WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Anatomy Term :

Definition  Neuron class of nine ventral cord motor neuron, innervates dorsal muscle. Name  DA neuron
Primary Identifier  WBbt:0005278

9 Children

Definition Name Synonym Primary Identifier
Ventral cord motor neurons, innervate dorsal muscles DA2 lineage name: ABplppapapa WBbt:0004869
Ventral cord motor neurons, innervate dorsal muscles DA6 lineage name: ABplpppaaap WBbt:0004861
Ventral cord motor neurons, innervate dorsal muscles DA7 lineage name: ABprpppaaap WBbt:0004859
Ventral cord motor neurons, innervate dorsal muscles DA3 lineage name: ABprppapapa WBbt:0004867
Ventral cord motor neurons, innervate dorsal muscles DA4 lineage name: ABplppapapp WBbt:0004865
Ventral cord motor neurons, innervate dorsal muscles DA5 lineage name: ABprppapapp WBbt:0004863
Ventral cord motor neurons, innervate dorsal muscles DA9 lineage name: ABplpppaaaa WBbt:0004857
Ventral cord motor neurons, innervate dorsal muscles DA1 lineage name: ABprppapaap WBbt:0004871
Ventral cord motor neurons, innervate dorsal muscles DA8 lineage name: ABprpapappp WBbt:0004858

18 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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:A-class-motor-neurons_larva_enriched
  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
  Single-cell RNA-Seq cell group 34 expressed in: Seam cells (grd+). CellRanger, DecontX, Monocle3, Louvain algorithm. WBPaper00065623:34
  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:A-class-motor-neurons_L1-larva_expressed
  Embryonic A-class motor neuron enriched genes. A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. WBPaper00030839:Embryo_A_Class
  Expressed transcripts enriched in embryonic motor neurons (identified by unc-4::GFP expressing cells). Comparisons of RMA normalized intensities for unc-4::GFP vs reference cells were statistically analyzed using Significance Analysis of Microarrays software (SAM, Stanford). A two-class unpaired analysis of the data was performed to identify genes that differ by 1.7-fold from the wildtype reference at a False Discovery Rate (FDR) of 1%. These genes were considered significantly enriched. WBPaper00025141:unc-4::GFP_Enriched_Genes
  Genes expressed in embryonic motor neurons (identified by unc-4::GFP expressing cells). Genes called Present by MAS 5.0 in 2 out of 3 unc-4::GFP hybridizations. WBPaper00025141:unc-4::GFP_Expressed_Genes
  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:A-class-motor-neurons_embryo_enriched
  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:A-class-motor-neurons_embryo_SelectivelyEnriched
  Larval A-class motor neuron enriched genes. A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. WBPaper00030839:Larval_A_Class
  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:A-class-motor-neurons_larva_SelectivelyEnriched
  Single-cell RNA-Seq cell group 6_2 expressed in neuron. scVI 0.6.0 WBPaper00065841:6_2
  Single-cell RNA-Seq cell group 136_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:136_0
  Single-cell RNA-Seq cell group 36 expressed in: Spermatheca bag proximal. CellRanger, DecontX, Monocle3, Louvain algorithm. WBPaper00065623:36
  Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at both embryonic and larval stages. 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_CoreEnriched
  Single-cell RNA-Seq cell group 6_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:6_0
  Single-cell RNA-Seq cell group 35 expressed in: Mature sperm. CellRanger, DecontX, Monocle3, Louvain algorithm. WBPaper00065623:35
  Single-cell RNA-Seq cell group 33 expressed in: AS; DA_VA; DB_VB; and SAB. CellRanger, DecontX, Monocle3, Louvain algorithm. WBPaper00065623:33

