of homeodomain proteins; during postembryonic development, mab-5 is required cell autonomously for specification of posterior cell fates, including hypodermal and neuronal fates, programmed cell deaths, cell proliferation and migration, and fate specification of the male-specific copulatory muscles and sensory rays; in addition, ectopic expression of mab-5 is sufficient to alter cell fates, such as direction of migration or sensory ray identity; in regions of the body where mab-5 expression overlaps with that of lin-39, another C. elegans HOM-C gene, the two genes appear to either compensate for one another's activity or act combinatorially to promote cell fates distinct from those where either gene is expressed alone; a mab-5:lacZ reporter fusion is expressed in cells in the posterior body region from the mid-gastrulation stage of embryogenesis through larval and adult stages; further, antibody staining reveals that MAB-5 expression in the V5 lineage is dynamic, switching on and off several times, while expression in V6 is continuous throughout most of the L1-L3 larval stages; early MAB-5 expression is V6 is dependent upon wild-type activity of pal-1, which encodes the C. elegans Caudal ortholog.
C08F8.8 C08F8.8 P W All gene names: nhr-67; C08F8.8; 4L939; CE18491; NHR67_CAEEL; NM_069693; WBGene00003657; WP:CE18491 WormBase description: nuclear hormone receptor
C10G8.6 C10G8.6 P W All gene names: ceh-34; C10G8.6; 5F794; CE20496; HM34_CAEEL; NM_072018; WBGene00000455; WP:CE20496 WormBase description: ceh-34 encodes a homeodomain protein, homologous to human SIX2 (OMIM:604994), that is expressed very weakly in the pharynxes of late embryos and early larvae; it has no known function. WormBase CDS description: homeobox protein
C11G6.4 C11G6.4 P W All gene names: nhr-28; C11G6.4; C11G6.4a.1; C11G6.4a.2; C11G6.4b.1; C11G6.4b.2; C11G6.4b.3; CE27061; CE37954; NHR28_CAEEL; WBGene00003624; WP:CE27061; WP:CE37954; XQ973 WormBase description: nuclear hormone receptor, nhr-28
C15C8.2 C15C8.2 P W All gene names: cky-1; C15C8.2; 5N221; CE30427; NM_073783; Q18018_CAEEL; WBGene00000521; WP:CE30427 WormBase description: cky-1 encodes a member of the basic-helix-loop-helix-PAS (bHLH-PAS) protein family; it is likely that CKY-1 together with AHA-1, another bHLH-PAS protein, has a role in pharyngeal function; CKY-1 is expressed in most non-neuronal pharyngeal cells. WormBase CDS description: Human ARNT-interacting protein like
C15H11.8 C15H11.8 P W All gene names: C15H11.8; 5O904; CE08185; WBGene00007616; WP:CE08185 WormBase description: DNA-directed RNA polymerase I like
C16A3.7 C16A3.7 P W All gene names: tag-182; C16A3.7; 3H467; CE04007; WBGene00007048; WBGene00015812; WP:CE04007 WormBase description: human NFX1; D. melanogaster shuttle craft protein
C16C10.4 C16C10.4 P W All gene names: C16C10.4; 3F261; CE01495; SAP18_CAEEL; WBGene00007625; WP:CE01495
C18A3.1 C18A3.1 P W All gene names: C18A3.1; 2G11; CE01793; WBGene00015939; WP:CE01793
C24G6.4 C24G6.4 P W All gene names: Csr-1; nhr-279; nhr-47; C24G6.4; C24G6.4.1; C24G6.4.2; 5F989; CE27727; NHR47_CAEEL; NM_072054; WBGene00003637; WP:CE27727 WormBase description: nhr-47 is predicted to encode a nuclear hormone receptor (NHR); gene expression of nhr-47 appears to be induced upon exposure of worm cultures to estradiol. WormBase CDS description: zinc finger protein
C25A1.2 C25A1.2 P W All gene names: fkh-10; C25A1.2; 1K740; CE08367; NM_060275; WBGene00001442; WP:CE08367 WormBase description: fkh-10 encodes one of 15 forkhead transcriptional regulators encoded by the C. elegans genome; by homology, FKH-10 is predicted to function as a transcription factor that regulates gene expression during development; however, as loss of fkh-10 activity via RNA-mediated interference (RNAi) does not result in any obvious abnormalities, the precise role of FKH-10 in C. elegans development and/or behavior is not yet known; nevertheless, reporter gene studies indicate that throughout larval and adult stages, fkh-10 expression is detected almost exclusively in six pairs of neuronal nuclei near the terminal bulb of the pharynx, suggesting that FKH-10 may have a specific function in neuronal differentiation. WormBase CDS description: nuclear factor 5 like
