WormMine: Gene WBGene00001481

• WormBase Gene ID: WBGene00001481
• Gene Name: fog-1
• Sequence Name: Y54E10A.4
• Brief Description: fog-1 encodes a cytoplasmic polyadenylation element binding (CPEB) protein; FOG-1 is required for specification of the sperm fate; FOG-1 binds its own 3'-UTR and fog-1 expression is directly regulated by FBF-1 and FBF-2.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA 3'-UTR binding activity. Involved in cell fate specification; germ-line sex determination; and spermatogenesis. Located in cytoplasm and nuclear periphery. Expressed in germ line.
• Biotype: SO:0001217
• Genetic Position: I :-4.47297 ±0.001409
• Length (nt): 6222

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001481

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y54E10A.4a.1	Y54E10A.4a.1	2118	I: 3211046-3217267
Transcript:Y54E10A.4b.1	Y54E10A.4b.1	1872	I: 3211046-3217021
Transcript:Y54E10A.4a.2	Y54E10A.4a.2	1592	I: 3212990-3217267
Transcript:Y54E10A.4c.1	Y54E10A.4c.1	1053	I: 3213879-3217021
Transcript:Y54E10A.4d.1	Y54E10A.4d.1	228	I: 3216794-3217021

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y54E10A.4a	Y54E10A.4a	1218	I: 3213118-3213202
CDS:Y54E10A.4d	Y54E10A.4d	228	I: 3216794-3217021
CDS:Y54E10A.4b	Y54E10A.4b	1860	I: 3211058-3211119
CDS:Y54E10A.4c	Y54E10A.4c	1053	I: 3213879-3213944

15 RNAi Result

• WBRNAi00087820
• WBRNAi00064341
• WBRNAi00004978
• WBRNAi00075634
• WBRNAi00061019
• WBRNAi00004977
• WBRNAi00061199
• WBRNAi00061209
• WBRNAi00061214
• WBRNAi00081940
• WBRNAi00081941
• WBRNAi00057349
• WBRNAi00064344
• WBRNAi00061210
• WBRNAi00061211

139 Allele

• gk963902
• gk964159
• gk963438
• q181
• q180
• q182
• q187
• q218
• q219
• q229
• q241
• q243
• q242
• q250
• q248
• q253
• q254
• q255
• q272
• q271
• q273
• q311
• q325
• q329
• q372
• q379
• q382
• q380
• q155
• q507

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001481
• Start: 3211046
• End: 3217267
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_3217268..3217287
• Length (nt): 20
• Chromosome Location: I: 3217268-3217287
• Organism: Caenorhabditis elegans

153 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_upregulated
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_aging
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
	Transcripts that showed significantly increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:daf-2(e1370)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:germline-precursors_blastula-embryo_expressed
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	Transcripts that showed significantly decreased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6.	DESeq2, log2 fold change > 2, adjusted p-value < 0.005.	WBPaper00055103:thoc-5(wy822)_downregulated
	Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:hda-1(RNAi)_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_downregulated

11 Expression Patterns

• Primary Identifier: Expr4653
• Remark: No detailed description expression patterns in other life stages.
• Pattern: In L4 germ lines, authors also examined SP56, the earliest known marker of sperm differentiation: SP56 antibodies recognize a minor sperm protein in primary, secondary, and mature spermatocytes. SP56 was first seen approximately 6 hr after the molt from L3 to L4 (3 hr, n = 17; 6 hr, n = 14; 10 hr, n = 19), where staining was limited to the proximal-most germ cells. As animals matured through the L4 stage, the SP56 domain expanded distally to include an increasing number of cells. Importantly, FOG-1 and SP56 were not present in the same cells at the same time. Instead, FOG-1 staining preceded SP56 staining in both time and space. For example, the proximal-most germ cells expressed FOG-1 in late L3 and early L4 ; those same cells expressed SP56 in mid-L4 (6 hr), when the FOG-1 domain had moved distally. Authors conclude that in wild-type larvae, FOG-1 is expressed transiently in germ cells destined for spermatogenesis. In wild-type larvae, FOG-1 became easily detectable in the second half of L2. In early L3 larvae, FOG-1 levels increased in the proximal region of most germ lines, and by late L3, FOG-1 staining was strong in that proximal region of all germ lines. FOG-1 remained abundant for approximately the first half of the L4 stage, although its location moved distally within the germ line.

