WormMine: AnatomyTerm WBbt:0005451

• Definition: type of cells that make up muscle layers in the pharynx.
• Name: pharyngeal muscle cell
• Primary Identifier: WBbt:0005451

13 Children

Definition	Name	Synonym	Primary Identifier
first layer pharyngeal muscle cell.	pm1	M1	WBbt:0003744
seventh pharyngeal muscle cell layer	pm7	m7	WBbt:0003721
third pharyngeal muscle cell layer	pm3	M3	WBbt:0003740
eighth pharyngeal muscle cell layer (single cell)	pm8	lineage name: MSaaapapp	WBbt:0004302
fifth pharyngeal muscle cell layer	pm5	M5	WBbt:0003737
fourth pharyngeal muscle cell layer	pm4	M4	WBbt:0003739
sixth pharyngeal muscle cell layer	pm6	m6	WBbt:0003724
second layer pharyngeal muscle cell.	pm2	m2	WBbt:0003742
precursor cell of pm4.	pm4 precursor		WBbt:0008272
precursor cell of pm3.	pm3 precursor		WBbt:0008271
precursor cell of pm2 syncytium.	pm2 precursor		WBbt:0008270
precursor cell of pm1 syncytium.	pm1 precursor		WBbt:0008269
precursor cell of pm5 syncytium.	pm5 precursor		WBbt:0008273

10 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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:pharyngeal-muscle_L1-larva_expressed
	Proteins expressed in pharyngeal muscle cytoplasm, according to tissue specific APX enzyme expression using myo-2 promoter driven NES(cytoplasm)-GFP-APX, followed with mass spectrometry.	Fold change > 2.	WBPaper00051245:pharyngeal-muscle_cytoplasm_expressed
	Single-cell RNA-Seq cell group 24_1 expressed in muscle.	scVI 0.6.0	WBPaper00065841:24_1
	Single-cell RNA-Seq cell group 26_1 expressed in pharynx.	scVI 0.6.0	WBPaper00065841:26_1
	Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.	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:pharyngeal-muscle_embryo_enriched
	Single-cell RNA-Seq cell group 26_0 expressed in muscle.	scVI 0.6.0	WBPaper00065841:26_0
	Single-cell RNA-Seq cell group 26_2 expressed in muscle.	scVI 0.6.0	WBPaper00065841:26_2
	Genes that show selective expression in a subset of cell types vs broadly expressed in many cell types. Correspond to 20% - 57% of enriched_genes for a given cell type.	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:pharyngeal-muscle_embryo_SelectivelyEnriched
	Proteins expressed in pharyngeal muscle nucleus, according to tissue specific APX enzyme expression using myo-2 promoter driven NLS(nucleus)-GFP-APX, followed with mass spectrometry.	Fold change > 2.	WBPaper00051245:pharyngeal-muscle_nucleus_expressed
	Proteins specifically expressed in pharyngeal muscle, according to tissue specific APX enzyme expression using myo-2 promoter, followed with mass spectrometry.	Fold change > 2.	WBPaper00051245:pharyngeal-muscle_specific

405 Expression Patterns

• Primary Identifier: Expr4895
• Remark: Picture: Figure S4F.
• Pattern: EVA-1::GFP expression was observed along the VNC, body wall muscles, Also expressed in pharyngeal muscles and hypodermis.
• Subcellular Localization: Exclusively localized on or near the cell surface membrane.

• Primary Identifier: Expr4864
• Pattern: A-class motor neuron: enriched in embryo (2.0) and larva (2.1). Neuronal expression include: DA, DB, VA, VB, DD, VD, head neurons. Also expressed in other cells: Pharyngeal muscle. Pan-neuronal: enriched in embryo (1.7) and larva (3.5).

• Primary Identifier: Expr4850
• Pattern: A-class motor neuron: enriched in embryo (2.6); not expressed in larva. Neuronal expression include: DD, head and tail neurons. Also expressed in other cells: Body muscle, pharyngeal muscle. Pan-neuronal: expressed in embryo; enriched in larva (6.5).

• Primary Identifier: Expr4841
• Pattern: A-class motor neuron: expressed in embryo; not expressed in larva. Neuronal expression include: All ventral cord motor neurons, head and tail neurons, PLN. Also expressed in other cells: Pharyngeal muscle, vulval muscle, anal depressor, hypodermis. Pan-neuronal: enriched in embryo (1.8); not expressed in larva.

• Primary Identifier: Expr4843
• Pattern: A-class motor neuron: expressed in larva; enriched in embryo (2.0). Neuronal expression include: Bright in head neurons, few tail neurons. weak in all ventral cord motor neurons. Touch neurons, PDE. Also expressed in other cells: Intestine, head muscle, pharyngeal muscle, hypodermis, distal tip cell. Pan-neuronal: expressed in larva; enriched in embryo(3.0).