C27A12.5 C27A12.5 P W All gene names: ceh-2; C27A12.5; C27A12.5.1; C27A12.5.2; 1G622; CE20530; NM_059345; WBGene00000429; WP:CE20530 WormBase description: ceh-2 encodes a homeodomain protein homologous to Drosophila empty spiracles (EMS) and the vertebrate EMX1 and EMX2 proteins (OMIM:600034, 600035); although the exact biological role of CEH-2 in C. elegans development and/or behavior is not yet known, expression in pharyngeal neurons and muscle, as well as vulval cells (vulB1, vulB2, and vulC) at late stages of development suggests that CEH-2 may play a role in terminal differentiation events in diverse cell types. WormBase CDS description: homeobox protein
C27C12.6 C27C12.6 P W All gene names: dmd-4; C27C12.6; CE23560; WBGene00007776; WP:CE23560; XP476 WormBase description: doublesex protein like
C29G2.5 C29G2.5 P W All gene names: srt-58; C29G2.5; 5D53; CE08466; NM_071304; WBGene00016233; WP:CE08466 WormBase description: 7TM chemoreceptor, srt family
C33D3.1 C33D3.1 P W All gene names: elt-2; C33D3.1; CE31430; ELT2_CAEEL; GATA; NM_077354; WBGene00001250; WP:CE31430; XL101 WormBase description: elt-2 encodes a GATA-type transcription factor most similar to the vertebrate GATA4-6 transcription factors required for cardiac and endoderm development (OMIM:601656, 600576); in C. elegans, ELT-2 is required redundantly with ELT-7 for initiating and maintaining terminal differentiation of the intestine; ELT-2 is expressed solely in the intestine, beginning embryonically at the 2E-cell stage and continuing in all intestinal cells throughout the life of the animal; in the regulatory hierarchy controlling endoderm development, ELT-2 lies downstream of the maternal regulators SKN-1 and POP-1 and the embryonic GATA factors MED-1/-2, and END-1/-3; in turn, ELT-2, along with ELT-7, likely regulates transcription of a number of intestine-specific terminal differentiation genes such as ges-1, ifb-2, pha-4, and the stress-induced mtl-2; ELT-2 also positively autoregulates, presumably to ensure maintenance of intestinal differentiation WormBase CDS description: zinc finger protein (GATA type)
C33G8.8 C33G8.8 P W All gene names: nhr-139; C33G8.8; 5H466; CE06917; WBGene00016365; WP:CE06917 WormBase description: zinc finger protein
C36A4.8 C36A4.8 P W All gene names: brc-1; C36A4.8; 3E944; CE31438; NM_065379; WBGene00000264; WP:CE31438 WormBase description: The brc-1 gene encodes a homolog of human BRCA1 (mutated in early onset breast and ovarian cancer; OMIM:113705); BRC-1 forms a heterodimer with BRD-1, which constitutes an E3 ubiquitin ligase; after irradiation, the DNA checkpoint proteins ATL-1 and MRE-11 are required for BRC-1/BRD-1 heterodimers to associate with the E2 ubiqutin-conjugating enzyme LET-70/Ubc5 and with RAD-51, and to ubiquitylate damaged chromatin; brc-1(RNAi) animals have excess chromosomal nondisjunction, abnormally high levels of CEP-1-dependent germ cell apoptosis (both with and without gamma-irradiation) and hypersensitivity to gamma-irradiation (e.g., abnormal sterility after irradiation); BRC-1 and BRD-1 bind one another, probably through their N-terminal RING domains, in yeast two-hybrid experiments and pull-down assays; BRC-1/BRD-1 heterodimers may interact with RAD-51 and other proteins via mutual binding to UBC-9; brc-1 is genetically dispensable for the induction of nuclear ATL-1 foci by gamma-irradiation or hydroxyurea. WormBase CDS description: Zinc finger, C3HC4 type (RING finger)
C36E8.1 C36E8.1 P W All gene names: C36E8.1; C36E8.1.1; C36E8.1.2; 3F90; CE00909; WBGene00007980; WP:CE00909; YPJ1_CAEEL
C46A5.9 C46A5.9 P W All gene names: hcf-1; C46A5.9; 4I536; CE26914; NM_068878; WBGene00001827; WP:CE26914
C56C10.8 C56C10.8 P W All gene names: icd-1; C56C10.8; C56C10.8.1; C56C10.8.2; 2G878; BTF3_CAEEL; CE02573; NM_062935; WBGene00002045; WP:CE02573 WormBase description: Transcription factor BTF3 (human)
F09C6.8 F09C6.8 P W All gene names: nhr-262; F09C6.8; 5R385; CE15767; WBGene00008619; WP:CE15767 WormBase description: Zinc finger, C4 type (two domains)
F09C6.9 F09C6.9 P W All gene names: nhr-116; F09C6.9; 5R395; CE37501; NM_074872; WBGene00003706; WP:CE37501 WormBase description: nuclear hormone receptor
F10G2.9 F10G2.9 P W All gene names: nhr-263; F10G2.9; 5H820; CE35274; WBGene00017367; WP:CE35274 WormBase description: zinc finger protein
F10G7.2 F10G7.2 P W All gene names: tsn-1; F10G7.2; F10G7.2.1; F10G7.2.2; 2E999; CE02626; NM_062438; WBGene00006626; WP:CE02626 WormBase description: human 100 kDa activator protein
F16B4.9 F16B4.9 P W All gene names: nhr-178; F16B4.9; 5C82; CE17680; WBGene00017510; WP:CE17680 WormBase description: nuclear hormone receptor
F16H11.4 F16H11.4 P W All gene names: ceh-1; F16H11.4; CE04399; HM01_CAEEL; NM_076395; WBGene00000428; WP:CE04399; XF268 WormBase description: ceh-1 encodes a protein that contains a homeobox domain.
