WormMine: Gene WBGene00001410

• WormBase Gene ID: WBGene00001410
• Gene Name: feh-1
• Sequence Name: Y54F10AM.2
• Brief Description: feh-1 encodes the single C. elegans member of the Fe65 protein family that affects embryonic and larval viability and pharyngeal pumping; the PTB2 domain binds to cytosolic domain of C. elegans APL-1 in vitro; expressed in the neuromuscular structures of the pharynx and in a subset of neurons.
• Organism: Caenorhabditis elegans
• Automated Description: Enables amyloid-beta binding activity. Involved in embryo development; feeding behavior; and nematode larval development. Located in actin filament. Expressed in nerve ring; pharynx; tail neurons; and ventral cord neurons. Human ortholog(s) of this gene implicated in Alzheimer's disease and cognitive disorder. Is an ortholog of human APBB2 (amyloid beta precursor protein binding family B member 2).
• Biotype: SO:0001217
• Genetic Position: III :-12.3627 ±0.181296
• Length (nt): 10765

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001410

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y54F10AM.2a.1	Y54F10AM.2a.1	2274	III: 2549920-2560668
Transcript:Y54F10AM.2b.1	Y54F10AM.2b.1	2273	III: 2549932-2560684
Transcript:Y54F10AM.2d.2	Y54F10AM.2d.2	2190	III: 2550065-2560640
Transcript:Y54F10AM.2c.2	Y54F10AM.2c.2	2233	III: 2550068-2560681
Transcript:Y54F10AM.2c.1	Y54F10AM.2c.1	2107	III: 2555208-2560672
Transcript:Y54F10AM.2d.1	Y54F10AM.2d.1	2114	III: 2555208-2560684

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y54F10AM.2a	Y54F10AM.2a	1998	III: 2549932-2549975
CDS:Y54F10AM.2b	Y54F10AM.2b	1923	III: 2549932-2549975
CDS:Y54F10AM.2c	Y54F10AM.2c	1665	III: 2555915-2555933
CDS:Y54F10AM.2d	Y54F10AM.2d	1590	III: 2555915-2555933

3 RNAi Result

• WBRNAi00057399
• WBRNAi00063449
• WBRNAi00063448

248 Allele

• gk962532
• gk964281
• gk963940
• WBVar01912953
• gk168950
• gk838702
• gb561
• ttTi41569
• gk943616
• gk402826
• WBVar01407939
• gk865363
• gk880900
• gk737716
• WBVar01983845
• gk962595
• WBVar01328153
• WBVar01328158
• WBVar01328156
• WBVar01328160
• WBVar01328162
• WBVar01328147
• WBVar01541013
• WBVar01548725
• WBVar01548724
• WBVar01548727
• WBVar01548726
• WBVar01548729
• WBVar01548728
• WBVar01548730

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001410
• Start: 2549920
• End: 2560684
• 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_chrIII_2560685..2561709
• Length (nt): 1025
• Chromosome Location: III: 2560685-2561709
• Organism: Caenorhabditis elegans

228 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:AVE-neuron_L1-larva_expressed
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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
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
	Genes that showed increased expression in wdr-5(ok1417) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:wdr-5(ok1417)_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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 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
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
	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
	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 increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_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
	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
	Transcripts that showed significantly increased expression in wdr-5(ok1417);skn-1(lax188) comparing to in skn-1(lax188) at day 2 adult stage.	fold change > 2	WBPaper00058711:wdr-5(ok1417)_upregulated

8 Expression Patterns

• Primary Identifier: Expr1030844
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1865
• Pattern: FEH-1 antibodies in whole-mount immunofluorescence analysis showed a largely prominent localisation of the protein in the pharynx at all stages of development, from three-fold stage embryos to adults. Barely detectable staining could be observed also in some neurons in the nerve ring and in the nerve chord and in the tail. In the pharynx the fluorescent signals start from the most terminal end of the organ and extend posteriorly to the second pharyngeal bulb and the attachment to the intestine.
• Subcellular Localization: Part of the protein appears to uniformly fill the cytoplasm of the expressing cells but an important fraction appears to associate with some sub-cellular compartment/structure in the shape of filaments that form, at the level of the second bulb, a characteristic basket-like structure.

• Primary Identifier: Expr1866
• Pattern: Expression of reporters confirmed that the main site of synthesis is the pharynx, but it is also expressed in some neurons in the nerve ring, in the ventral chord and in the tail. During embryogenesis, the expression of the constructs is detectable unambiguously only after proliferation has ceased and the embryo has elongated to the two- to three-fold stage. Expression of the reporters does not change substantially from embryogenesis and hatching to larval stages and adults. Expression is strong in several neurons and in pharyngeal cells. The very strong GFP signal detected in the pharynx did not allow the identification of feh-1-expressing cells among those forming this organ. The analysis of nuclear-targeted beta-galactosidase, expressed under the control of the feh-1 gene promoter, clearly identified, in agreement with GFP reporter activity, the nuclei of some extrapharyngeal neurons, as well as neurons of the ventral nerve chord and of the tail. Furthermore, in the procorpus and in the first pharyngeal bulb, the nuclei of m3 and m4 muscle cells are also stained. The staining of the nuclei in the second bulb, where the density is higher, did not unambiguously reveal the identity of feh-1-expressing cells.
• Subcellular Localization: The GFP clearly outlines the shape of the expressing neurons with their processes (e.g. in the ventral nerve chord).

• Primary Identifier: Expr2011748
• 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: Expr1020162
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Chronogram110
• Remark: Original chronogram file: chronogram.1117.xml
• Reporter Gene: [Y54F10AM.2:gfp] transcriptional fusion.

• Primary Identifier: Expr1160831
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2029986
• 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).

14 GO Annotation

9 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001410
• Start: 2549920
• End: 2560684
• Strand: 1

14 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Proteins that showed significantly decreased expression in feh-1(-) (generated by applying feh-1 dsRNA to feh-1 -/+ P0) embryos comparing to control RW3625 embryos injected with empty vector, according to 2D-DIGE analysis.	Student's t-test. Ratio > 1.75, p-value < 0.01.	WBPaper00031674:feh-1(gb561)(RNAi)_downregulated
	Proteins that showed significantly increased expression in feh-1(-) (generated by applying feh-1 dsRNA to feh-1 -/+ P0) embryos comparing to control RW3625 embryos injected with empty vector, according to 2D-DIGE analysis.	Student's t-test. Ratio > 1.75, p-value < 0.01.	WBPaper00031674:feh-1(gb561)(RNAi)_upregulated

1 Sequence

• Length: 10765

1 Sequence Ontology Term