WormMine: Gene WBGene00001345

• WormBase Gene ID: WBGene00001345
• Gene Name: fos-1
• Sequence Name: F29G9.4
• Brief Description: fos-1 encodes two basic region-leucine zipper (bZip) transcription factors, FOS-1A and FOS-1B, that are the sole C. elegans orthologs of the fos bZip transcription factor family; during hermaphrodite development, FOS-1A activity is required cell autonomously in the gonadal anchor cell for basement-membrane removal and subsequent anchor cell invasion of the vulval epithelium; in addition, fos-1 activity is also required for proper vulval and uterine development, fertility, and oogenesis; in late-L3 larvae, a FOS-1A translational fusion protein is expressed at high levels in the anchor cell nucleus and at lower levels in uterine cells, while a FOS-1B reporter is expressed at low levels in the anchor cell, uterine, and vulval cells; transcriptional reporters additionally reveal that fos-1b is expressed in most cells of late L3 larvae; in affecting anchor cell invasion, FOS-1A appears to act by regulating the expression of three AC-expressed genes: cdh-3/cadherin, him-4/hemicentin, and zmp-1/matrix metalloproteinase, which likely function together to promote anchor cell invasion.
• Organism: Caenorhabditis elegans
• Automated Description: Enables several functions, including RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; chromatin binding activity; and identical protein binding activity. Involved in several processes, including determination of adult lifespan; negative regulation of stress response to copper ion; and regulation of gene expression. Located in nucleus. Part of RNA polymerase II transcription regulator complex. Expressed in several structures, including gonad; neurons; uterine pi cell; ventral uterine precursor; and vulval cell.
• Biotype: SO:0001217
• Genetic Position: V :-0.462278 ±0.00249
• Length (nt): 12487

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001345

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F29G9.4a.1	F29G9.4a.1	1608	V: 6003601-6016083
Transcript:F29G9.4a.2	F29G9.4a.2	2298	V: 6008068-6016087
Transcript:F29G9.4b.1	F29G9.4b.1	1404	V: 6008566-6015691
Transcript:F29G9.4a.3	F29G9.4a.3	3580	V: 6009063-6016087
Transcript:F29G9.4a.4	F29G9.4a.4	1722	V: 6010808-6016087
Transcript:F29G9.4a.5	F29G9.4a.5	1477	V: 6011211-6016087

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F29G9.4a	F29G9.4a	996	V: 6011296-6011352
CDS:F29G9.4b	F29G9.4b	1404	V: 6008566-6008823

43 RNAi Result

• WBRNAi00107709
• WBRNAi00107708
• WBRNAi00107796
• WBRNAi00107797
• WBRNAi00045945
• WBRNAi00078880
• WBRNAi00115880
• WBRNAi00008727
• WBRNAi00025320
• WBRNAi00031590
• WBRNAi00085548
• WBRNAi00099794
• WBRNAi00100404
• WBRNAi00063265
• WBRNAi00100778
• WBRNAi00099188
• WBRNAi00071534
• WBRNAi00099592
• WBRNAi00099390
• WBRNAi00115829
• WBRNAi00112405
• WBRNAi00107547
• WBRNAi00092156
• WBRNAi00100030
• WBRNAi00100217
• WBRNAi00100591
• WBRNAi00107483
• WBRNAi00078883
• WBRNAi00116172
• WBRNAi00061041

184 Allele

• gk963301
• WBVar02060208
• gk963591
• gk963553
• gk963042
• gk963041
• gk964259
• gk964351
• gk963850
• otn12393
• WBVar01862500
• WBVar01862502
• WBVar01862501
• WBVar01862504
• WBVar01862503
• WBVar01588351
• WBVar01588352
• WBVar01588353
• WBVar01588354
• tm1757
• gk395593
• WBVar01973703
• WBVar01973702
• WBVar01973701
• WBVar01973700
• WBVar01973697
• WBVar01973699
• WBVar01973698
• gk760749
• gk236386

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001345
• Start: 6003601
• End: 6016087
• Strand: 1

4 Data Sets

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

0 Downstream Intergenic Region

158 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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 no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	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
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	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 GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 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_age_regulated_developing
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 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_developing
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
	Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	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
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray

13 Expression Patterns

• Primary Identifier: Expr1030820
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1200089
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr7530
• Remark: Clone: pUL#IAH8H3
• Pattern: Weak, infrequent, unconvincing expression seen in nerve cells in the head, nerve cord and tail from L1 to adult in 2 of 5 lines generated. Also see probably background expression in very anterior head body wall muscle cells.

• Primary Identifier: Expr2011872
• 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: Expr3686
• Pattern: Transgenic animals containing the fos-1a::YFP-TX and -TL reporters showed the same expression pattern at all times examined, and fos-1a::YFP-TL protein localized to the nucleus. fos-1a::YFP-TL also rescued the AC-invasion defect when expressed in fos-1(ar105) mutants. fos-1a was expressed at the highest level in the AC and at lower levels in neighboring somatic gonad cells during AC invasion. No expression of fos-1a was detected in vulval cells. In contrast, both the fos-1b::CFP-TX and -TL reporters directed expression in vulval cells and the AC. fos-1b::CFP-TL also drove expression in neighboring uterine cells, whereas fos-1b::CFP-TX did not, suggesting the presence of a downstream uterine enhancer element in fos-1b::CFP-TL. Unlike fos-1a expression, levels of fos-1b::CFP-TL protein were not greater in the AC compared to neighboring cells. Moreover, whereas the fos-1a reporters drove expression almost exclusively in the somatic gonad cells, the fos-1b reporters directed expression in nearly all cells at the L3 stage.
• Subcellular Localization: fos-1a::YFP-TL protein localized to the nucleus

• Primary Identifier: Expr1020029
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr11182
• Pattern: fos-1b::cfp is expressed in a subset of vulval progeny. During the mid-L4 stage, CFP fluorescence is brighter in presumptive vulD cells compared with vulE and vulF cells. This pattern is dynamic, such that by late-L4 stage, the presumptive vulE and vulF cells were much brighter compared with the presumptive vulD cells.

• Primary Identifier: Expr11183
• Pattern: fos-1a::yfp was undetectable in vulval cells during the L3 and L4 stages.

• Primary Identifier: Expr11184
• Pattern: The authors observed that a fos-1a translational fusion is expressed throughout the VU intermediate prescursor cells, including pi cells.

• Primary Identifier: Expr11185
• Pattern: plastFOS-1c::YFP showed expression primarily in the early dorsal and ventral uterus during L3 and L4 stages. Importantly, expression was observed in all VU intermediate precursors including pi cells. Furthermore, the authors confirmed that plastFOS-1c::YFP co-localized with cells expressing an egl-13 pi marker from the late L3 induction stage through generation of pi descendants.

• Primary Identifier: Expr1149842
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1200246
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2030110
• 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).

34 GO Annotation

15 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001345
• Start: 6003601
• End: 6016087
• Strand: 1

34 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 12487

1 Sequence Ontology Term