F16H11.5 F16H11.5 P W All gene names: nhr-45; F16H11.5; CE33052; NM_076396; Q19496_CAEEL; WBGene00003635; WP:CE33052; XF276 WormBase description: zinc finger DNA-binding protein
F19B2.5 F19B2.5 P W All gene names: F19B2.5; F19B2.C; 5U632; CE20697; WBGene00008944; WP:CE20697
F20D1.4 F20D1.4 P W All gene names: F20D1.4; CE09497; WBGene00008976; WP:CE09497; XP602 WormBase description: transcriptional activator protein PUR-alpha like
F21H11.3 F21H11.3 P W All gene names: sdf-13; tbx-2; F21H11.3; F21H11.3.1; F21H11.3.2; 3G222; CE01245; NM_065687; TBX2_CAEEL; WBGene00006543; WP:CE01245 WormBase description: tbx-2 encodes one of 21 C. elegans T-box transcription factors; during development, tbx-2 activity is required for normal adaptation, but not chemotaxis, to attractive odorants sensed by the AWC amphid neurons; tbx-2 is also required redundantly with unc-3 and unc-31 for negative regulation of dauer formation, and large-scale RNAi screens reveal an essential role for tbx-2 in early larval development, normal rates of postembryonic growth, and locomotory behavior; antibodies to TBX-2 detect expression in the cytoplasm of amphid and pharyngeal neurons in larvae and adults, suggesting that TBX-2 function may be controlled, in part, by regulation of its subcellular localization; in addition, in situ hybridization studies indicate that tbx-2 mRNA is expressed during mid-embryogenesis; tbx-2 expression in the AWC amphid neurons is sufficient to rescue the olfactory adaptation defects seen in tbx-2 mutant animals.
F26C11.2 F26C11.2 P W All gene names: ceh-4; unc-4; F26C11.2; 2K188; CE01560; NM_063737; UNC4_CAEEL; WBGene00006744; WP:CE01560 WormBase description: The unc-4 gene encodes a paired-class homeodomain protein with homologs in Drosophila and vertebrates; UNC-4 is required for establishing the identity of the A class motor neurons DA and VA, and is thus required for movement, axon guidance, and synapse formation; UNC-4 is negatively regulated by VAB-7, and UNC-4 activity requires UNC-37; unc-4 is expressed in the A-type motor neurons, DA and VA, the six VC motor neurons that innervate the vulval muscles, and the three SAB motor neurons; unc-4 is also expressed in the pharyngeal I5 motor neuron and the AVF neurons in the retrovesicular ganglion. WormBase CDS description: homeobox protein (otd subfamily)
F28B12.2 F28B12.2 P W All gene names: egl-44; F28B12.2; F28B12.2e.1; F28B12.2e.2; F28B12.2e.3; F28B12.2f.1; F28B12.2f.2; 2G229; CE27143; CE33378; CE33379; CE33380; CE33381; CE33382; EGL44_CAEEL; NM_062785; NM_171007; NM_171850; NM_182104; NM_182105; NM_182106; WBGene00001208; WP:CE27143; WP:CE33378; WP:CE33379; WP:CE33380; WP:CE33381; WP:CE33382 WormBase description: The egl-44 gene encodes a putative transcription regulatory protein of 471 amino acids similar to vertebrate transcription enhancer factor (TEF) proteins.
F31E3.1 F31E3.1 P W All gene names: ceh-20; F31E3.1; 3I71; CE01241; HM20_CAEEL; WBGene00000443; WP:CE01241 WormBase description: ceh-20 encodes the C. elegans ortholog of the homeodomain co-factor Extradenticle (Exd/Pbx); together with ceh-40 and unc-62, ceh-20 activity is required for embryonic viability; ceh-20 is also required as a cofactor for LIN-39- and MAB-5- dependent postembryonic mesoderm patterning; in addition, ceh-20 is required for regulating post-embryonic migrations of the Q neuroblast descendants and for regulating vulval development; a CEH-20::GFP fusion protein is expressed in embryos and postembryonically in many cell types including the Q, P, and V cells and their descendants; CEH-20 localizes to the nucleus.
F32H2.2 F32H2.2 P W All gene names: mdt-31; F32H2.2; 1J543; CE09877; MED31_CAEEL; NM_060012; WBGene00007026; WP:CE09877 WormBase description: Yeast SOH1 protein like
F35H10.6 F35H10.6 P W All gene names: F35H10.6; 4J65; CE38515; WBGene00018071; WP:CE38515
F38A6.1 F38A6.1 P W All gene names: Ce-fkh-1; fkh-1; pha-4; F38A6.1; 5V229; CE15998; NM_075605; Q17381_CAEEL; WBGene00004013; WP:CE15998 WormBase description: Fork head domain, eukaryotic transcription factors
F38H12.3 F38H12.3 P W All gene names: nhr-181; F38H12.3; 5E571; CE17809; WBGene00018189; WP:CE17809 WormBase description: nuclear hormone receptor
F39H2.3 F39H2.3 P W All gene names: F39H2.3; 1J241; CE37516; WBGene00009563; WP:CE37516 WormBase description: S.pombe hypothetical protein C21E11.07 like
F40G9.11 F40G9.11 P W All gene names: mxl-2; F40G9.11; 3A804; CE19858; NM_064772; WBGene00003510; WP:CE19858
F41B5.10 F41B5.10 P W All gene names: nhr-183; F41B5.10; 5C738; CE17819; WBGene00018266; WP:CE17819 WormBase description: nuclear hormone receptor
F41B5.9 F41B5.9 P W All gene names: nhr-182; F41B5.9; 5C734; CE10232; WBGene00018265; WP:CE10232 WormBase description: nuclear hormone receptor