86 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr4864 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).  
    Expr4865 A-class motor neuron: enriched in embryo (1.8) and larva (1.8). Neuronal expression include: DA, DB, DD, VA, VB, VD, AS, head neurons. Also expressed in other cells: Head muscle. Pan-neuronal: enriched in embryo (1.8) and larva (1.5).  
    Expr4866 A-class motor neuron: enriched in embryo (2.1) and larva (1.9). Neuronal expression include: DA, DB, VA, VB. Pan-neuronal: enriched in embryo (1.9) and larva (2.2).  
    Expr4867 A-class motor neuron: enriched in embryo (5.3) and larva (3.7). Neuronal expression include: DA, DB, VA, VB, AS, head neurons. Also expressed in other cells: Body muscle, intestine. Pan-neuronal: enriched in embryo (3.9) and larva (8.3).  
    Expr4868 A-class motor neuron: enriched in embryo (5.1) and larva (1.7). Neuronal expression include: DA, DB, VA, VB, VD. Also expressed in other cells: Intestine, hypodermis. Pan-neuronal: enriched in embryo (1.9) and larva (2.7).  
    Expr4869 A-class motor neuron: enriched in embryo (3.6) and larva (3.1). Neuronal expression include: DA, DB, VA, VB, VC, touch neurons, head and tail neurons. Pan-neuronal: enriched in embryo (2.3) and larva (4.0).  
    Expr4860 A-class motor neuron: enriched in embryo (4.0) and larva (2.2). Neuronal expression include: DA, DB, VA, VB, head and tail neurons. Pan-neuronal: expressed in embryo; enriched in larva (2.3).  
    Expr4862 A-class motor neuron: enriched in embryo (1.9) and larva (2.1). Neuronal expression include: DA, VB, DB, VD, DD, bright in AS, also head and tail neurons. Pan-neuronal: expressed in embryo; enriched in larva (3.5).  
    Expr4856 A-class motor neuron: expressed in embryo; enriched in larva (1.9). Neuronal expression include: L2 -- DA, VA, VB, VD, bright in touch neurons, head and tail neurons L3 -- all ventral cord motor neurons. Pan-neuronal: expressed in embryo; enriched in larva (5.9).  
    Expr4858 A-class motor neuron: enriched in embryo (2.8) and larva (3.1). Neuronal expression include: DA, VB, AS, DB, DD, HSN, VC4&5, AIY, head neurons. Also expressed in other cells: Muscle, intestine. Pan-neuronal: expressed in embryo; enriched in larva (1.5).  
    Expr4851 A-class motor neuron: enriched in embryo (1.7); not expressed in larva. Neuronal expression include: DA, VD, AS, VB, DB. Also expressed in other cells: Body muscle. Pan-neuronal: expressed in embryo; enriched in larva (2.7).  
    Expr4845 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).  
    Expr4846 A-class motor neuron: not expressed in embryo or larva. Neuronal expression include: All VNC motor neuron classes, except DD, head and tail neurons. Pan-neuronal: enriched in larva (4.9); not expressed in embryo.  
    Expr4847 A-class motor neuron: enriched in embryo (2.3); not expressed in larva. Neuronal expression include: DA, DB, DD, VD, AS. Pan-neuronal: enriched in larva (1.7); not expressed in embryo.  
    Expr4848 A-class motor neuron: expressed in larva; enriched in embryo (1.8). Neuronal expression include: VA, VB, DA, DB, AS, touch neurons. Also expressed in other cells: Body muscle, pharyngeal neurons. Pan-neuronal: enriched in larva (1.8); not expressed in embryo.  
    Expr13427 To confirm that lgc-46 is expressed in A-MNs, we created a transgenic strain coexpressing GFP and mStrawberry under the control of Plgc-46 and the A-MN-specific promoter Punc-4, respectively. In the transgenic worms, GFP expression was observed in ventral cord MNs, many head neurons, and some neurons in the tail. All mStrawberry-positive neurons were colabelled by GFP, suggesting that lgc-46 is expressed in A-MNs. In addition, GFP was observed in some ventral cord motor neurons not labelled by mStrawberry, which could be GABAergic MNs that reportedly express lgc-46.  
