WormMine: Gene WBGene00007732

• WormBase Gene ID: WBGene00007732
• Gene Name: spe-44
• Sequence Name: C25G4.4
• Brief Description: spe-44 encodes a SAND (for Sp100, Aire, NucP41/75, DEAF-1) domain-containing protein that is one of four C. elegans proteins related to the mammalian glucocorticoid modulatory element-binding proteins GMEB-1 and GMEB-2; SPE-44 is one of the earliest markers of sperm fate and its activity is essential for regulation of sperm-specific genes during spermatogenesis; microarray analyses indicate the SPE-44 is required for expression of a number of sperm-specific genes, including those that encode the Major Sperm Proteins (MSPs), members of the small sperm-specific protein family, other SPE proteins such as SPE-7, and the ELT-1 GATA transcription factor; when expressed in yeast, SPE-44 can directly activate transcription of a lacZ reporter gene containing the spe-7 promoter region; spe-44 expression coincides with commitment to the sperm fate at the L3 larval stage, and persists throughout spermatogenesis in hermaphrodites and males; SPE-44 protein is first detected in the early meiotic zone, co-localizes with meiotic autosomes in the pachytene region, and becomes non-chromosomal before disappearing in karyosome stage nuclei; spe-44 expression is controlled by terminal regulators of the germline sex determination pathway, such as fem-1, fem-3, and fog-1.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific. Involved in positive regulation of transcription by RNA polymerase II and spermatogenesis. Located in autosome. Expressed in germ line; sperm; and in male. Is an ortholog of human GMEB1 (glucocorticoid modulatory element binding protein 1) and GMEB2 (glucocorticoid modulatory element binding protein 2).
• Biotype: SO:0001217
• Genetic Position: IV :5.96572 ±0.006805
• Length (nt): 2153

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00007732

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C25G4.4.1	C25G4.4.1	1631	IV: 12452063-12454215

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C25G4.4	C25G4.4	1275	IV: 12452285-12452715

4 RNAi Result

• WBRNAi00041213
• WBRNAi00011180
• WBRNAi00076159
• WBRNAi00029204

35 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk964475
• ok1400
• WBVar00192525
• WBVar00192523
• WBVar00192524
• fx110
• WBVar01454583
• WBVar01859651
• WBVar01569898
• WBVar01954059
• gk214633
• gk214634
• gk214631
• gk214632
• gk214629
• gk214630
• gk214627
• gk214628
• cxTi5803
• gk382651
• gk552172
• gk767178
• gk583100
• gk920932
• gk557765
• gk515003

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00007732
• Start: 12452063
• End: 12454215
• 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_chrIV_12451336..12452062
• Length (nt): 727
• Chromosome Location: IV: 12451336-12452062
• Organism: Caenorhabditis elegans

133 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
	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
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	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_SM
	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 dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_downregulated
	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
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 48 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_48h_downregulated
	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:coelomocytes_L2-larva_expressed
	Transcripts that were regulated by both set-6(ok2195) and baz-2(tm0235) at 2-day post L4 adult hermaphrodite stage.	N.A.	WBPaper00059356:set-6(ok2195)_baz-2(tm0235)_regulated
	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:glr-1(+)-neurons_L2-larva_expressed
	Transcripts that showed significantly decreased expression in rbr-2(tm3141) comparing to in N2 animals.	Mapped reads were analyzed for transcript assembly and differential expression using Cufflinks 2.1.1 with a filter of twofold difference and FDR correction (P < 0.05).	WBPaper00050080:rbr-2(tm3141)_downregulated
	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
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:hda-1(RNAi)_upregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
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
	Genes that show significant variation due to strain by stage interaction.	An analysis of variance (one-way ANOVA) test was used to see which genes changed significantly over developmental time, using the strain and stage of each array as the parameters. qvalue, an R-package, was used to obtain false-discovery rates (FDR). Significant genes have an FDR of less than .05.	WBPaper00032479:CB4856vsN2_LifeStageProfile_Variation
	Genes with significant increase of expression in UPF1 smg-2(RNAi) comparing to control.	Bioconductor package LIMMA was used to determine differentially expressed genes. The P-values were adjusted for multiple testing with a false-discovery rate (50). Probe sets with fold-change > 1.5 and q-value < 0.05 were used as a cut-off for C. elegans microarrays	WBPaper00042561:smg-2(RNAi)_upregulated
	Top 300 transcripts enriched in ABalppppapa, ABpraaapapa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:OLL_parent

