Romagnolo et al 2002 Fig3b TF, 28 genes

Gene list file name:Romagnolo2002.Fig3b_28TF.txt
Type of gene identifier:MA primer pair (sjj)
Description:Romagnolo et al 2002 Fig3b 28 Transcripton Factors  
Organism:Caenorhabditis elegans (nematode)
Gene list type:Experimental

Gene name             Source Gene ID          Annotation                                                  Date       Added by    

B0564.10 B0564.10 P W All gene names: unc-30; B0564.10; 4N887; CE05183; CE36087; NM_070125; WBGene00006766; WP:CE05183; WP:CE36087 WormBase description: unc-30 encodes a paired-like homeodomain transcription factor orthologous to vertebrate Pitx homeodomain proteins, such as mouse Pitx2; UNC-30 controls the terminal differentiation of all 19 type D GABA-ergic motor neurons by directly regulating the expression of UNC-25/GAD and UNC-47/VGAT, which are responsible for GABA formation and secretion, respectively; UNC-30 is expressed most strongly in type D motor neurons during early L1 and L2 larval stages. WormBase CDS description: homeobox protein (otd subfamily)
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Romagnolo et al 2002  Fig3b TF                               

C09F5.3 C09F5.3 P W All gene names: C09F5.3; 3B280; CE39319; WBGene00015649; WP:CE39319
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF                                    

C15F1.5 C15F1.D P W All gene names: C15F1.5; 2H258; CE20510; CE39557; WBGene00015796; WP:CE20510; WP:CE39557 WormBase description: zinc finger protein
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, herm sperm, Reinke                             
                                              et al 2004, wt vs glp-4 enriched genes, Reinke et al                               
                                              2004, list of genes in cluster order, Reinke et al                                 
                                              2004, spermatogenesis enriched genes, Reinke et al                                 
                                              2004, list of genes in cluster D, Reinke et al 2004,                               
                                              fem3 enriched genes, Romagnolo et al 2002  Fig3b TF                                

C17E7.5 C17E7.5 P W All gene names: nhr-157; C17E7.5; 5E340; CE08265; WBGene00015900; WP:CE08265 WormBase description: nuclear hormone receptor
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, intrinsic, Reinke                              
                                              et al 2004, wt vs glp-4 enriched genes, Reinke et al                               
                                              2004, GO categories, Romagnolo et al 2002  Fig3b TF,                               
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

C17E7.7 C17E7.7 P W All gene names: nhr-159; C17E7.7; 5E348; CE17412; WBGene00015902; WP:CE17412 WormBase description: nuclear hormone receptor
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF,                                   
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

C25E10.1 C25E10.1 P W All gene names: nhr-30; C25E10.1; 5J523; CE06863; WBGene00016091; WP:CE06863 WormBase description: zinc finger-containing protein
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF                                    

C26B2.4 C26B2.4 P W All gene names: nhr-258; C26B2.4; 4I809; CE34709; WBGene00016126; WP:CE34709 WormBase description: nuclear hormone receptor
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF                                    

C27B7.5 C27B7.5 P W All gene names: C27B7.5; 4J667; CE03034; WBGene00007762; WP:CE03034 WormBase description: Zinc finger, CCHC class
                                              
Member of lists (Publications lists):
                                              Jiang et al 2001  Fig1                                            
                                              hermaphrodite-enriched TF, Jones et al 2001  Non dauer                             
                                              genes P<0.05, Reinke et al 2004, list of genes in                                  
                                              cluster F, Reinke et al 2004, fem1 enriched genes,                                 
                                              Reinke et al 2004, Fig2b shared gemlines, Reinke et al                             
                                              2004, list of genes in cluster order, Reinke et al                                 
                                              2004, oogenesis enriched genes, Reinke et al 2004, wt                              
                                              vs glp-4 enriched genes, Reinke et al 2004, wt males vs                            
                                              glp4 male enriched , Reinke et al 2004, wt herm vs wt                              
                                              male enriched gen, Reinke et al 2004, GO categories,                               
                                              Romagnolo et al 2002  Fig3b TF, ViswanathanM et al 2005                            
                                               S2 sir-2.1 regulated                                                              

C29F9.5 C29F9.5 P W All gene names: C29F9.5; 3A735; CE08453; WBGene00016220; WP:CE08453
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, IVb male soma                                  
                                              enriched genes, Romagnolo et al 2002  Fig3b TF, Shen et                            
                                              al 2005  T1 hif-1 depend hypoxia                                                   

C34H3.2 C34H3.A P W All gene names: odd-2; C34H3.2; CE23571; NM_076631; WBGene00003846; WP:CE23571; XG778 WormBase description: odd-2 encodes a protein with homology to the Drosophila ODD-SKIPPED family members and affects larval viability; expressed in the intestine. WormBase CDS description: C2H2-type zinc finger protein
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Romagnolo et al 2002  Fig3b TF                               

