WormMine: Gene WBGene00000238

• WormBase Gene ID: WBGene00000238
• Gene Name: bar-1
• Sequence Name: C54D1.6
• Brief Description: bar-1 encodes a beta-catenin; during C. elegans development, BAR-1 likely functions as a transcriptional coactivator whose activity is required for Q neuroblast migration, P12 cell fate specification, and P3.p through P8.p vulval cell fate specification at two different stages of development; in specifying vulval cell fates, bar-1 interacts with Wnt and MAPK signaling pathways to regulate proper expression of the LIN-39 homeodomain transcription factor, overexpresion of which can partially rescue the bar-1 mutant phenotype; in yeast two-hybrid assays, BAR-1 interacts strongly with the POP-1/TCF transcription factor, and when fused to the Gal4 DNA binding domain, BAR-1 can function in yeast as a transcriptional coactivator; during larval development, BAR-1 expression begins in P3.p through P8.p at the late L1 stage and then disappears from these cells by the mid-L3 stage; BAR-1 is also expressed in P12, in the seam cells, and in cells of the somatic gonad; BAR-1 subcellular localization, assessed using an integrated transgene, reveals localization to the cytoplasm, nucleus, and cell junctions; genetic mosaic analyses indicate that, in P4.p and in P12, bar-1 acts cell autonomously to specify cell fates.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II-specific DNA-binding transcription factor binding activity and transcription coactivator activity. Involved in several processes, including nematode larval development; reproductive behavior; and response to stress. Located in several cellular components, including adherens junction; cytosol; and nucleus. Expressed in several structures, including gonad; intestine; and vulva.
• Biotype: SO:0001217
• Genetic Position: X :-1.81008 ±0.003566
• Length (nt): 4621

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000238

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C54D1.6.1	C54D1.6.1	2592	X: 7166005-7170625

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C54D1.6	C54D1.6	2436	X: 7166152-7166387

65 RNAi Result

• WBRNAi00101812
• WBRNAi00101813
• WBRNAi00101386
• WBRNAi00101392
• WBRNAi00101363
• WBRNAi00101365
• WBRNAi00066967
• WBRNAi00066979
• WBRNAi00067124
• WBRNAi00067391
• WBRNAi00067512
• WBRNAi00067581
• WBRNAi00067639
• WBRNAi00067818
• WBRNAi00043132
• WBRNAi00024903
• WBRNAi00008554
• WBRNAi00097720
• WBRNAi00099916
• WBRNAi00071876
• WBRNAi00101459
• WBRNAi00100757
• WBRNAi00099310
• WBRNAi00071621
• WBRNAi00099714
• WBRNAi00101710
• WBRNAi00099512
• WBRNAi00101104
• WBRNAi00088907
• WBRNAi00087089

90 Allele

• gk964260
• WBVar01927133
• gk963778
• gk963873
• gk963874
• WBVar02064659
• gk315567
• gk844478
• gk882255
• gk409899
• gk409900
• gk923361
• gk360423
• gk793920
• gk531223
• gk557421
• gk481729
• gk467985
• gk318402
• gk542013
• gk371652
• gk578691
• gk538364
• gk615207
• gk603759
• gk779388
• gk721003
• gk799978
• gk811190
• gk318403

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000238
• Start: 7166005
• End: 7170625
• 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

138 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 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
	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:bodywall-muscle_L1-larva_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 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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_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
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
	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 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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	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
	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 animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
	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
	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 (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:GABAergic-motor-neurons_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: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

14 Expression Patterns

• Primary Identifier: Expr2009530
• 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: Expr1030152
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr12634
• Pattern: A BAR-1::GFP translational fusion is faintly expressed throughout the body, with highest expression in the posterior gut, consistent with reports that egl-5 also is expressed and functions in the posterior end.

• Primary Identifier: Expr1395
• Pattern: Similar expression patterns were obtained using either the BAR-1 antibodies in immunocytochemistry experiments or by direct observation of the functional BAR-1-GFP. BAR-1 is present in P3.p through P8.p in the late L1/early L2 stage and disappears in the mid-L3 stage before the first divisions of P3.p-P8.p. Did not observe BAR-1 in P1.p, P2.p, P9.p, P10.p or P11.p at this time. P6.p occasionally showed higher BAR-1 expression than the other vulval precursor cells, and was often observed to be the last vulval precursor cell to lose BAR-1 staining. In addition to the vulval precursor cells, BAR-1 is expressed in several other postembryonic cells, including the seam cells , cells in the somatic gonad and P12.
• Subcellular Localization: In the vulval precursor cells, BAR-1 is predominantly cytoplasmic, with some protein present in the nucleus and some at cell junctions.

