WormMine: Gene WBGene00002245

• WormBase Gene ID: WBGene00002245
• Gene Name: lag-1
• Sequence Name: K08B4.1
• Brief Description: lag-1 encodes a transcription factor orthologous to members of the CSL (CBF1, Suppressor of Hairless, LAG-1) family that is highly conserved amongst metazoans; during development, LAG-1 functions as a downstream effector in both the lin-12- and glp-1-mediated Notch-like signaling pathways and accordingly, is required for such processes as germline induction, AC/VU lateral signaling, and embryonic development; LAG-1 can bind a consensus CSL family binding site found in multiple copies in the predicted regulatory regions of lin-12, glp-1, and lag-1, thus implicating LAG-1 as an important component of the positive feedback loop observed in the LIN-12/GLP-1 signaling pathway.
• Organism: Caenorhabditis elegans
• Automated Description: Enables Notch binding activity; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and transcription coactivator binding activity. Involved in several processes, including cell differentiation; dauer exit; and regulation of DNA-templated transcription. Located in nucleus. Part of RNA polymerase II transcription regulator complex and chromatin. Expressed in several structures, including P4.p; P5.p; P6.p; P7.p; and P8.p. Human ortholog(s) of this gene implicated in Adams-Oliver syndrome and dilated cardiomyopathy. Is an ortholog of human RBPJ (recombination signal binding protein for immunoglobulin kappa J region).
• Biotype: SO:0001217
• Genetic Position: IV :2.97979 ±0.005015
• Length (nt): 15249

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002245

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K08B4.1b.1	K08B4.1b.1	2552	IV: 6095407-6110641
Transcript:K08B4.1a.1	K08B4.1a.1	2572	IV: 6095407-6110655
Transcript:K08B4.1d.1	K08B4.1d.1	4541	IV: 6101512-6110641
Transcript:K08B4.1c.1	K08B4.1c.1	1884	IV: 6101519-6110114

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K08B4.1c	K08B4.1c	1884	IV: 6101519-6101587
CDS:K08B4.1a	K08B4.1a	2022	IV: 6095416-6095504
CDS:K08B4.1b	K08B4.1b	2016	IV: 6095416-6095504
CDS:K08B4.1d	K08B4.1d	2373	IV: 6104337-6105099

83 RNAi Result

• WBRNAi00114292
• WBRNAi00114057
• WBRNAi00114136
• WBRNAi00114215
• WBRNAi00106568
• WBRNAi00106589
• WBRNAi00081743
• WBRNAi00081742
• WBRNAi00081744
• WBRNAi00081747
• WBRNAi00110326
• WBRNAi00066972
• WBRNAi00067042
• WBRNAi00067092
• WBRNAi00067139
• WBRNAi00067286
• WBRNAi00067335
• WBRNAi00067358
• WBRNAi00067465
• WBRNAi00067611
• WBRNAi00067648
• WBRNAi00050226
• WBRNAi00008970
• WBRNAi00066906
• WBRNAi00078881
• WBRNAi00112332
• WBRNAi00027675
• WBRNAi00022788
• WBRNAi00068427
• WBRNAi00068426

226 Allele

• otn10002
• gk964500
• gk963722
• gk963417
• gk963375
• gk963416
• q358
• q386
• q385
• q410
• q416
• q418
• q426
• q476
• WBVar02068717
• WBVar02020657
• WBVar02020656
• WBVar02020655
• WBVar01650006
• WBVar01650007
• WBVar00189300
• WBVar00189301
• WBVar00189302
• WBVar00189303
• WBVar00189304
• WBVar00189305
• WBVar00189306
• WBVar00189307
• WBVar00189295
• WBVar00189296

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002245
• Start: 6095407
• End: 6110655
• 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

167 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 food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
	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 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 old adults stage (214 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_aging
	Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 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_aging
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	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
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	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
	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
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated

8 Expression Patterns

• Primary Identifier: Expr1031319
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr16001
• Pattern: At L1, mNeonGreen expression is observed in several neurons in the head including ADF neuron. Strong LAG-1 expression in ADF neuron is maintained at all larval stages and throughout the life of the animal.

• Primary Identifier: Expr1153920
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr10711
• Pattern: lag-1::YFP is expressed in the pre-AC/pre-VU cells before specification. It is also expressed in VU cells, but not the AC, after specification.

• Primary Identifier: Expr2013004
• 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: Expr15941
• Pattern: LAG-1::mKate2, revealed a dynamic expression pattern in the VPCs during vulval induction. In order to achieve a more quantitative analysis, and potentially reveal more subtle dynamics, we quantitated LAG-1::GFP fluorescence, as GFP appeared brighter overall than mKate2. We observed that both LAG-1::GFP and LAG-1::mKate2 accumulated to a higher level in P5.p and P7.p compared with other VPCs (secondary fate pattern). This accumulation pattern is consistent with LIN-12 activation in the VPCs and suggests a positive feedback mechanism.

• Primary Identifier: Expr1022836
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031236
• 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).

48 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002245
• Start: 6095407
• End: 6110655
• Strand: 1

48 Ontology Annotations

8 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts activated by lag-1(oz536oz537), in the gld-2(q497)gld-1(q485); glp-1(ar202) background at young adult stage after 48 hours of 1mM auxin treatment.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_activated_48hr-auxin
	Transcripts interacting with LAG-1 at L4 larva stage in germline ChIP-Seq analysis.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_interacting_germline
	Transcripts interacting with LAG-1 at L4 larva stage in whole animal ChIP-Seq analysis.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_interacting_WholeAnimal
	Transcripts activated by lag-1(oz536oz537), in the gld-2(q497)gld-1(q485); glp-1(ar202) background at young adult stage after 2 hours of 1mM auxin treatment.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_activated_2hr-auxin
	Transcripts activated by lag-1(oz536oz537), in the gld-2(q497)gld-1(q485); glp-1(ar202) background at young adult stage after 4 hours of 1mM auxin treatment.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_activated_4hr-auxin
	Transcripts repressed by lag-1(oz536oz537), in the gld-2(q497)gld-1(q485); glp-1(ar202) background at young adult stage after 2 hours of 1mM auxin treatment. No gene was found.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_repressed_2hr-auxin
	Transcripts repressed by lag-1(oz536oz537), in the gld-2(q497)gld-1(q485); glp-1(ar202) background at young adult stage after 4 hours of 1mM auxin treatment.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_repressed_4hr-auxin
	Transcripts repressed by lag-1(oz536oz537), in the gld-2(q497)gld-1(q485); glp-1(ar202) background at young adult stage after 48 hours of 1mM auxin treatment.	edgeR fold change >= 2, FDR <= 0.05.	WBPaper00059440:LAG-1_repressed_48hr-auxin

1 Sequence

• Length: 15249

1 Sequence Ontology Term

• Name: gene

10 Strains

• WBStrain00022545
• WBStrain00022552
• WBStrain00030024
• WBStrain00034581
• WBStrain00051949
• WBStrain00051599
• WBStrain00051810
• WBStrain00052019
• WBStrain00054794
• WBStrain00007146

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_6094072..6095406
• Length (nt): 1335
• Chromosome Location: IV: 6094072-6095406
• Organism: Caenorhabditis elegans