F43G9.11 F43G9.11 P W All gene names: ces-1; F43G9.11; 1J211; CE17821; NM_059937; Q93721_CAEEL; WBGene00000468; WP:CE17821 WormBase description: ces-1 encodes a C2H2-type zinc finger transcription factor that is a member of the Snail family of proteins that includes Drosophila Scratch, Snail, and Slug, and human SNAIL and SLUG; although the normal function of CES-1 is not fully understood, gain-of-function mutations indicate that CES-1 can function as a transcriptional repressor that blocks programmed cell death in specific neurons by inhibiting expression of the cell-death activator EGL-1; in regulating EGL-1 expression, CES-1 appears to antagonize the transcriptional activity of the bHLH proteins, HLH-2 and HLH-3; despite its cell-type specific role in apoptosis, CES-1 expression is reportedly detected in many embryonic nuclei from the 100-cell stage of embryogenesis through the beginning of morphogenesis, with some CES-1 expression remaining at later embryonic stages; genetic studies indicate that CES-1 is negatively regulated by the bZIP transcription factor CES-2, which can bind CES-1 upstream sequences in vitro and thus may directly regulate CES-1 transcription in vivo WormBase CDS description: Zinc finger, C2H2 type (5 domains)
F43G9.12 F43G9.12 P W All gene names: F43G9.12; 1J219; CE17822; WBGene00009672; WP:CE17822 WormBase description: Human GC-rich sequence DNA-binding factor (GCF) like
F44C4.2 F44C4.2 P W All gene names: nhr-37; F44C4.2; 5H103; CE07250; WBGene00018412; WP:CE07250 WormBase description: zinc finger-containing protein
F44C8.2 F44C8.2 P W All gene names: nhr-134; F44C8.2; 5C711; CE17823; NH134_CAEEL; NM_071209; WBGene00003724; WP:CE17823 WormBase description: nuclear hormone receptor
F44C8.3 F44C8.3 P W All gene names: nhr-18; F44C8.3; 5C707; CE30796; NHR18_CAEEL; NM_071207; WBGene00003617; WP:CE30796 WormBase description: The nhr-18 gene encodes a member of the superfamily of nuclear receptors, which is one of the most abundant class of transcriptional regulators; nuclear receptors have a well conserved DNA binding domain and a less conserved C-terminal ligand binding domain; the human homolog of nhr-18, CYP21, when mutated leads to congenital adrenal hyperplasia (OMIM:201910). WormBase CDS description: nuclear hormone receptor
F44C8.6 F44C8.6 P W All gene names: nhr-56; F44C8.6; 5C699; CE27385; CE38959; NM_071204; WBGene00003646; WP:CE27385; WP:CE38959 WormBase description: nhr-56 encodes a member of the superfamily of nuclear receptors, which is one of the most abundant class of transcriptional regulators; nuclear receptors have a well conserved DNA binding domain and a less conserved C-terminal ligand binding domain.
F44E2.6 F44E2.6 P W All gene names: F44E2.6; 3J934; CE00184; WBGene00018419; WP:CE00184; YL56_CAEEL WormBase description: Transcription regulation
F44E7.8 F44E7.8 P W All gene names: nhr-142; F44E7.8; 5G266; CE35972; Q8MXK0_CAEEL; WBGene00018430; WP:CE35972 WormBase description: nuclear hormone receptor
F45E4.2 F45E4.2 P W All gene names: plp-1; F45E4.2; F45E4.2.1; F45E4.2.2; 4I399; CE10494; NM_068840; WBGene00004046; WP:CE10494 WormBase description: plp-1 encodes a protein containing three PUR repeats that are predicted to bind DNA/RNA and has similarity to the mammalian transcription factor pur alpha, and is required for embryonic development, development of the pharynx, and affects formation of the intestine; interacts with an Lef-1 site within the end-1 promoter and binding is regulated by phosphorylation
F45E6.2 F45E6.2 P W All gene names: atf-6; F45E6.2; CE17828; NM_077693; Q20435_CAEEL; WBGene00000222; WP:CE17828; XN103 WormBase description: atf-6 is an ortholog of mammalian ATF6alpha, a proximal sensor required for the unfolded protein response (UPR) in the endoplasmic reticulum (ER); ATF6alpha is a transmembrane protein, with a bZIP transcription factor domain in its cytosolic amino terminus that is released and activated by proteolytic cleavage upon ER stress; either ire-1 or xbp-1 deletions are synthetically lethal with atf-6 or pek-1 deletions, producing arrest in L2 larvae; RNAi of Y56A3A.2 (a S2P protease homolog) is synthetically lethal with ire-1(RNAi), consistent with the hypothesis that Y56A3A.2 cleaves ATF-6; atf-6 regulates few genes that are transcriptionally induced by UPR, but regulates roughly one-quarter of genes that require UPR constitutively; pdr-1 transcripts are strongly upregulated in a atf-6(ok551) mutant background, but atf-6(ok551);pdr-1(lg103) double mutants have a grossly normal phenotype ; atf-6 is dispensable for proper localization of GLR-1 glutamate receptors. WormBase CDS description: YIB9 like
F46F3.1 F46F3.1 P W All gene names: ceh-27; F46F3.1; 5M140; CE36695; NM_073551; WBGene00000449; WP:CE36695 WormBase description: ceh-27 encodes a homeodomain protein of the NK-2 class that contains Drosophila scarecrow and human NKX-2 (OMIM:606727); CEH-27 activity is essential for embryogenesis and appears to be required for maintaining hypodermal integrity during movement as embryos lacking CEH-27 burst at a breach in the ventral hypodermis upon commencement of muscle contractions; CEH-27 expression is first detected in the ~100-cell embryo in what appear to be MS-derived cells while in later embryos expression is seen in a number of cells in the anterior head region. WormBase CDS description: homeobox protein (NK-2 subfamily)
F48G7.11 F48G7.11 P W All gene names: nhr-190; F48G7.11; 5B120; CE35318; WBGene00018622; WP:CE35318 WormBase description: nuclear hormone receptor