• Primary Identifier: Expr3089
• Pattern: GFP expression was seen in hypodermal seam cells. This expression began in the mid-L1 stage and was present in all larval stages and the adult. GFP expression was seen in sheath cells of the somatic gonad. Expression was also seen in a subset of ventral cord neurons (VCNs) and in the anchor cell of the gonad that was not previously observed with antibody staining or a BAR-1 translational GFP reporter. Expression is seen in 7 to 15 neurons between the posterior bulb of the pharynx and the anus in L1 animals 1 h after hatching, indicating that some embryonically derived neurons in the ventral cord are expressing bar-1. During the rest of the L1 and L2 stages, the number of GFP-expressing neurons increases to 20 40 per animal. By the L4 stage, the number of ventral cord neurons showing GFP expression anterior to the vulva is 0 9, and posterior to the vulva is 11 24. In regard to vulval development, GFP expression from the transcriptional fusion was first seen in Pn.p cells after their birth in the L1 stage. This expression persisted in the L2 and L3 stages and continued throughout the divisions of the VPCs until the early L4 stage. In the adult, strong GFP expression is confined to the vulval muscles, but faint expression is still seen in adult vulval cells.

• Primary Identifier: Expr12877
• Pattern: An 11-kb regulatory region upstream of the bar-1/b-catenin gene fused to GFP is not expressed in cloacal cells or in the trailing gonad but is strongly expressed in the linker cell.

• Primary Identifier: Expr1021743
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2027767
• 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: Expr12041
• Pattern: BAR-1-GFP expression first appeared in P11.p in the late L1 stage. In the early-to-middle L2 stage, BAR-1-GFP accumulated in the cytoplasm of P11.p in a punctate pattern, presumably resulting from the stabilization of BAR-1 in response to increased Wnt signaling. The punctate GFP fluorescence in the cytoplasm of P11. p rapidly decreased during the mid-to-late L2 stage. By the mid-L3 stage, just before P11.p divides, BAR-1-GFP expression appeared to be brighter in the nucleus than in the cytoplasm. The switch of cytoplasmic-to-nuclear BAR-1-GFP accumulation is initiated in the mid-to-late L2 stage, coincident with the time window critical for the specification of HCG cell fates. BAR-1-GFP expression was undetectable in P10.p prior to cell division but became visible in the nucleus of the posterior daughter, P10.pp, suggesting that Wnt signaling through BAR-1 likely acts during fate execution of some descendants of the P10.p lineage. Although we did not observe lin-17::GFP expression in P9.p, faint, mostly cytoplasmic expression of BAR-1-GFP was sometimes seen in P9.p up to the mid-L2 stage, just before P9.p fuses with hyp7.

• Primary Identifier: Expr12038
• Pattern: BAR-1-GFP expression first appeared in P11.p in the late L1 stage. In the early-to-middle L2 stage, BAR-1-GFP accumulated in the cytoplasm of P11.p in a punctate pattern, presumably resulting from the stabilization of BAR-1 in response to increased Wnt signaling. The punctate GFP fluorescence in the cytoplasm of P11. p rapidly decreased during the mid-to-late L2 stage. By the mid-L3 stage, just before P11.p divides, BAR-1-GFP expression appeared to be brighter in the nucleus than in the cytoplasm. The switch of cytoplasmic-to-nuclear BAR-1-GFP accumulation is initiated in the mid-to-late L2 stage, coincident with the time window critical for the specification of HCG cell fates. BAR-1-GFP expression was undetectable in P10.p prior to cell division but became visible in the nucleus of the posterior daughter, P10.pp, suggesting that Wnt signaling through BAR-1 likely acts during fate execution of some descendants of the P10.p lineage. Although we did not observe lin-17::GFP expression in P9.p, faint, mostly cytoplasmic expression of BAR-1-GFP was sometimes seen in P9.p up to the mid-L2 stage, just before P9.p fuses with hyp7.