C48E7.3 C48E7.3 P W All gene names: lpd-2; C48E7.3; 1G831; CE29953; NM_059405; WBGene00003059; WP:CE29953 WormBase description: lpd-2 encodes a predicted transcription factor with homology to transcription factors of the CCAAT/Enhancer Binding Protein family (C/EBPA and B, OMIM:116897, 189965, associated with the regulation of mammalian adipocyte differentiation); in C. elegans, LPD-2 activity is required for normal lipid metabolism and wild-type levels of lipogenic enzyme expression, as well as for larval development; in addition, LPD-2 may be part of a conserved pathway regulating lipogenesis, as LPD-2 appears to positively regulate expression of sbp-1, which encodes the C. elegans Sterol Regulatory Element Binding Protein (SREBP) homolog, a basic helix-loop-helix-type transcription factor also required for normal lipid metabolism and larval development.
                                              
Member of lists (Publications lists):
                                              Lund et al 2002   Fig3C                                           
                                              Germline-intrinsic, Reinke et al 2004, fem1 enriched                               
                                              genes, Reinke et al 2004, wt vs glp-4 enriched genes,                              
                                              Reinke et al 2004, oogenesis enriched genes, Reinke et                             
                                              al 2004, wt herm vs wt male enriched gen, Romagnolo et                             
                                              al 2002  Fig3b TF, ViswanathanM et al 2005  S2 sir-2.1                             
                                              regulated                                                                          

F19B10.9 F19B10.9 P W All gene names: sea-1; tbx-18; F19B10.9; CE09476; WBGene00004750; WP:CE09476
                                              
Member of lists (Publications lists):
                                              Jiang et al 2001  Fig1                                            
                                              hermaphrodite-enriched TF, Jones et al 2001  Non dauer                             
                                              genes P<0.05, Reinke et al 2004, fem1 enriched genes,                              
                                              Reinke et al 2004, list of genes in cluster order,                                 
                                              Reinke et al 2004, oogenesis enriched genes, Reinke et                             
                                              al 2004, wt vs glp-4 enriched genes, Reinke et al 2004,                            
                                              wt herm vs wt male enriched gen, Reinke et al 2004, GO                             
                                              categories, Reinke et al 2004, list of genes in cluster                            
                                              E, Romagnolo et al 2002  Fig3b TF, ViswanathanM et al                              
                                              2005  S2 daf-16 Resveratrol, ViswanathanM et al 2005                               
                                              S2 sir-2.1 regulated                                                               

F26B1.7 F26B1.7 P W All gene names: let-381; F26B1.7; 1G898; CE28006; NM_059425; WBGene00002601; WP:CE28006 WormBase description: let-381 encodes a forkhead transcription factor and was identified in a screen for essential genes; let-381 is essential for development at different times as mutants exhibit embryonic and early larval lethality, with a few developing to sterile adults; inactivation of let-381 using RNA interference results in adults with mesodermal cell lineage defects and a reduced number of coelomocytes; reporter-gene assays indicate LET-318 is expressed when the embryo starts to elongate and continues to be expressed through all larval stages and into the adult. WormBase CDS description: fork-head domain-type transcription factors
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF,                                   
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F43G9.11 F43G9.11 P W All gene names: ces-1; F43G9.11; 1J211; CE17821; NM_059937; 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)
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Non dauer genes                                 
                                              P<0.05, McCarroll et al 2004  SFig1-4 conserved w/                                 
                                              Drosoph, Reinke et al 2004, list of genes in cluster                               
                                              order, Romagnolo et al 2002  Fig3b TF                                              

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
                                              
Member of lists (Publications lists):
                                              Baugh et al 2005, PAL-1 target genes,                             
                                              Kwon et al 2004 T1 late-induction Ethanol-response,                                
                                              McCarroll et al 2004  SFig1-4 conserved w/ Drosoph,                                
                                              Reinke et al 2004, intrinsic, Reinke et al 2004, wt vs                             
                                              glp-4 enriched genes, Reinke et al 2004, wt herm vs wt                             
                                              male enriched gen, Romagnolo et al 2002  Fig3b TF,                                 
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

F55D12.4 F55D12.4 P W All gene names: unc-55; F55D12.4; 1I472; CE05957; NM_059780; WBGene00006790; WP:CE05957 WormBase description: nuclear hormone receptor
                                              
Member of lists (Publications lists):
                                              McCarroll et al 2004  SFig1-4                                     
                                              conserved w/ Drosoph, Romagnolo et al 2002  Fig3b TF,                              
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

K06B4.10 K06B4.10 P W All gene names: nhr-199; K06B4.10; 5Q176; CE11800; WBGene00010604; WP:CE11800 WormBase description: Zinc finger, C4 type (two domains) (2 domains)
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF                                    

M02H5.1 M02H5.G P W All gene names: nhr-99; M02H5.1; 5A955; CE25947; NM_070813; WBGene00003689; WP:CE25947 WormBase description: nhr-99 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.
                                              
Member of lists (Publications lists):
                                              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 TF                                              

