WormMine: Gene WBGene00001208

• WormBase Gene ID: WBGene00001208
• Gene Name: egl-44
• Sequence Name: F28B12.2
• Brief Description: egl-44 encodes a transcription enhancer factor of the TEA domain (TEAD) class; egl-44 activity is required to repress the touch cell fate in some cells and to promote aspects of HSN differentiation; EGL-44 physically interacts with YAP-1, a C. elegans Yes-associated protein (YAP) homolog, and when co-expressed, the two proteins are able to activate a TEAD reporter; an EGL-44::GFP fusion protein is expressed in nuclei of various cells including the hypodermis, pharynx, intestine, and neurons including the FLP and HSN neurons; in the FLP neurons, EGL-44 positively regulates expression of EGL-46, a zinc-finger transcription factor also required for regulating neuronal differentiation.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and transcription coactivator binding activity. Involved in several processes, including generation of neurons; positive regulation of exit from mitosis; and regulation of transcription by RNA polymerase II. Located in nucleus. Part of RNA polymerase II transcription regulator complex. Expressed in several structures, including anterior hypodermis; body wall musculature; ganglia; neurons; and pharynx. Human ortholog(s) of this gene implicated in Sveinsson chorioretinal atrophy. Is an ortholog of human TEAD2 (TEA domain transcription factor 2) and TEAD4 (TEA domain transcription factor 4).
• Biotype: SO:0001217
• Genetic Position: II :-0.841979 ±0.008666
• Length (nt): 12029

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001208

Genomics

13 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F28B12.2c.2	F28B12.2c.2	2076	II: 5928802-5940818
Transcript:F28B12.2b.2	F28B12.2b.2	2100	II: 5928802-5940821
Transcript:F28B12.2g.1	F28B12.2g.1	1479	II: 5928830-5940228
Transcript:F28B12.2h.1	F28B12.2h.1	1458	II: 5928830-5940228
Transcript:F28B12.2b.3	F28B12.2b.3	2126	II: 5933486-5940821
Transcript:F28B12.2a.1	F28B12.2a.1	2107	II: 5933493-5940830
Transcript:F28B12.2i.1	F28B12.2i.1	1482	II: 5933537-5940228
Transcript:F28B12.2b.1	F28B12.2b.1	2024	II: 5936441-5940815
Transcript:F28B12.2c.1	F28B12.2c.1	2003	II: 5936441-5940815
Transcript:F28B12.2f.1	F28B12.2f.1	1308	II: 5936657-5940228
Transcript:F28B12.2k.1	F28B12.2k.1	1287	II: 5936657-5940228
Transcript:F28B12.2d.1	F28B12.2d.1	1873	II: 5937047-5940817
Transcript:F28B12.2j.1	F28B12.2j.1	1872	II: 5937051-5940799

Other

10 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F28B12.2g	F28B12.2g	1479	II: 5928830-5928871
CDS:F28B12.2h	F28B12.2h	1458	II: 5928830-5928871
CDS:F28B12.2i	F28B12.2i	1482	II: 5933537-5933581
CDS:F28B12.2j	F28B12.2j	1257	II: 5937095-5937251
CDS:F28B12.2a	F28B12.2a	1461	II: 5933537-5933581
CDS:F28B12.2b	F28B12.2b	1437	II: 5936441-5936484
CDS:F28B12.2c	F28B12.2c	1416	II: 5936441-5936484
CDS:F28B12.2d	F28B12.2d	1236	II: 5937095-5937251
CDS:F28B12.2f	F28B12.2f	1308	II: 5936657-5936665
CDS:F28B12.2k	F28B12.2k	1287	II: 5936657-5936665

8 RNAi Result

• WBRNAi00089841
• WBRNAi00045781
• WBRNAi00014028
• WBRNAi00086261
• WBRNAi00089990
• WBRNAi00090149
• WBRNAi00090308
• WBRNAi00090569

161 Allele

• gk963801
• gk963053
• gk964349
• WBVar01603953
• WBVar00244433
• WBVar00244432
• WBVar01373555
• WBVar01373566
• WBVar01719972
• WBVar01719973
• h9605
• tm4799
• WBVar00550737
• cas3
• cas6
• cas19
• cas58
• cas140
• n998
• WBVar02002753
• WBVar00103968
• st12173
• WBVar01766331
• ttTi1420
• gk922956
• gk586395
• gk588677
• gk834876
• gk321096
• gk398180

