WormMine: Gene WBGene00001441

• WormBase Gene ID: WBGene00001441
• Gene Name: fkh-9
• Sequence Name: K03C7.2
• Brief Description: fkh-9 encodes a member of the forkhead domain transcription factor family.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including axon regeneration; determination of adult lifespan; and learning or memory. Acts upstream of or within ERAD pathway and defense response to other organism. Located in nucleus. Expressed in several structures, including intestine; neurons; pharyngeal-intestinal valve; rectal valve cell; and somatic nervous system.
• Biotype: SO:0001217
• Genetic Position: X :-9.33097 ±0.020127
• Length (nt): 10117

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001441

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K03C7.2c.3	K03C7.2c.3	2667	X: 3816847-3820572
Transcript:K03C7.2a.1	K03C7.2a.1	2051	X: 3816851-3826963
Transcript:K03C7.2b.1	K03C7.2b.1	1941	X: 3816853-3820570
Transcript:K03C7.2c.2	K03C7.2c.2	1573	X: 3816860-3818488
Transcript:K03C7.2c.4	K03C7.2c.4	2939	X: 3816860-3820572
Transcript:K03C7.2c.1	K03C7.2c.1	1678	X: 3816894-3819630

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K03C7.2b	K03C7.2b	843	X: 3817951-3818144
CDS:K03C7.2a	K03C7.2a	903	X: 3817951-3818144
CDS:K03C7.2c	K03C7.2c	285	X: 3817951-3818144

5 RNAi Result

• WBRNAi00049806
• WBRNAi00113577
• WBRNAi00022899
• WBRNAi00092043
• WBRNAi00107444

133 Allele

• gk963725
• gk964260
• WBVar02063490
• tm8858
• gk276721
• gk794362
• gk276728
• gk886864
• WBVar00077279
• WBVar00077280
• WBVar02026968
• WBVar02026969
• WBVar02026970
• WBVar01814090
• WBVar02091812
• gk544796
• qd327
• gk331890
• gk633655
• gk809409
• gk691526
• gk849107
• gk865047
• gk915394
• gk918012
• gk412273
• gk793273
• gk818350
• gk573045
• gk500818

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001441
• Start: 3816847
• End: 3826963
• 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_chrX_3816430..3816846
• Length (nt): 417
• Chromosome Location: X: 3816430-3816846
• Organism: Caenorhabditis elegans

193 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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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
	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
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 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 that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_upregulated
	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 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
	Expression Pattern Group C, enriched for genes involved in metabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_C
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:oscillating_dev_expression
	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
	Transcripts that showed significantly decreased expression in miR-85(n4117), comparing to in N2 at 20C.	DESeq2 FDR < 0.05	WBPaper00061800:miR-85(n4117)_downregulated_20C
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly increased expression in wdr-23(mac32) embryos from parents fed with E. coliHB101, comparing to N2 embryos parents fed with E. coli HB101.	DESeq2, Fold Change > 2 or < 0.5.	WBPaper00059566:wdr-23(mac32)_upregulated

13 Expression Patterns

• Primary Identifier: Expr1030866
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9734
• Pattern: Although weaker, GFP expression looks similar to UL3218 (generated by the same strategy as UL3146 but with gfp inserted just before the fkh-9 stop codon). GFP was seen from the comma stage embryo. From the L1 stage, GFP was seen in neurons and hypodermis in the head, but the fluorescence signal was much brighter before hatching.

• Primary Identifier: Expr9738
• Pattern: Very broad GFP expression was seen from late embryogenesis to mature adult. Many cells in the head showed expression including neurons, the pharynx and hypodermis. Many neurons in the tail also showed expression. Body wall GFP expression was observed throughout the length of the body, in the hypodermis and possibly muscle, and was most apparent in the L4. There was also intestinal expression but this varied considerably in intensity between individuals. Finally GFP expression was also observed in the vulva in the L4, probably in the vulval muscles, and possibly in the rectal muscles. Expression was brightest in the L4s and young adults.

• Primary Identifier: Expr9834
• Pattern: GFP expression was observed from early embryogenesis to the mature adult. GFP was localized to many nuclei in the head and tail from L1 to adult The expression appeared to be mainly neuronal, with possibly some hypodermal expression as well. There was also expression in the rectal-intestinal valve and rectal cells, and some faint intestinal expression in adults. The brightest fluorescence was seen just prior to hatching.

• Primary Identifier: Expr13963
• Pattern: FKH-9 expression was expressed in both neurons and intestinal nuclei consistent with published reports (Hope et al. 2003; Kaletsky et al. 2015).

• Primary Identifier: Expr9809
• Pattern: GFP expression was observed from just before hatching to mature adult. Broad neuronal GFP expression was observed in the head and tail, but not in the ventral nerve cord. GFP was most prominent in the pharynx in larvae, in possibly all pharyngeal cells including muscle. The pharyngeal expression was fainter but still visible in the adult. GFP was also present in intestinal nuclei throughout development but again more faintly in the adult.

• Primary Identifier: Expr2337
• Remark: Reporter gene fusion type not specified.
• Pattern: Expression in the nervous system was extensive, possibly including all nerve cells in the head and tail ganglia and the nerve cord. Expression was also observed throughout the digestive system: in all cells of the pharynx, in the pharyngeal-intestinal valve, in all cells of the intestine and in the intestinal-rectal valve. Both neuronal and non-neuronal expression was observed through all larval stages and into the adult.

• Primary Identifier: Expr2011811
• 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: Expr1153525
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr9830
• Pattern: Low levels of GFP were seen in all postembryonic stages in a few neurons in the head and tail. GFP in the intestine was observed less frequently and usually only in the posterior 2 to 4 nuclei and anterior 1 or 2 nuclei, a distribution that has been considered an artefact of the reporter gene technology.

• Primary Identifier: Expr1016177
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2030049
• 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: Expr12663
• Subcellular Localization: FKH-9-GFP localized to nuclei.

23 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001441
• Start: 3816847
• End: 3826963
• Strand: -1

23 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10117

1 Sequence Ontology Term