WormMine: Gene WBGene00004011

• WormBase Gene ID: WBGene00004011
• Gene Name: pha-2
• Sequence Name: M6.3
• Brief Description: pha-2 encodes a homeodomain protein that is orthologous to vertebrate Hex proteins required for the development of B lymphocytes and organs derived from foregut endoderm; in C. elegans, pha-2 is essential for proper development and morphogenesis of the pm5 pharyngeal muscles cells during late stages of embryogenesis; in regulating pm5 fate specification, PHA-2 appears to act downstream of the organ identity factor PHA-4, and upstream of ceh-22, whose expression it may negatively regulate in pm5; a rescuing PHA-2::GFP reporter is expressed in pharyngeal cells, intestinal-rectal cells, and postembryonic head neurons.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including eating behavior; muscle structure development; and nematode pharyngeal gland morphogenesis. Located in nucleus. Expressed in head neurons; intestine; pharynx; and rectal gland cell. Is an ortholog of human HHEX (hematopoietically expressed homeobox).
• Biotype: SO:0001217
• Genetic Position: X :-19.5325 ±0.007965
• Length (nt): 3626

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004011

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:M6.3.1	M6.3.1	1109	X: 633368-636993

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:M6.3	M6.3	645	X: 633719-633862

2 RNAi Result

• WBRNAi00095212
• WBRNAi00051034

62 Allele

• gk963652
• gk963725
• WBVar02063464
• WBVar01690006
• WBVar01690008
• WBVar01690007
• WBVar01600336
• WBVar01600337
• WBVar00074364
• WBVar00074367
• WBVar00074366
• WBVar00074365
• WBVar01979039
• WBVar01979040
• gk485765
• gk361205
• gk812694
• gk640713
• gk522530
• gk549967
• gk555892
• gk526130
• gk898069
• gk608132
• gk603731
• gk596915
• gk702159
• gk507111
• gk600170
• gk723881

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004011
• Start: 633368
• End: 636993
• 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_chrX_632869..633367
• Length (nt): 499
• Chromosome Location: X: 632869-633367
• Organism: Caenorhabditis elegans

60 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
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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Coexpression clique No. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:sre-33-ZK1025.1_8337
	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
	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
	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 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 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 that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly decreased 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)_downregulated
Starvation	Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl)	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:starvation_regulated_LowSalt
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:S.marcescens_24hr_upregulated_TilingArray
	Transcripts that showed significantly increased expression in animals fed with JM103 bacteria producing Cry5B, comparing to control animals fed with JM103.	ANOVA, p-value < 0.05.	WBPaper00056167:Cry5B_upregulated
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
	Transcripts that showed significantly increased expression in dpy-7(e88) animals comparing to N2 animals.	Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.	WBPaper00053771:up_at_dpy-7(e88)
	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:intestine_L1-larva_expressed
	Transcripts that showed significantly decreased expression in 100-cell stage embryo of let-418(RNAi) animals, comparing to in control RNAi (with gfp control vector) animals.	DESeq and EdgeR were used. A threshold of 1.5 log2 fold change and a p value <10 % were applied. let-418: wild-type; let-418(RNAi)-treated embryos; chd-3: chd-3(eh4);controlGFP(RNAi)-treated embryos; chd-3_let-418: chd-3(eh4); let-418(RNAi)-treated embryos. All fold changes are calculated versus wild-type;control(RNAi)-treated embryos. 1h and 3h correspond to the 24- and 100-cell stages, respectively.	WBPaper00050163:let-418(RNAi)_downregulated_100-cell-embryo
	Transcripts that showed differential expression in dauer mir-34(gk437) vs dauer mir-34(OverExpression) animals at 20C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_dauer_20C
	Transcripts that showed differential expression in dauer N2 vs dauer mir-34(gk437) animals at 20C.	N.A.	WBPaper00050488:N2_vs_mir-34(gk437)_regulated_dauer_20C
	Genes that showed flat mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:flat_dev_expression
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly increased 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_upregulated_hpx-2(dg047)
Bacteria: B.subtilis	Transcripts that showed significantly increased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult.	edgeR 3.16.5, FDR < 0.05, fold change > 2.	WBPaper00059117:B.subtilis_upregulated