F49E10.5 F49E10.5 P W All gene names: F49E10.5; CE29966; WBGene00018642; WP:CE29966; XG491 WormBase description: tag-45 encodes a D-isomer specific 2-hydroxyacid dehydrogenase. WormBase CDS description: dehydrogenase
F49E12.6 F49E12.6 P W All gene names: F49E12.6; 2I705; CE37018; WBGene00009899; WP:CE37018 WormBase description: The F49E12.6 gene encodes a protein with two E2F domains that may be involved in apoptosis. WormBase CDS description: RBB3 like protein
F52C12.5 F52C12.5 P W All gene names: elt-6; F52C12.5; F52C12.5.1; F52C12.5.2; 4C685; CE31536; NM_067743; WBGene00001253; WP:CE31536
F58E6.10 F58E6.10 P W All gene names: unc-42; F58E6.10; 5K244; CE39164; NM_073118; Q20455_CAEEL; WBGene00006778; WP:CE39164 WormBase description: unc-42 encodes a paired-like homeodomain protein of the Q50 class; UNC-42 is required to specify the fate of ASH sensory neurons, AVA, AVD, and AVE interneurons, and a subset of motor neurons; unc-42 mutants fail to express cell-surface receptors required for differentiated neuronal function (sra-6, srb-6, glr-1, glr-5, and glr-6); UNC-42 is also required for AVKR and HSNL growth cones to follow the PVPR and PVQL pioneer axons, for axonal outgrowth in the backward command interneurons AVA, AVD, and AVE, and for inhibition of ectopic FMRFamide-positive and GABAergic axons; unc-42 mutants are defective in mechanosensation, backward motion, and regulation of egg-laying. WormBase CDS description: Homeobox domain
H01A20.1 H01A20.1 P W All gene names: nhr-3; H01A20.1; CE18798; NHR3_CAEEL; NM_078022; WBGene00003602; WP:CE18798; XP179 WormBase description: nhr-3 encodes a member of the superfamily of nuclear receptors which is one of the most abundant class of transcriptional regulators; nuclear receptors have a well conserved DNA binding domain and a less conserved C-terminal ligand binding domain; nhr-3 has been identified and characterised as a gene affected by ethanol exposure in a microarray analysis of all C. elegans ORFs. WormBase CDS description: Zinc finger, C4 type (two domains)
H21P03.1 H21P03.1 P W All gene names: mbf-1; H21P03.1; 4M244; CE18819; NM_069765; WBGene00003148; WP:CE18819 WormBase description: Helix-turn-helix
K02B12.1 K02B12.1 P W All gene names: ceh-6; K02B12.1; 1J76; CE28045; HM06_CAEEL; NM_059903; WBGene00000431; WP:CE28045 WormBase description: ceh-6 encodes a POU family homeodomain protein, homologous to human POU3F4 (OMIM:304400, mutated in conductive deafness 3) that affects embryonic viability, locomotion, and molting, and that regulates ectodermal and excretory function; CEH-6 is expressed dynamically during development and expression includes neurons, the excretory cell, and ectodermal cells. WormBase CDS description: Homeobox domain, Pou domain - N-terminal to homeobox domain
K02B9.4 K02B9.4 P W All gene names: elt-3; K02B9.4; CE23844; NM_077920; WBGene00001251; WP:CE23844; XO559 WormBase description: The elt-3 gene encodes a GATA transcription factor expressed in the embryonic hypodermis; specifically, it is expressed in expressed in all of the major hypodermal cells except the lateral seam cells. WormBase CDS description: GATA-binding transcription factor like
K07C11.1 K07C11.1 P W All gene names: pax-1; K07C11.1; 5I707; CE07344; NM_072719; WBGene00003937; WP:CE07344 WormBase description: DNA-binding transcription factor
K08F8.2 K08F8.2 P W All gene names: atf-2; K08F8.2; 2J43; CE03468; NM_063460; Q21361_CAEEL; WBGene00000220; WP:CE03468 WormBase description: transcription factor
K11G9.4 K11G9.4 P W All gene names: egl-46; K11G9.4; 5H160; CE07377; NM_072293; WBGene00001210; WP:CE07377 WormBase description: egl-46 encodes a predicted transcription factor and conserved member of a TFIIA-like zinc finger protein family that affects coordinated locomotion, morphology and process formation of the touch cells, male mating efficiency, HSN cell migration, differentiation, and axonal outgrowth, serotonin production and also affects terminal divisions of the Q neuroblasts; acts to inhibit touch cell fate in FLP cells together with egl-44 and is expressed dynamically in neurons, specifically in touch cells, FLP, and HSN neurons. WormBase CDS description: zinc finger protein
R03E9.1 R03E9.1 P W All gene names: mdl-1; R03E9.1; CE04784; NM_076735; WBGene00003163; WP:CE04784; XH361 WormBase description: human Max-interacting bHLH-Zip protein
R04B5.4 R04B5.4 P W All gene names: nhr-12; R04B5.4; 5K564; CE06214; NHR12_CAEEL; NM_073188; WBGene00003611; WP:CE06214 WormBase description: Zinc finger, C4 type (two domains)
R05D11.6 R05D11.6 P W All gene names: R05D11.6; 1J173; CE32473; WBGene00011034; WP:CE32473
R08B4.2 R08B4.2 P W All gene names: alr-1; sns-10; R08B4.2; CE03536; WBGene00011138; WBGene00044330; WP:CE03536; XL742 WormBase description: homeobox protein (otd subfamily)
R11E3.5 R11E3.5 P W All gene names: nhr-104; R11E3.5; 4F550; CE31719; CE31720; CE37269; NM_171326; NM_171327; WBGene00003694; WP:CE31719; WP:CE31720; WP:CE37269 WormBase description: nhr-104 encodes a member of the superfamily of nuclear receptors, which is one of the most abundant class of transcriptional regulators; nuclear receptors have a well conserved DNA binding domain and a less conserved C-terminal ligand binding domain.
