WormMine: Gene WBGene00001210

• WormBase Gene ID: WBGene00001210
• Gene Name: egl-46
• Sequence Name: K11G9.4
• Brief Description: egl-46 encodes a transcription factor with similarity to the TFIIA-like zinc-finger protein family; egl-46 activity is required for coordinated locomotion, morphology and process formation of the touch cells, male mating efficiency, HSN cell migration, differentiation, and axonal outgrowth, serotonin production and also terminal divisions of the Q neuroblasts; egl-46 acts to inhibit touch cell fate in FLP cells together with egl-44; EGL-46 is a nuclear protein expressed dynamically in neurons, including the touch receptor neurons, ventral cord neurons, FLP, and HSN neurons; egl-46 expression in FLP cells, but not HSN cells, is dependent upon EGL-44.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in several processes, including detection of chemical stimulus; generation of neurons; and positive regulation of exit from mitosis. Located in nucleus. Expressed in several structures, including QL.aa; QL.pp; QR.aa; QR.pp; and neurons. Is an ortholog of human INSM2 (INSM transcriptional repressor 2).
• Biotype: SO:0001217
• Genetic Position: V :0.132676 ±0.000364
• Length (nt): 2451

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001210

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K11G9.4.1	K11G9.4.1	1401	V: 6679123-6681573

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K11G9.4	K11G9.4	861	V: 6679657-6679872

15 RNAi Result

• WBRNAi00000978
• WBRNAi00089839
• WBRNAi00050621
• WBRNAi00017027
• WBRNAi00070206
• WBRNAi00092905
• WBRNAi00089916
• WBRNAi00090076
• WBRNAi00090234
• WBRNAi00090355
• WBRNAi00090402
• WBRNAi00090449
• WBRNAi00090496
• WBRNAi00107177
• WBRNAi00115952

62 Allele

• gk963301
• gk963553
• gk963042
• gk963041
• gk964259
• gk964351
• gk963850
• gk962860
• WBVar01588499
• gk692
• sy628
• WBVar01973893
• WBVar01973894
• gk237789
• gk237788
• gk237787
• gk237791
• gk237790
• WBVar00272134
• WBVar01740839
• WBVar00272133
• gk613927
• cas16
• WBVar01460335
• gk678654
• cas18
• gk908123
• cas24
• gk797723
• cas25

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001210
• Start: 6679123
• End: 6681573
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_6679109..6679122
• Length (nt): 14
• Chromosome Location: V: 6679109-6679122
• Organism: Caenorhabditis elegans

258 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
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 and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	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 increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_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 that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	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
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:ASE_parent
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	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_hel-1(gk148684)-background
	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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_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 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
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
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell 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:dopaminergic-neurons_L3-L4-larva_expressed
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell 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:hypodermis_L3-L4-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell 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:PVD-OLL-neurons_L3-L4-larva_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 increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus.	Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2.	WBPaper00059824:rnp-6(dh1127)_regulated_S.aureus

12 Expression Patterns

• Primary Identifier: Expr11222
• Pattern: egl-46 was only expressed in a subset of the Q cell lineage. Initially, egl-46 was not expressed in the Q neuroblast, and in the Q.a lineage it started to be expressed in the Q.a cell, whereas in the Q.p lineage its expression was restricted to Q.paa and was absent from Q.pap.

• Primary Identifier: Expr1030769
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13832
• Pattern: egl-46 is expressed in the HSN at L4 coinciding with the onset of differentiation. egl-46 is also expressed in other neurons, including the NSM serotonergic neuron, but not in the ADF serotonergic neuron. egl-46 initiates its expression at postnatal stages. egl-46 expression is maintained in HSN after differentiation.

• Primary Identifier: Expr12068
• Pattern: An egl-46 transcriptional reporter confirmed the previously published expression pattern for egl-46 in the FLP, HSN and PVD neurons and other neurons in the head. In addition, the egl-46 reporter colocalized with egl-13::gfp reporter (expressed in BAG, URX, AQR and PQR) in the BAG neurons at the L2 and L3 stages of larval development; suggesting that egl-46 is expressed during short temporal window in the BAG neurons, as has been observed in other neurons previously (WU et al. 2001). Note: we only rarely observed colocalization with the BAG marker, suggesting that the egl-46 promoter drives expression in the BAG neurons in a transient manner.

• Primary Identifier: Expr878
• Pattern: Fluorescence was first seen in some embryonic cells after gastrulation. All expression was confined to nuclei. Several cells in the head and tail, most of which appeared to be neuronal, were fluorescent in larvae and adults. The expression in at least some of the cells varied with time. Authors observed strongest expression and most continuous expression (lasting into the adult) in the FLP cells. The two HSN cells were seen in comma-stage to 1.5-fold stage embryos. Sometimes saw egl-1(+)-dependent expression in cells in the normal HSN position in L1 and L2 larvae, but never in L3 or older animals. In addition to these cells, GFP fluorescence was also found in 11 pairs of ventral cord neurons in the late L1 stage but not later. As many as 10 cells also fluoresced in the heads of L1 larvae. One cell in the tail also fluoresced at hatching, and two additional cells fluoresced at the end of the L1 stage and the beginning of the L2 stage. All of these cells lost their fluorescence as the animals matured. Unexpectedly, the touch cells also expressed the gfp::egl-46 fusion. This expression was transient (mainly in L2 larvae) and much fainter than the expression in the FLP cells (the postembryonically derived AVM and PVM cells fluoresced strongest). Some PVM fluorescence was seen at the L3 stage. gfp::egl-46 was also expressed in the PVD neurons. egl-46 is expressed transiently in the Q lineages.
• Subcellular Localization: All expression was confined to nuclei.

• Primary Identifier: Expr2963
• Remark: Reporter gene fusion type not specified.
• Pattern: Expressed in male sensory rays.

• Primary Identifier: Expr2697
• Remark: Reporter gene fusion type not specified.
• Pattern: In male, egl-46 expressed in FLP cells, ventral cord neurons and PVD. egl-46::cfp was expressed in the HOB neuron beginning at the L4 stage and continuing throughout adulthood. No detectable expression was seen in the HOA hook neuron.

• Primary Identifier: Expr2011225
• 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: Expr13960
• Pattern: egl-46 and egl-44 were normally expressed in the FLP neurons but not the TRNs. egl-44 and egl-46 were transiently expressed in the early embryos in HSN neurons before they migrated and differentiated.

• Primary Identifier: Expr2029461
• 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: Expr1154327
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1024687
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

33 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001210
• Start: 6679123
• End: 6681573
• Strand: -1

33 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2451

1 Sequence Ontology Term