• Primary Identifier: Expr12039
• Pattern: BAR-1-GFP expression first appeared in P11.p in the late L1 stage. In the early-to-middle L2 stage, BAR-1-GFP accumulated in the cytoplasm of P11.p in a punctate pattern, presumably resulting from the stabilization of BAR-1 in response to increased Wnt signaling. The punctate GFP fluorescence in the cytoplasm of P11. p rapidly decreased during the mid-to-late L2 stage. By the mid-L3 stage, just before P11.p divides, BAR-1-GFP expression appeared to be brighter in the nucleus than in the cytoplasm. The switch of cytoplasmic-to-nuclear BAR-1-GFP accumulation is initiated in the mid-to-late L2 stage, coincident with the time window critical for the specification of HCG cell fates. BAR-1-GFP expression was undetectable in P10.p prior to cell division but became visible in the nucleus of the posterior daughter, P10.pp, suggesting that Wnt signaling through BAR-1 likely acts during fate execution of some descendants of the P10.p lineage. Although we did not observe lin-17::GFP expression in P9.p, faint, mostly cytoplasmic expression of BAR-1-GFP was sometimes seen in P9.p up to the mid-L2 stage, just before P9.p fuses with hyp7.

• Primary Identifier: Expr12045
• Pattern: BAR-1-GFP expression first appeared in P11.p in the late L1 stage. In the early-to-middle L2 stage, BAR-1-GFP accumulated in the cytoplasm of P11.p in a punctate pattern, presumably resulting from the stabilization of BAR-1 in response to increased Wnt signaling. The punctate GFP fluorescence in the cytoplasm of P11. p rapidly decreased during the mid-to-late L2 stage. By the mid-L3 stage, just before P11.p divides, BAR-1-GFP expression appeared to be brighter in the nucleus than in the cytoplasm. The switch of cytoplasmic-to-nuclear BAR-1-GFP accumulation is initiated in the mid-to-late L2 stage, coincident with the time window critical for the specification of HCG cell fates. BAR-1-GFP expression was undetectable in P10.p prior to cell division but became visible in the nucleus of the posterior daughter, P10.pp, suggesting that Wnt signaling through BAR-1 likely acts during fate execution of some descendants of the P10.p lineage. Although we did not observe lin-17::GFP expression in P9.p, faint, mostly cytoplasmic expression of BAR-1-GFP was sometimes seen in P9.p up to the mid-L2 stage, just before P9.p fuses with hyp7.

• Primary Identifier: Expr12040
• Pattern: BAR-1-GFP expression first appeared in P11.p in the late L1 stage. In the early-to-middle L2 stage, BAR-1-GFP accumulated in the cytoplasm of P11.p in a punctate pattern, presumably resulting from the stabilization of BAR-1 in response to increased Wnt signaling. The punctate GFP fluorescence in the cytoplasm of P11. p rapidly decreased during the mid-to-late L2 stage. By the mid-L3 stage, just before P11.p divides, BAR-1-GFP expression appeared to be brighter in the nucleus than in the cytoplasm. The switch of cytoplasmic-to-nuclear BAR-1-GFP accumulation is initiated in the mid-to-late L2 stage, coincident with the time window critical for the specification of HCG cell fates. BAR-1-GFP expression was undetectable in P10.p prior to cell division but became visible in the nucleus of the posterior daughter, P10.pp, suggesting that Wnt signaling through BAR-1 likely acts during fate execution of some descendants of the P10.p lineage. Although we did not observe lin-17::GFP expression in P9.p, faint, mostly cytoplasmic expression of BAR-1-GFP was sometimes seen in P9.p up to the mid-L2 stage, just before P9.p fuses with hyp7.

• Primary Identifier: Expr1147100
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

80 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000238
• Start: 7166005
• End: 7170625
• Strand: -1