9 Expression Patterns

• Primary Identifier: Expr2034277
• 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: Expr1033347
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1200179
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr10041
• Pattern: In situ hybridizations of dissected gonads were performed to ascertain the precise spatial pattern of spe-44 expression. The fem- 3(gf) and fem-1(lf) mutations were used to restrict hermaphrodite gametogenesis to sperm or oocyte production, respectively. Abundant expression was first detected in fem-3(gf) animals during the L3 stage in the early meiotic germline. DAPI staining of the chromatin indicated that expression coincides with early pachytene of meiosis I. By contrast, spe-44 expression was undetectable in fem-1(lf) germlines at any stage of development. Thus, spe-44 expression is restricted to the sperm-producing germline at a time and place consistent with the regulation of sperm gene expression.

• Primary Identifier: Expr11705
• Pattern: Expression of spe-44 was first detected with quantitative RT-PCR in age-synchronized populations of wild-type hermaphrodites at the L3 larval stage, when gametes become committed to the sperm cell fate. Transcript levels of spe-44 declined through the L4 and adult stages, when gametogenesis switches from sperm to oocyte production. In wild-type L4 and adult males, which produce sperm continuously, spe-44 expression levels were higher than in hermaphrodites at the same stages. Peak expression is observed during L3 at the onset of sperm fate specification.

• Primary Identifier: Expr11706
• Subcellular Localization: Temporally, SPE-44 labeling was first detectable in L3 male germlines and persisted through adulthood. Spatially, SPE-44 labeling was absent in the distal stem cell niche and mitotic zone, initiated in the early meiotic zone, colocalized with chromosomes in the pachytene region, and became non-chromosomal before disappearing altogether in karyosome stage nuclei. Closer examination revealed that SPE-44 localized along the length of most but not all of the pachytene chromosomes. The unpaired X chromosome was a likely candidate for SPE-44 exclusion: X is singularly devoid of sperm genes, and contains chromatin modifications consistent with transcriptional silencing. SPE-44 is localized to autosomes (which contain sperm genes) but not X (which does not), consistent with a role as an early acting and positive regulator of sperm gene transcription. SPE-44 exhibits the properties predicted for a regulator of sperm gene expression: the protein appears at the onset of sperm fate specification prior to the production of sperm proteins, is bound to the chromatin of committed and developing spermatocytes, and disappears in the karyosome stage coincident with the global cessation of transcription. Labeling of SPE-44 in hermaphrodite gonads likewise correlates with sperm production. The protein is first detectable in L3 at the time of sperm fate specification and in young L4 hermaphrodites undergoing spermatogenesis, but is absent in adult hermaphrodites that are undergoing oogenesis.

• Primary Identifier: Expr2016042
• 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: Expr1014891
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1145249
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

13 GO Annotation

7 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00007732
• Start: 12452063
• End: 12454215
• Strand: -1

13 Ontology Annotations

6 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with significantly decreased expression in spe-44(ok1400) comparing to N2.	Microarray data were analyzed by Microarray Suite 5.0 (Affymetrix) and Genomics Suite (Partek) software, using a p-value threshold of 0.05 for differential expression.	WBPaper00041071:spe-44_downregulated
	Transcripts that showed significantly increased expression in spe-44(fx110) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:spe-44(fx110)_upregulated
	Transcripts that showed significantly decreased expression in nhr-23(kry61);spe-44(fx110) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:nhr-23(kry61);spe-44(fx110)_downregulated
	Transcripts that showed significantly increased expression in nhr-23(kry61);spe-44(fx110) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:nhr-23(kry61);spe-44(fx110)_upregulated
	Transcripts that showed significantly decreased expression in spe-44(fx110) comparing to in control male animals.	DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.	WBPaper00064502:spe-44(fx110)_downregulated
	Genes with significantly increased expression in spe-44(ok1400) comparing to N2.	Microarray data were analyzed by Microarray Suite 5.0 (Affymetrix) and Genomics Suite (Partek) software, using a p-value threshold of 0.05 for differential expression.	WBPaper00041071:spe-44_upregulated

1 Sequence

• Length: 2153

1 Sequence Ontology Term

• Name: gene

8 Strains

• WBStrain00031119
• WBStrain00031120
• WBStrain00033484
• WBStrain00033487
• WBStrain00034724
• WBStrain00036311
• WBStrain00051870
• WBStrain00051868

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_12454216..12455049
• Length (nt): 834
• Chromosome Location: IV: 12454216-12455049
• Organism: Caenorhabditis elegans