• Primary Identifier: Expr1030884
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2422
• Pattern: The fog-1L transcript could not be detected in the Glp mutants. Thus, fog-1L is either produced in the germ line or produced in the soma following induction by germ cells.

• Primary Identifier: Expr2423
• Pattern: Anti-fog-1 probes was observed specific to the large transcript stain the germ cells of extruded gonads. The most intense staining stretches from germ cells in early meiosis through primary spermatocytes.

• Primary Identifier: Expr3514
• Remark: Gene_regulation: In fbf-1 fbf-2 mutants, FOG-1 levels were elevated compared with wild-type. In both L2 and L3, FOG-1 was easily detectable or abundant in all fbf-1 fbf-2 germ cells. Therefore, FBF repression is required for maintaining low FOG-1 in L2 germlines and for establishing the FOG-1 spatial gradient in L3 germlines. To assess FOG-1 in germlines that possess proliferative cells throughout the entire tissue, germlines that are tumorous were stained in the presence and absence of FBF. The quantity of FOG-1 protein was low in gld-3 nos-3 tumorous germlines, but consistently higher in fbf-1 fbf-2 gld-3 nos-3 tumorous germlines. The FBF represses fog-1 expression in vivo and that FBF is required for establishing the temporal and spatial pattern of FOG-1 expression. This adult male pattern of fog-1 expression was confirmed by in situ hybridization using an antisense probe to detect fog-1 mRNA; no RNA was seen with a sense probe. Germlines dissected from fog-1(q250) mutant males had no detectable FOG-1 protein, consistent with its being a null allele and demonstrating specificity of the antibody.
• Pattern: In contrast to adult male germlines, no FOG-1 was detected in adult hermaphrodites. Therefore, FOG-1 expression is sexually dimorphic in adults. FOG-1 is graded in spermatogenic germlines: FOG-1 is low or undetectable in proliferating cells but abundant in cells entering the meiotic cell cycle and destined for spermatogenesis. By contrast, FOG-1 is not detected in oogenic germlines. In wild-type animals, FOG-1 protein was observed in the germline and was predominantly cytoplasmic. In L2s, FOG-1 became detectable, but staining was faint. In L3s, the level of FOG-1 remained low distally in proliferating germ cells, but FOG-1 was abundant more proximally in germ cells that had entered meiosis and were destined for spermatogenesis. Temperature shift experiments with a fog-1(ts) allele showed that FOG-1 specifies spermatogenesis in L3 when germ cells enter meiosis, consistent with the idea that the abundant FOG-1 in early meiotic germ cells is specifying the sperm fate. In adult male germlines, FOG-1 was spatially graded: FOG-1 was either not detected or barely visible in the distal half of the mitotic region, became detectable in the proximal half of the mitotic region where some germ cells have entered pre-meiotic S phase, intensified in the transition zone and remained high in distal pachytene germ cells; no FOG-1 was detected in more proximal pachytene cells.
• Subcellular Localization: cytoplasmic

• Primary Identifier: Expr12583

• Primary Identifier: Expr2011865
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr3797
• Pattern: Expression not detected in the ventral hypodermis of L1, L2, or L3 larvae.

• Primary Identifier: Expr2030103
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1015132
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1160785
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

24 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001481
• Start: 3211046
• End: 3217267
• Strand: 1

24 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	FOG-1associated mRNAs identified by RIP-ChIP	To identify transcripts enriched in RIP samples, background corrected and normalized data were analyzed with the Bioconductor package Siggenes (siggenes 1.38.0) using two-class significance analysis of microarrays (SAM function).	WBPaper00048762:FOG-1_associated

1 Sequence

• Length: 6222

1 Sequence Ontology Term

• Name: gene

9 Strains

• WBStrain00022633
• WBStrain00022660
• WBStrain00022661
• WBStrain00022628
• WBStrain00022517
• WBStrain00022535
• WBStrain00022541
• WBStrain00022595
• WBStrain00004543

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_3210273..3211045
• Length (nt): 773
• Chromosome Location: I: 3210273-3211045
• Organism: Caenorhabditis elegans