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001208
• Start: 5928802
• End: 5940830
• 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_chrII_5940831..5940862
• Length (nt): 32
• Chromosome Location: II: 5940831-5940862
• Organism: Caenorhabditis elegans

180 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	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
	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 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 pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_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 detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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 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 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
	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
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:A-class-motor-neurons_L2-larva_expressed
	Transcripts that showed significantly increased expression in nuo-6(qm200) 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:nuo-6(qm200)_upregulated
	Transcripts that showed significantly increased expression in hda-1[KKRR]-smo-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(ne4748)_upregulated
	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
	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 increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) 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:mep-1(ne4629)_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:hypodermis_L3-L4-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:intestine_L2-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 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 decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated

12 Expression Patterns

• Primary Identifier: Expr1030767
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1019829
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr9769
• Pattern: Widespread GFP expression. GFP was observed in many nuclei in the head, both inside and outside of the pharynx, in different cell types probably including neurons, hypodermis and muscle. In the anterior half of head the GFP showed a diffuse distribution over most of the pharynx as if poorly localized to the nucleus. The GFP becomes tightly nuclear-localized more posteriorly with expression in body wall muscle, intestine, spermathecae and hypodermis, and several neuronal cells in the tail.

• Primary Identifier: Expr13958
• Pattern: egl-44 expression was much more restricted then zag-1, being found only in the FLP, ADL, and SAB neurons, as well as a few VA and VB motor neurons. Moreover, egl-44 was widely expressed in hypodermis, pharynx, and intestine, whereas zag-1 expression was absent in these tissues.

• Primary Identifier: Expr877
• Remark: A C-terminal GFP fusion (EGL-44::GFP) fluoresced in pharyngeal muscle cells and some intestinal nuclei. Because this reporter did not rescue the Egl phenotype, it may not reflect accurately the egl-44 expression pattern. A free C terminus may be important for function, because an N-terminal protein fusion (GFP::EGL-44) partially rescued the Egl phenotype, and authors believe the pattern of fluorescence is more likely to represent the true expression pattern of the gene.
• Pattern: GFP was detected in various nuclei starting from before gastrulation through adulthood. Newly hatched larvae expressed GFP in nuclei of the hypodermis (hyp3, hyp4, hyp6, and hyp7), intestine, pharyngeal muscle cells, and neurons (in the head and in the ventral, retrovesicular, preanal, and lumbar ganglia). In the second larval stage (L2), more hypodermal nuclei fluoresced in the body and the tail. In adults, GFP fluorescence was much fainter in the hypodermal cells and no longer delectable in some neurons in the head and tail. Other neuronal expression and the intestinal expression remained. GFP::EGL-44 was expressed in two cell types, the FLP and HSN cells, whose cell fate is altered in egl-44 mutants. The fluorescence in the FLP cells was maintained from the L1 larval stage through adulthood. In contrast to the FLP cells, which expressed the fusion postembryonically, the HSN neurons fluoresced only embryonically, at the 1.5-fold stage. Authors confirmed the identity of these embryonic HSN cells by noting the absence of this fluorescence in egl-1(n487) mutants, animals in which the HSN neurons die at this time. GFP::EGL-44 expression was not seen in the touch cells.
• Subcellular Localization: nuclei.

• Primary Identifier: Expr9752
• Pattern: Non-nuclear localized GFP was observed in the intestine in all stages and later also in the spermathecae.

• Primary Identifier: Expr9761
• Pattern: Nuclear-localized GFP, from embryo to adult. Lots of cells showed GFP expression in the head. GFP was also observed in the intestine and hypodermis.

• Primary Identifier: Expr2011223
• 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: Expr13959
• 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: Expr1149695
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr11221
• Pattern: egl-44 was expressed throughout the Q cell lineage.

• Primary Identifier: Expr2029459
• 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).

37 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001208
• Start: 5928802
• End: 5940830
• Strand: 1

37 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 12029

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00026952
• WBStrain00027009
• WBStrain00033855
• WBStrain00051997

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_5927313..5928801
• Length (nt): 1489
• Chromosome Location: II: 5927313-5928801
• Organism: Caenorhabditis elegans