WormMine: Gene WBGene00001061

• WormBase Gene ID: WBGene00001061
• Gene Name: dpl-1
• Sequence Name: T23G7.1
• Brief Description: dpl-1 encodes the C. elegans ortholog of mammalian DP, the E2F-heterodimerization partner; dpl-1 is a class B synMuv gene whose activity is required for oogenesis as well as embryonic asymmetry and vulval development; in addition, dpl-1 acts with a subset of class B synMuv genes and the MCD-1 zinc-finger protein to promote the killing process during programmed cell death; DPL-1 is a nuclear protein that is widely expressed throughout development in both somatic and germ cell lineages.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in several processes, including gonad development; negative regulation of Ras protein signal transduction; and negative regulation of vulval development. Located in nucleus. Expressed in germ line; gonad; and hyp7 syncytium. Human ortholog(s) of this gene implicated in mismatch repair cancer syndrome. Is an ortholog of human TFDP1 (transcription factor Dp-1); TFDP2 (transcription factor Dp-2); and TFDP3 (transcription factor Dp family member 3).
• Biotype: SO:0001217
• Genetic Position: II :1.08207 ±0.005888
• Length (nt): 2656

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001061

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T23G7.1.1	T23G7.1.1	2198	II: 9169910-9172565
Transcript:T23G7.1.2	T23G7.1.2	2196	II: 9169910-9172563

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T23G7.1	T23G7.1	1797	II: 9169957-9169965

19 RNAi Result

• WBRNAi00076033
• WBRNAi00115776
• WBRNAi00053981
• WBRNAi00008156
• WBRNAi00053980
• WBRNAi00078813
• WBRNAi00106667
• WBRNAi00019108
• WBRNAi00075705
• WBRNAi00076032
• WBRNAi00035891
• WBRNAi00086555
• WBRNAi00111696
• WBRNAi00062980
• WBRNAi00062981
• WBRNAi00084459
• WBRNAi00086705
• WBRNAi00115246
• WBRNAi00115242

41 Allele

• gk963801
• gk963053
• gk962682
• gk962798
• WBVar01604415
• bs21
• n3316
• n3319
• WBVar01393947
• WBVar02002904
• n3380
• bs169
• n2994
• gk325158
• gk550929
• zu355
• sam13
• gk907016
• gk531422
• gk559590
• gk680868
• gk446673
• gk533243
• gk393617
• gk685
• WBVar00174497
• WBVar00174498
• WBVar00174495
• WBVar01720457
• WBVar00174496

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001061
• Start: 9169910
• End: 9172565
• 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

125 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 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
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	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
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
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
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_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
	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
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
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)
Bacteria: B.thuringiensis	Transcripts in N2 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_N2
	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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated
	Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_upregulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes

10 Expression Patterns

• Primary Identifier: Expr1030671
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1200005
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr882
• Pattern: In wild-type animals, DPL-1 protein was expressed in most and perhaps all cells throughout development and was localized to nuclei. The P(3-8).p nuclei and nuclei of the hypodermal syncytium, hyp7, both expressed DPL-1. DPL-1 was also present in the descendants of P3.p to P8.p. In addition to somatic nuclei, immature germ cell and oocyte nuclei were also sites of strong DPL-1 expression. In wild-type animals, DPL-1 protein was expressed in most and perhaps all cells throughout development and was localized to nuclei. The P(38).p nuclei and nuclei of the hypodermal syncytium, hyp7, both expressed DPL-1. DPL-1 was also present in the descendants of P3.p to P8.p. In addition to somatic nuclei, immature germ cell and oocyte nuclei were also sites of strong DPL-1 expression.
• Subcellular Localization: nuclei

• Primary Identifier: Expr10271
• Pattern: Inferred expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/

• Primary Identifier: Expr4030
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Broadly expressed in gonad.

• Primary Identifier: Expr2011050
• 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: Expr1025828
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029287
• 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: Expr1200124
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr1157526
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

24 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001061
• Start: 9169910
• End: 9172565
• Strand: 1

24 Ontology Annotations

6 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes whose expression is either up- or downregulated in efl-1, dpl-1 or lin-35 mutants relative to controls.	For each set of mutant data, the repeats were averaged, and a Z test [Z=(observedexpected)\/SE] was performed in Excel. A moderate correction for multiple testing (~17,600 genes) was performed by multiplying the calculated P-value by 10,000. After this correction, all genes with up- or downregulation greater than twofold, P<0.05 in any given mutant were selected. The hypergeometric probability test was used to calculate the significance of overlap of gene groups. Authors determined whether transcripts of Group I-IV genes are bound by GLD-1, based on a minimum criteria of >1.5 enrichment in GLD-1 immunoprecipitated samples compared to control immunoprecipitations (P < 0.01).	WBPaper00027758:Regulated_genes_not_in_group
	Genes with lower expression in efl-1, dpl-1 and lin-35 mutants than in control gonads.	For each set of mutant data, the repeats were averaged, and a Z test [Z=(observedexpected)\/SE] was performed in Excel. A moderate correction for multiple testing (~17,600 genes) was performed by multiplying the calculated P-value by 10,000. After this correction, all genes with up- or downregulation greater than twofold, P<0.05 in any given mutant were selected. The hypergeometric probability test was used to calculate the significance of overlap of gene groups. Authors determined whether transcripts of Group I-IV genes are bound by GLD-1, based on a minimum criteria of >1.5 enrichment in GLD-1 immunoprecipitated samples compared to control immunoprecipitations (P < 0.01).	WBPaper00027758:Group_II
	Transcripts that showed significantly decreased expression in dpl-1(n2994) comparing to in N2 animals at starved L1 larva stage.	A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.	WBPaper00062056:dpl-1(n2994)_downregulated
	Transcripts that showed significantly increased expression in dpl-1(n2994) comparing to in N2 animals at starved L1 larva stage.	A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.	WBPaper00062056:dpl-1(n2994)_upregulated
	Genes with higher expression in one or more mutants of efl-1, dpl-1 and lin-35 relative to controls.	For each set of mutant data, the repeats were averaged, and a Z test [Z=(observedexpected)\/SE] was performed in Excel. A moderate correction for multiple testing (~17,600 genes) was performed by multiplying the calculated P-value by 10,000. After this correction, all genes with up- or downregulation greater than twofold, P<0.05 in any given mutant were selected. The hypergeometric probability test was used to calculate the significance of overlap of gene groups. Authors determined whether transcripts of Group I-IV genes are bound by GLD-1, based on a minimum criteria of >1.5 enrichment in GLD-1 immunoprecipitated samples compared to control immunoprecipitations (P < 0.01).	WBPaper00027758:Group_III
	Genes downregulated in dpl-1(n3316) and efl-1(n3639) mutants.	For each set of mutant data, the repeats were averaged, and a Z test [Z=(observedexpected)\/SE] was performed in Excel. A moderate correction for multiple testing (~17,600 genes) was performed by multiplying the calculated P-value by 10,000. After this correction, all genes with up- or downregulation greater than twofold, P<0.05 in any given mutant were selected. The hypergeometric probability test was used to calculate the significance of overlap of gene groups. Authors determined whether transcripts of Group I-IV genes are bound by GLD-1, based on a minimum criteria of >1.5 enrichment in GLD-1 immunoprecipitated samples compared to control immunoprecipitations (P < 0.01).	WBPaper00027758:Group_I

1 Sequence

• Length: 2656

1 Sequence Ontology Term