• Primary Identifier: Expr4845
• Pattern: A-class motor neuron: expressed in larva; enriched in embryo (2,5). Neuronal expression include: DA, DB, DD, VA, VB, VD, AS head and tail neurons. Also expressed in other cells: Body muscle, head muscle, pharyngeal muscle. Pan-neuronal: enriched in embryo (2.1) and larva (1.8).

• Primary Identifier: Expr4840
• Pattern: A-class motor neuron: expressed in embryo; not expressed in larva. Neuronal expression include: All ventral cord motor neurons, head and tail neurons, touch neurons. Also expressed in other cells: Intestine, vulval muscle, pharyngeal muscle, anal depressor, body muscle. Pan-neuronal: enriched in embryo (1.8); not expressed in larva.

• Primary Identifier: Expr4809
• Remark: Picture: Figure 8. Staining was greatly reduced in unc-87(e843).
• Pattern: The antibody react with body wall muscle, pharyngeal muscle, anal depressor and sphincter muscle, intestinal muscles, vulval muscles and uterine muscles. In all cases, UNC-87 was contained withing the pattern observed with phalloidin or anti-actin antibodies, suggesting colocalization with thin filaments..
• Subcellular Localization: Immunohistochemical staining of wild type adult body wall muscle revealed a atriated pattern. The striations are interupted periodically along their length by unstained regions. Double labelling experiments showed that anti-UNC-87 staining pattern corresponded with that of the monoclonal antibody MH44. This pattern represent the I band. At the center of the I band are the dense bodies, these correspond to the unstained regions within the striations.

• Primary Identifier: Expr4699
• Pattern: Expressed in pharyngeal muscle and neuron.

• Primary Identifier: Expr4755
• Pattern: frh-1::gfp1 showed a complex expression pattern, which includes a number of neurons in the head. This construct also stains the muscle cells of the pharynx, intestinal cells, body wall muscle cells and spermatheca. This construct was expressed in neurons that showed dendritic projections toward the mouth, suggesting that they may be sensory amphidic neurons. Costaining with DiI, which stains amphidic neurons in C. elegans, confirmed the amphidic nature of these cells.

• Primary Identifier: Expr4757
• Pattern: frh-1::gfp3, which does not contain the frh-1 gene but contains all the 5 sequence present in frh-1::gfp1, was not expressed in amphid neurons, suggesting the presence of a regulatory sequence within the frh-1 gene that would drive the expression of the gene in head neurons. On the other hand, the frh-1::gfp3 was expressed in the pharynx, gut cells, spermatheca, and body wall muscles, as the frh-1::gfp1, indicating that frh-1::gfp1 would contain most of the necessary sequences for frataxin expression.

• Primary Identifier: Expr4759
• Remark: The specificity of binding of anti-Ce-GnRHR antibody to GnRHR was demonstrated by the lack of staining throughout the worm (including the germline, pharyngeal muscle and intestinal cells) when the antibody was preincubated with its antigen (the C-terminus amino acids 386 to 401).
• Pattern: To better localize cellular staining in worms, authors permeabilized worms and performed whole-mount fluorescent immunohistochemistry. These experiments indicated that Ce-GnRHR was localized to the nucleus of maturing oocytes and intestinal cells, to sperm, pharyngeal muscles, but not other cells such as hypodermal cells. Similar staining of these structures was evident for both the anti-human-GnRHR1 and anti-Ce-GnRHR antibodies. Ce-GnRHR staining clearly illustrates an increase in the size of the oocyte nuclei as they mature along the gonadal arm. Upon fertilization, Ce-GnRHR staining becomes diffuse throughout the developing egg, although staining appears to increase during egg development. Only uniform background autofluorescence was apparent in worms treated with secondary antibody alone. Ce-GnRHR also was detected along the myofilament lattice of the pharyngeal muscles. staining along the three parallel muscles that comprise the pharyngeal musculature beginning at the tip of the head and extending to the pharyngeal bulb, staining of all 8 pharyngeal muscle (pm1 to 8) domains, but not in the gaps between contractile zones of adjacent pharyngeal muscle domains. staining of myofilaments that run radially towards the lumen and which are most obvious in the bulbs. These results indicate Ce-GnRHR is present on the pharyngeal musculature.
• Subcellular Localization: Ce-GnRHR was localized to the nucleus of maturing oocytes and intestinal cells, to sperm, pharyngeal muscle.

• Primary Identifier: Expr4742
• Pattern: The anti-CeTNI-2 antibody strongly stained the body wall muscle, and faintly the pharyngeal muscle, vulval muscles and anal muscles.
• Subcellular Localization: At high magnification the anti-CeTNI-2 antibody stained the thin filaments in the I-band regions that also contain actin.

• Primary Identifier: Expr4743
• Pattern: The anti-CeTNI-4 antibody stained only the pharynx muscles.

• Primary Identifier: Expr4707
• Pattern: Expressed in body wall and pharyngeal muscle and intestine.

• Primary Identifier: Expr4709
• Pattern: Expressed in pharyngeal muscle.

• Primary Identifier: Expr4703
• Pattern: Expressed in body wall, pharyngeal and vulva muscle, H cell.