80 Ontology Annotations

7 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes that showed increased expression in bar-1(ga80) animal comparing to in N2.	All statistical analyses were performed using the statistical programming language R (version 2.13.1 x 64). A linear model was used to determine the effect and significance of the genotype on the expression levels (probe intensity + genotype + error). Using permutations of the original data in the same linear model, authors determined thresholds adjusted for multiple testing (FDR 0.05: -log10(p) > 2; FDR 0.01: -log10(p) > 3). To correct for the developmental difference between bar-1(ga80) and N2 authors used the developmental gene expression data from Snoek et al. (2014) together with the gene expression data generated for this study (bar-1(ga80) vs. N2) in one linear model (probe intensity, sample age + genotype + error). The intensities were corrected for batch effect and for sample age authors used an age of 44 hours for the bar-1(ga80) samples (as estimated), and 48 hours for the N2 samples.	WBPaper00045257:bar-1(ga80)_upregulated
	Genes that showed decreased expression in bar-1(ga80) animal comparing to in N2.	All statistical analyses were performed using the statistical programming language R (version 2.13.1 x 64). A linear model was used to determine the effect and significance of the genotype on the expression levels (probe intensity + genotype + error). Using permutations of the original data in the same linear model, authors determined thresholds adjusted for multiple testing (FDR 0.05: -log10(p) > 2; FDR 0.01: -log10(p) > 3). To correct for the developmental difference between bar-1(ga80) and N2 authors used the developmental gene expression data from Snoek et al. (2014) together with the gene expression data generated for this study (bar-1(ga80) vs. N2) in one linear model (probe intensity, sample age + genotype + error). The intensities were corrected for batch effect and for sample age authors used an age of 44 hours for the bar-1(ga80) samples (as estimated), and 48 hours for the N2 samples.	WBPaper00045257:bar-1(ga80)_downregulated
	Genes that were considered as putative WNT pathway targets because they have higher expression in WNT overactivated (by delNTbar-1 overexpression in huIs10) animals comparing to in N2.	Genes that were considered as putative WNT pathway targets based on the following criteria. (1) an average fold change of 1.5-fold or more in deIs10; huIs1 (Wnt pathway overactivation) compared to control (N2); (2) present and increased calls in at least two of three biological replicates; (3) ANOVA P <=0.05; and (4) ratio of average fold change >= 1.5-fold between Wnt pathway overactivated (deIs10; huIs1) and underactivated (deIs10; deIs26) conditions.	WBPaper00046887:WNT-target
	Genes showing a statistically-significant decrease in gene expression of 2 fold or greater in response to expre ssion of delNTBAR-1 protein.	Criteria used for selection of BAR-1 responsive gene targets were (1) at least a twofold change in signal response to (del)NTBAR-1 overexpression compared with control average, (2) concurrence in directional change for at least two of the three (del)NTBAR-1 induced replicates (e.g., increase or decrease of signal), and (3) an analysis of variance p-value of <=0.05.	WBPaper00044857:BAR-1_downregulated
	Transcripts that showed significantly increased expression in Q neuroblast descendant cells expressing a constitutively active, N terminally truncated form of BAR-1 (beta-catenin) (del-N-BAR-1 Q) (huIs179).	Differential gene expression analysis was done with DESeq2 R-package using an FDR based on adjusted P < 0.05. (The threshold was reset from FDR < 0.1 to FDR < 0.05 by WormBase curator.)	WBPaper00061210:huIs179_upregulated
	Genes showing a statistically-significant increase in gene expression of 2 fold or greater in response to expre ssion of delNTBAR-1 protein.	Criteria used for selection of BAR-1 responsive gene targets were (1) at least a twofold change in signal response to (del)NTBAR-1 overexpression compared with control average, (2) concurrence in directional change for at least two of the three (del)NTBAR-1 induced replicates (e.g., increase or decrease of signal), and (3) an analysis of variance p-value of <=0.05.	WBPaper00044857:BAR-1_upregulated
	Transcripts that showed significantly decreased expression in Q neuroblast descendant cells expressing a constitutively active, N terminally truncated form of BAR-1 (beta-catenin) (del-N-BAR-1 Q) (huIs179).	Differential gene expression analysis was done with DESeq2 R-package using an FDR based on adjusted P < 0.05. (The threshold was reset from FDR < 0.1 to FDR < 0.05 by WormBase curator.)	WBPaper00061210:huIs179_downregulated

1 Sequence

• Length: 4621

1 Sequence Ontology Term

• Name: gene

8 Strains

• WBStrain00023612
• WBStrain00034113
• WBStrain00034116
• WBStrain00034115
• WBStrain00004839
• WBStrain00004823
• WBStrain00007434
• WBStrain00004838

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_7170626..7170851
• Length (nt): 226
• Chromosome Location: X: 7170626-7170851
• Organism: Caenorhabditis elegans