R11H6.5 R11H6.5 P W All gene names: R11H6.5; 5P92; CE12778; WBGene00011253; WP:CE12778 WormBase description: Human NF45 protein like
R13.1 R13.1 P W All gene names: R13.1; 4L589; WBGene00011256
T05A12.4 T05A12.4 P W All gene names: T05A12.4; 4H661; CE37666; CE37667; WBGene00020235; WP:CE37666; WP:CE37667 WormBase description: helicase
T06C12.13 T06C12.13 P W All gene names: nhr-213; T06C12.13; 5Q374; CE16363; NH213_CAEEL; WBGene00011520; WP:CE16363 WormBase description: Zinc finger, C4 type (two domains)
T06C12.6 T06C12.6 P W All gene names: nhr-102; T06C12.6; 5Q354; CE16356; NM_074566; WBGene00003692; WP:CE16356 WormBase description: Zinc finger, C4 type (two domains)
T06C12.7 T06C12.7 P W All gene names: nhr-84; T06C12.7; 5Q356; CE16357; NM_074567; WBGene00003674; WP:CE16357 WormBase description: Zinc finger, C4 type (two domains)
T08A9.1 T08A9.1 P W All gene names: T08A9.1; CE04916; WBGene00020334; WP:CE04916; XH957 WormBase description: T08A9.1 is orthologous to the human gene LIKELY ORTHOLOG OF MOUSE COILED COIL FORMING PROTEIN 1 (RB1CC1; OMIM:606837), which when mutated leads to disease. WormBase CDS description: keratin
T08H4.3 T08H4.3 P W All gene names: ast-1; T08H4.3; 2E418; CE19576; WBGene00020368; WP:CE19576 WormBase description: ast-1 encodes a novel ETS-box transcription factor; AST-1 is required for the proper navigation of some interneuron axons to their targets, for differentiation of the ventral cord pioneer neuron AVG, and for pharyngeal morphogenesis; AST-1 is transiently expressed in many head neurons late in their differentiation and axon outgrowth, and in a few pharyngeal cells; AST-1 is at first nuclear, but then relocates to spots in cell bodies and even neuronal processes; hypomorphic ast-1 mutants have axons extending laterally, and crossing over from the right axon tract to the left axon bundle; null ast-1(hd92) mutants are inviable, failing to attach a working pharynx to their cuticle during development and then starving as L1 larvae; behaviorally, hypomorphic ast-1 animals are at least superficially normal, indicating that the ventral nerve cord can tolerate at least some miswiring; AST-1 regulates odr-2 expression, while ast-1 expression is itself regulated by lin-11. WormBase CDS description: ETS protein
T09A5.6 T09A5.6 P W All gene names: mdt-10; T09A5.6; 2I144; CE01087; MED10_CAEEL; NM_063249; WBGene00007014; WP:CE01087
T12D8.1 T12D8.1 P W All gene names: tag-350; T12D8.1; 3O745; CE16398; WBGene00011729; WP:CE16398 WormBase description: PHD-finger. (2 domains), SET domain
T12F5.4 T12F5.4 P W All gene names: lin-59; T12F5.4; 1E282; CE13601; LIN59_CAEEL; NM_058805; WBGene00003040; WP:CE13601
T13F2.2 T13F2.2 P W All gene names: T13F2.2; T13F2.2.1; T13F2.2.2; 4K562; CE13621; TCP4_CAEEL; WBGene00011743; WP:CE13621 WormBase description: single-stranded DNA binding protein P9
T19B10.11 T19B10.11 P W All gene names: mxl-1; T19B10.11; 5L725; CE16417; NM_073455; WBGene00003509; WP:CE16417 WormBase description: Helix-loop-helix DNA-binding domain
T19E7.2 T19E7.2 P W All gene names: skn-1; T19E7.2; T19E7.2c.1; T19E7.2c.2; T19E7.2c.3; T19E7.2c.4; T19E7.2c.5; T19E7.2c.6; 4G416; CE27591; CE31238; CE31239; NM_171345; NM_171346; NM_171347; SKN1_CAEEL; WBGene00004804; WP:CE27591; WP:CE31238; WP:CE31239 WormBase description: skn-1 encodes a transcription factor with similarity to the basic region of bZip transcription factors; during early embryogenesis, maternally provided SKN-1 is required for specification of the EMS blastomere, a mesendodermal precursor that gives rise to pharyngeal, muscle, and intestinal cells; later, during postembryonic development, SKN-1 functions in the p38 MAPK-mediated oxidative stress response pathway, as well as in regulation of lifespan; SKN-1 is detected at highest levels in nuclei of the P1 blastomere and its descendants through the 8-cell stage of embryogenesis; later in embryogenesis, SKN-1 is observed in all hypodermal and intestinal nuclei, with reporter constructs indicating that intestinal expression begins as early as the 50-100-cell stage; in larvae and young adults, SKN-1 reporters are expressed in the intestine and ASI neurons, with expression in intestinal nuclei greatly enhanced under stress-inducing conditions.