T01G6.7 T01G6.7 P W All gene names: nhr-55; T01G6.7; 5A957; CE37786; NM_070814; WBGene00003645; WP:CE37786 WormBase description: nhr-55 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: zinc finger protein
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF                                    

T26C11.5 T26C11.5 P W All gene names: ceh-41; T26C11.5; CE05024; NM_075939; WBGene00000462; WP:CE05024; XC466 WormBase description: ceh-41 encodes a a ONECUT class CUT homeobox protein with a single N-terminal OCAM domain; the OCAM domain is a nematode-specific motif conserved between CEH-21, CEH-41, and T02B5.2; ceh-41 is one of three nematode-specific ONECUT genes in a cluster with ceh-21 and ceh-39; ceh-41 has no obvious function in mass RNAi assays. WormBase CDS description: paired-type homeobox protein
                                              
Member of lists (Publications lists):
                                              Reinke et al 2004, fem1 enriched                                  
                                              genes, Reinke et al 2004, mixed oogenesis soma,                                    
                                              Romagnolo et al 2002  Fig3b TF, 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                                                                      

T27B7.5 T27B7.5 P W All gene names: nhr-227; T27B7.5; 5C765; CE14239; WBGene00020851; WP:CE14239 WormBase description: zinc finger protein
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF,                                   
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

W03C9.4 Y17G7A.2 P W All gene names: egl-29; lin-29; W03C9.4; Y17G7A.2; 2M208; CE28257; NM_064144; WBGene00003015; WP:CE28257 WormBase description: lin-29 encodes a zinc finger transcription factor of the C2H2 type that affects the heterochronic development of the vulva, egg laying system, cuticle, and the molting cycle; expressed in uterine and vulval muscle cells, seam cells, pharynx, head neurons, ventral cord neurons, preanal ganglion, distal tip cells, anchor cell, vulval cells, and cells in the tail. WormBase CDS description: transcription factor lin-29
                                              
Member of lists (Publications lists):
                                              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, Romagnolo et al 2002  Fig3b TF, 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                                                                    

Y32B12B.6 Y32B12B.6 P W All gene names: nhr-233; tag-122; Y32B12B.6; 5R50; CE19066; WBGene00006471; WP:CE19066 WormBase description: nuclear hormone receptor
                                              
Member of lists (Publications lists):
                                              Jones et al 2001  Dauer specific genes                            
                                              P<0.05, Romagnolo et al 2002  Fig3b TF, Wang et al 2003                            
                                               S7 SAGE genes in the dataset, Wang et al 2003  S8 SAGE                            
                                              genes in the dauer exit                                                            

Y53C12C.1 Y53C12C.1 P W All gene names: Y53C12C.1; 2K112; CE14906; WBGene00013147; WP:CE14906 WormBase description: Y53C12C.1 encodes a divergent paired-like homeodomain protein that does not belong to the Q50, K50, or S50 classes; it has no obvious function in mass RNAi assays. WormBase CDS description: 'Paired box' domain, Homeobox domain
                                              
Member of lists (Publications lists):
                                              Portman et al 2004  T1 25 candidate                               
                                              ray genes, Romagnolo et al 2002  Fig3b TF                                          

ZK1240.6 ZK1240.6 P W All gene names: ZK1240.6; 2C612; CE15539; WBGene00022871; WP:CE15539
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF,                                   
                                              ViswanathanM et al 2005  S2 sir-2.1 regulated                                      

ZK488.4 ZK488.4 P W All gene names: nhr-251; ZK488.4; 5B75; CE15357; WBGene00022756; WP:CE15357 WormBase description: zinc finger protein
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF, 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                                                               

ZK6.4 ZK6.4 P W All gene names: nhr-253; ZK6.4; 5A873; CE19643; WBGene00022639; WP:CE19643 WormBase description: zinc finger protein
                                              
Member of lists (Publications lists):
                                              Romagnolo et al 2002  Fig3b TF,                                   
                                              ViswanathanM et al 2005  S2 daf-16 Resveratrol                                     

ZK909.4 ZK909.4 P W All gene names: ces-2; ZK909.4; 1P559; CE15479; NM_061209; WBGene00000469; WP:CE15479 WormBase description: ces-2 encodes a basic region leucine-zipper (bZIP) transcription factor, most similar in sequence and binding specificity to the PAR (proline- and acid-rich) subfamily of bZIP proteins; ces-2 is required to activate programmed cell death in the sister cells of the serotoninergic neurosecretory motor (NSM) neurons, and is transcriptionally inhibited by activated LET-60(G12V). WormBase CDS description: albumin D-binding protein like
                                              
Member of lists (Publications lists):
                                              Portman et al 2004  T1 newly found                                
                                              ray-genes in25c, Portman et al 2004  T1 25 candidate                               
                                              ray genes, Reinke et al 2004, list of genes in cluster                             
                                              order, Reinke et al 2004, list of genes in cluster E,                              
                                              Romagnolo et al 2002  Fig3b TF