• Primary Identifier: Expr4704
• Pattern: Expressed in head muscle, pharyngeal muscle, vulva muscle and neurons.

• Primary Identifier: Expr4705
• Pattern: Expressed in pharyngeal muscle and neuron.

• Primary Identifier: Expr4940
• Pattern: strong bwm, vul, mu int, occaisonal weak pharyngeal, spermatheca, faint VNC, head neurons; embryonic bwm starts at 3-fold and very strong in L1s.

• Primary Identifier: Expr4931
• Pattern: strong bwm, pharyngeal, vulval, and anal depressor; a bit mosaic; starts at 3-fold?

• Primary Identifier: Expr4934
• Pattern: strong bwm, pharyngeal, vul, anal, mu int, sphincter muscles; no embryonic seen

• Primary Identifier: Expr4936
• Pattern: strong pharyngeal muscle, tail and head neurons, strong bean and later embryonic bwm?; strong GFP emb/Ls are lumpy dumpy or worse

• Primary Identifier: Expr4923
• Pattern: strong pharyngeal and bwm; no vul or anal seen; no embryonic seen

• Primary Identifier: Expr4919
• Pattern: Strong pharyngeal, vulval, bwm, anal dep, mu int; 3-fold earliest embryonic.

• Primary Identifier: Expr4911
• Remark: Picture: Fig S5.
• Pattern: A transcriptional fusion of the unc-50 promoter to GFP is expressed in all cell types throughout development. unc-50::gfp expression was seen in the head of adult hermaphrodite. Expression is seen in the pharyngeal muscle, head neurons, and epidermis. Expression is also present in the gut, ventral cord motor neurons, and epidermal seam cells. In the mid body region expression is seen in the gut, seam cells, uterus, vulva muscles, and distal tip cell. In the tail region unc-50 expression can be detected in the epidermis and enteric muscles.

• Primary Identifier: Expr4378
• Pattern: The C17E4.3::GFP reporter is expressed in the developing embryo and L1 larval stages, in three distinct sheath/socket cells in the head region close to the anterior bulb of the pharynx and several cells around the anus. Expression is also seen in several pharyngeal muscle cells. Dye filling tests confirmed that the processes extending to the nose were not from amphid neurons, but rather from socket cells.

• Primary Identifier: Expr4350
• Pattern: Localized differently within cells and GFP fluorescence was seen in body wall muscle, distal tip cells, enteric muscle and cells of the posterior intestine. Within the pharynx, cca-1 expression is observed in most if not all pharyngeal muscle cells but is most prominent in those of the procorpus and in pm8, the most posterior cell in the terminal bulb.

• Primary Identifier: Expr4349
• Pattern: Transgenic animals carrying this construct show GFP fluorescence in a variety of cells, with robust expression in the pharyngeal muscle. GFP expression was also observed in many neurons, including specific subsets in the head, pharynx, ventral nerve cord and anal ganglia.

• Primary Identifier: Expr4264
• Pattern: Expressed in body wall muscle cells, pharyngeal muscles, rectal gland cells, vulval and uterine muscles, and a subset of neurons in the head and ventral nerve cord. The expression was first detected in the embryo at the 1.5-fold stage and continued to be expressed until adulthood. In this stage, cells with position corresponding to P cells showed also GFP expression. In order to determine if the expression of GFP was in epidermal lineages, including P cells and their descendants, authors prepared double transgenic lines expressing GFP from promoter 1 of nhr-40 on the background of SU93 line that expresses an AJM::GFP membrane marker. This confirmed the expression of nhr-40::gfp in epidermal precursors P cells and their neuronal progeny within the ventral neuronal cord. However, the GFP was not observed in ventral epidermal cells that originated from P cells. The nhr-40::gfp was not observed in seam cells that are also marked by an AJM::GFP. The muscle pattern of expression was partially lost with truncations of this promoter fragments (-1013 and -682 bp); however, other aspects of expression were retained.

5 Life Stages

Remark	Definition	Other Name	Public Name	Primary Identifier
	The second stage larva. At 25 Centigrade, it ranges 25.5-32.5 hours after fertilization, 11.5-18.5 hours after hatch.		L2 larva Ce	WBls:0000027
	The fourth stage larva. At 25 Centigrade, it ranges 40-49.5 hours after fertilization, 26-35.5 hours after hatch.		L4 larva Ce	WBls:0000038
	The first stage larva. At 25 Centigrade, it ranges 14-25.5 hours after fertilization, 0-11.5 hours after hatch.		L1 larva Ce	WBls:0000024
	The stage that begins when a C.elegans individual is fully-developed and has reached maturity.		adult Ce	WBls:0000041
	The third stage larva. At 25 Centigrade, it ranges 32.5-40 hours after fertilization, 18.5-26 hours after hatch.		L3 larva Ce	WBls:0000035

2 Parents

Definition	Name	Synonym	Primary Identifier
	pharyngeal cell		WBbt:0005460
muscle of the alimentary organ system.	alimentary muscle		WBbt:0005820