T22H6.6 T22H6.6 P W All gene names: gei-3; T22H6.6; CE31625; NM_077736; WBGene00001560; WP:CE31625; XN414 WormBase description: gei-3 encodes a member of the high mobility group (HMG) protein family; interacts with GEX-3 in yeast two-hybrid assays.
T24G10.2 T24G10.2 P W All gene names: T24G10.2; 3G532; CE37993; WBGene00020779; WP:CE37993
T26H2.9 T26H2.9 P W All gene names: nhr-79; T26H2.9; 5T682; CE31072; NHR79_CAEEL; NM_075333; WBGene00003669; WP:CE31072 WormBase description: Zinc finger, C4 type (two domains)
T27A1.6 T27A1.6 P W All gene names: Ce-tbx-12; mab-9; tbx-12; T27A1.6; 2A811; CE24016; NM_061349; TBX12_CAEEL; WBGene00003106; WP:CE24016 WormBase description: mab-9 encodes a member of the T-box family of transcriptional regulators containing a 200-amino acid T-box DNA-binding domain most similar to mouse Brachyury; mab-9 is involved in hindgut and mail tail development, specifically affecting the fate of two posterior blast cells in the hindgut, B and F; in the male this results in a grossly abnormal tail lacking spicules, and renders them incapable of mating; in the hermaphrodite this results in hindgut defects; mab-9 may also be part of a network of T-box genes that includes tbx-8, tbx-9 and vab-7 and is important for the correct patterning of posterior cells in the developing embryo; mab-9 affects movement to some extent though the basis for this defect is unknown; MAB-9 localizes to the nucleus of B and F and their descendents during development. WormBase CDS description: transcription regulator
T27B7.1 T27B7.1 P W All gene names: nhr-59; T27B7.1; 5C756; CE30194; NHR59_CAEEL; NM_071223; WBGene00003649; WP:CE30194
T27B7.4 T27B7.4 P W All gene names: nhr-115; T27B7.4; 5C771; CE35785; NH115_CAEEL; NM_071228; WBGene00003705; WP:CE35785 WormBase description: zinc finger protein
W03A3.1 W03A3.1 P W All gene names: ceh-10; mig-11; W03A3.1; 3G889; CE07563; HM10_CAEEL; NM_065850; WBGene00000435; WP:CE07563 WormBase description: 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.
W05E10.3 W05E10.3 P W All gene names: ceh-32; W05E10.3; W05E10.3.1; W05E10.3.2; 5M182; CE29364; HM32_CAEEL; NM_073557; WBGene00000453; WP:CE29364 WormBase description: ceh-32 encodes a Six/sine oculis-type homeodomain protein most closely related to the Six3/6 subfamily that contains Drosophila OPTIX and human SIX3 (OMIM:603714, which when mutated leads to holoprosencephaly 2); CEH-32 appears to be essential for development and required for proper head morphogenesis; during embryogenesis, CEH-32 is expressed in hypodermal and neuronal precursors, and at later stages, in the descendants of these cells and in gonadal sheath cells; in some hypodermal cells, ceh-32 is a direct transcriptional target of VAB-3, a PAX-6 ortholog sufficient to induce ceh-32 expression in some cell types and able to bind the ceh-32 promoter in vitro. WormBase CDS description: homeobox protein (so subfamily)
W09C2.1 W09C2.1 P W All gene names: elt-1; W09C2.1; W09C2.1a.1; W09C2.1a.2; 4K383; CE03799; CE39113; ELT1_CAEEL; NM_069307; WBGene00001249; WP:CE03799; WP:CE39113 WormBase description: The elt-1 gene encodes a GATA transcription factor expressed in the embryonic hypodermis, and is essential for the production of most hypodermal cells. WormBase CDS description: elongation factor ELT
W10D5.1 W10D5.1 P W All gene names: mef-2; W10D5.1; 1J677; CE25156; NM_060040; WBGene00003182; WP:CE25156 WormBase description: mef-2 encodes a transcription factor that is the sole C. elegans member of the MEF2 subgroup of MADS box transcription factors; loss of mef-2 activity does not result in a strong visible phenotype, although mef-2 mutant adults are slightly dumpy (Dpy); in vitro, MEF-2 is able to bind a consensus MEF2 DNA binding site and interact with the class II histone deacetylase encoded by C10E2.3 (hda-4/hda-7); mef-2 mRNA is detected at all stages of development and expression of mef-2 reporter gene fusions begins in neurons during late embryogenesis and continues in all tissues throughout postembryonic development; mef-2 mutations do not appear to interact with mutations in other myogenic factors such as hlh-1, hlh-8, pha-1, and unc-120. WormBase CDS description: MEF-2 protein
Y102A5C.18 Y102A5C.18 P W All gene names: efl-1; mex-2; Y102A5C.18; Y102A5C.18.1; Y102A5C.18.2; 5R440; CE20390; NM_074888; WBGene00001161; WP:CE20390 WormBase description: efl-1 encodes a homolog of mammalian E2F that is required for embryonic asymmetry and that functions as a transcriptional repressor; during vulval development, efl-1, a class B synMuv gene, acts with class B synMuv genes dpl-1 and lin-35/Rb to antagonize receptor tyrosine kinase and Ras-mediated signaling; EFL-1 also negatively regulates the G1 to S phase cell cycle transition.