13 Expression Patterns

• Primary Identifier: Expr1031919
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3093
• Pattern: In larvae and adults, expression is observed in several cells of the head that likely correspond to extrapharyngeal neurons, including at least two amphid neurons, and also in intestinal cells (mostly the posterior cells) as well as the three rectal gland cells and 1 to 2 other unidentified rectal cells. In larvae and adult worms, very weak pharyngeal expression of pPHA-2::GFP-A persists in nuclei of the posterior bulb, metacorpus, and procorpus. While the pm4 and pm5 muscle cells were identified as positive nuclei in these transgenic animals, it was often difficult to identify with confidence the positive cells because the pPHA2::GFP-A construct itself caused a pharyngeal phenotype in a small fraction of the transgenic animals. The earliest unambiguous expression of pPHA2::GFP-A began in 4 to 8 cells of the pharyngeal primordium at around 280 to 300 min of embryonic development, which is after gastrulation and at a time when the pharyngeal primordium becomes clearly defined but before the formation of a surrounding basal lamina. Just before the comma stage (approximately 350 min), expression is observed in two groups of pharyngeal primordium cells: a strongly expressing posterior group comprising 10 to 12 cells and a small anterior group (usually 3 to 5 cells) expressing weak levels of the reporter. This pattern persists until the 3-fold stage. During the 2-to-3-fold transition, the posterior group of cells splits into two groups: one group of positive nuclei move into the forming metacorpus while a larger group remains associated with the posterior part of the primordium, where the anterior part of the posterior bulb is forming. Beginning at the 3-fold stage, or slightly before that, strong expression is also observed in several cells of the tail.
• Subcellular Localization: The fusion protein was mostly confined to the cell nucleus.

• Primary Identifier: Expr11835
• Remark: A 5' region of merely 470 bp (construct pPHA2::GFP-B) or even 158 bp (construct pPHA2::GFP-C) upstream of the pha-2 gene is sufficient to support weak PHA2::GFP expression in some cells of the pharyngeal primordium and some cells of the adult metacorpus, and strong expression in extrapharyngeal head cells, intestinal and rectal cells. However, these two constructs fail to rescue the pha-2 mutant and show no PHA2::GFP expression in the following pharyngeal cells, the pm5 muscles, the I4 interneuron, and the pharyngeal epithelial cells, indicating that expression of pha-2 in pharyngeal cells is essential for rescue.

• Primary Identifier: Expr7779
• Remark: Clone: pUL#IAH10A4
• Pattern: No expression

• Primary Identifier: Expr1200031
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr11834
• Pattern: Expression from the pPHA2::GFP-F construct was restricted to three types of pharyngeal cells: reproducible expression in the pharyngeal interneuron I4, and weak and rare (detected in <10% of transgenic worms) expression in pm5 muscle cells and in three pharyngeal epithelial cells.

• Primary Identifier: Expr11836
• Pattern: When the 2.7-kb promoter is present to drive a truncated pha-2 gene containing only the first three exons and first two introns, the complete pharyngeal expression profile of the full-length rescue-competent pPHA2::GFP-A construct is restored (pPHA2::GFP-E). This construct also supports expression in rectal gland cells, but shows no expression in the head neurons or intestine. This shows that important regulatory sequences exist within the first two introns and that these elements operate in concert with 5' sequences that are in the 500 to 2700 bp to drive robust expression of pha-2 in the pm5, I4, metacorpus cells, and pharyngeal epithelial cells.

• Primary Identifier: Expr11837
• Pattern: The pPHA2::GFP-D construct, which contains the third intron as well as part of the fourth exon, exhibited an expression profile similar to the pPHA2::GFP-E construct (Expr11836).

• Primary Identifier: Expr15636

• Primary Identifier: Expr1154747
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1026041
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2014880
• 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: Expr2033115
• 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).

22 GO Annotation

7 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004011
• Start: 633368
• End: 636993
• Strand: -1

22 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3626

1 Sequence Ontology Term