Y113G7B.23 Y113G7B.23 P W All gene names: psa-1; Y113G7B.23; 5U710; CE25208; NM_075505; Q9U2W6_CAEEL; WBGene00004203; WP:CE25208 WormBase description: psa-1 encodes an ortholog of SWI3, a component of the SWI/SNF complex that is conserved from yeast to mammals and that is involved in chromatin remodeling; psa-1 is probably required during mitosis of the T cells for asymmetric cell division, and in addition, is required for embryonic and larval development, as well as normal levels of fertility; psa-1 exhibits strong genetic interactions with lin-35/Rb, as psa-1 larval lethality and sterility at 20 degrees C are greatly enhanced in lin-35;psa-1 double mutants. WormBase CDS description: SWI/SNF protein
Y16B4A.1 Y16B4A.1 P W All gene names: unc-3; Y16B4A.1; CE29366; NM_078052; UNC3_CAEEL; WBGene00006743; WP:CE29366; XP401 WormBase description: The unc-3 gene encodes a protein with homology to immunoglobulin (Ig) domain-containing transcription factors such as OLF-1 or SU(H). WormBase CDS description: transcription factor OLF-1 like
Y22F5A.1 Y22F5A.1 P W All gene names: nhr-232; Y22F5A.1; 5K739; CE38441; WBGene00012494; WP:CE38441 WormBase description: Zinc finger, C4 type (two domains)
Y2H9A.1 Y2H9A.1 P W All gene names: mes-4; Y2H9A.1; 5N914; CE27781; MES4_CAEEL; NM_073932; WBGene00003222; WP:CE27781 WormBase description: mes-4 encodes a SET domain-containing protein that also contains three plant homeodomain (PHD) fingers; MES-4 is required maternally for normal germline development, but in contrast to MES-2, -3, and -6, does not appear to be required for somatic anteroposterior patterning; in germline development, MES-4 activity is essential for regulating active chromatin states and for excluding the MES-2/MES-3/MES-6 chromatin repression complex from the autosomes; MES-4 is also required for germline silencing of repetitive transgene arrays; MES-4 localizes to autosomes, and is detectable in the distal, mitotic region of the germline, in meiotic germ cells during late pachytene, and in oocytes; MES-4 is detected in all somatic and germline nuclei of the early embryo, but by the 100-cell stage, its expression becomes restricted to the primordial germ cells, Z2 and Z3; exclusion of MES-4 from X chromosomes requires the activity of the MES-2, -3, -6 complex WormBase CDS description: SET domain
Y39B6A.17 Y39B6A.17 P W All gene names: nhr-95; Y39B6A.17; Y39B6B.D; 5T552; CE31105; CE34507; NM_171590; WBGene00003685; WP:CE31105; WP:CE34507 WormBase description: nhr-95 encodes a member of the superfamily of nuclear receptors, which is one of the most abundant class of transcriptional regulators; nuclear receptors have a well conserved DNA binding domain and a less conserved C-terminal ligand binding domain. WormBase CDS description: nuclear hormome receptor
Y39B6A.47 Y39B6A.47 P W All gene names: nhr-145; Y39B6.C; Y39B6A.47; Y39B6B.C; 5T569; CE36621; WBGene00012703; WP:CE36621
Y40B10A.8 Y40B10A.8 P W All gene names: nhr-86; Y40B10A.8; 5C540; CE31110; NHR86_CAEEL; NM_071160; WBGene00003676; WP:CE31110
Y43F8C.10 Y43F8C.10 P W All gene names: dmd-3; Y43F8C.10; 5U124; CE39835; WBGene00012832; WP:CE39835 WormBase description: DM DNA binding domain
Y46H3D.6 Y46H3D.6 P W All gene names: nhr-237; Y46H3D.6; 5C104; CE24323; WBGene00021610; WP:CE24323 WormBase description: zinc finger protein
Y53C10A.12 Y53C10A.12 P W All gene names: hsf-1; Y53C10A.12; Y53C10A.12.1; Y53C10A.12.2; 1M546; CE22380; NM_060630; WBGene00002004; WP:CE22380 WormBase description: hsf-1 encodes the C. elegans heat-shock transcription factor ortholog; HSF-1 functions as a transcriptional regulator of stress-induced gene expression whose activity is required for heat-shock and proteotoxicity response, larval development, innate immunity, and regulation of adult lifespan. WormBase CDS description: HSF-type DNA-binding domain
Y57E12AL.5 Y57E12AL.5 P W All gene names: let-425; mdt-6; med-6; Y57E12AL.5; Y57E12_247.D; 5H538; CE25510; NM_072390; WBGene00003164; WP:CE25510 WormBase description: mdt-6 encodes a highly conserved transcriptional mediator of the Med6 family that includes Saccharomyces cerevisiae Med6 and human MED6 (OMIM:602984); MDT-6 is an essential gene required maternally for embryogenesis and zygotically for postembryonic transcriptional regulation of genes involved in the Ras and Wnt signaling pathways that mediate vulval and male tail formation, respectively; mdt-6 is expressed in all cells at all stages and localizes to the peripheral region of nuclei, where actively transcribed portions of the genome may be localized.
Y73E7A.2 Y73E7A.2 P W All gene names: Y73E7A.2; 1C79; CE32277; WBGene00022269; WP:CE32277
Y75B8A.14 Y75B8A.14 P W All gene names: Y75B8A.14; 3N306; CE23026; Q9XW68_CAEEL; WBGene00013550; WP:CE23026
ZC123.3 ZC123.3 P W All gene names: ZC123.3; 1B307; CE28153; WBGene00022518; WP:CE28153 WormBase description: zinc finger protein