Picture: Figure 1A.   Marker89   Marker for DA and DB motor axons.
Picture: Fig 3.   Expr8850 Neuronal Expression: AVA, AVB, AVE, PVC, AIB, AUA, AVG, RIB, RIC, SAA, SIA, SIB, RIF, RIM, RMD, RME, SMD, DA, DB, VA, VB, M5, NSM, MC, I3, MI?. Non-neuronal Expression: rectal epithelium, body wall muscle, spermethecae, vulva muscle.  
    Expr11295 Fairly weak expression in most animals, strongest expression in young larvae, pharynx: marginal cells and pm6, gut, rectal gland cells, about 10-15 pairs of head neurons incl. some IL's, some motoneurons (DA/DB?), 2-3 pairs of tail neurons  
    Expr8203 Expressed in DA, VB, AS, DB, DD, HSN, VC4 & 5, AIY, head neurons, muscles, intestine. acr-14::GFP is expressed in RME in the head and in ventral nerve cord (VNC) motor neurons.  
    Expr10808 ACR-2::GFP showed mostly diffused localization on neuronal soma, as well as processes in the ventral cord, sublateral cords, and nerve ring. In the ventral cord, expression of ACR-2::GFP was specifically observed in the VA, VB, DA, and DB motor neurons as reported previously (Jospin et al., 2009). Several additional cells (e.g., SDQ, vulva muscles) also expressed ACR-2::GFP, presumably because of the use of a longer promoter and inclusion of intronic sequences. However, staining of ACR-2::GFP was not seen in the dorsal nerve cord. Because the axonal processes of DA and DB motor neurons are major constituents of the dorsal nerve cord, lack of ACR-2::GFP signals in the dorsal nerve cord indicates that ACR-2 is unlikely to localize to presynaptic sites of these motor neurons.  
    Expr9444 nlg-1 is expressed in a subset of neurons in C. elegans adults, including ~20 cells in the ventral nerve cord and ~20 cells in the head. The nlg-1-expressing cells in the ventral nerve cord were identified as the cholinergic VA and DA motor neurons. Authors also identified the two AIY and two URB interneurons and the four URA motor neurons in the head, and the two PVD mechanosensory and two HSN motor neurons in the body, as nlg-1-expressing cells. Finally, faint Pnlg-1::YFP expression was also observed in body wall muscles. Bright punctate staining was observed in dendritic (postsynaptic) regions. Clear punctate staining was also observed in presynaptic regions of each neuronal type. For example, in the DA9 motor neuron, bright NLG-1::YFP puncta were present in the ventral postsynaptic domain, and dimmer puncta were present in the dorsal presynaptic region. Puncta were excluded from the synapse-poor region between the cell body and dorsal presynaptic region and from the anterior asynaptic region of the dorsal process. To further study the punctate staining in the presynaptic region, NLG-1::YFP localization was examined in animals expressing the tagged synaptic vesicle protein mCherry::RAB-3 in DA9. In the dorsal axon, NLG-1::YFP puncta partially colocalized with puncta containing mCherry::RAB-3, suggesting that NLG-1::YFP localization is perisynaptic. Sub-cellular localization within the body wall muscle: Muscle cell membrane +/- Muscle arms
    Expr9932 ric-7 promoter expresses nuclear localized Cherry in many neurons, including both cholinergic and GABAergic motor neurons. GFP-tagged RIC-7 constructs was expressed in the cholinergic DA neurons (using the unc-129 promoter). The RIC-7::GFP protein was localized in a punctate distribution in both cell bodies and dorsal cord axons. The majority of RIC-7 puncta co-localized with an SV marker (mCherry-tagged Endophilin), suggesting that RIC-7 is targeted to synapses.
    Expr10058 lin-14 was broadly expressed in C. elegans neurons, with strong expression in neurons starting in the late embryonic stage. Analysis of the expression patterns of lin-14 and lin-4 revealed overlapping expression of the two genes in several neurons, including AVM, ALM, PVM, PLM, DD, VD, DA, DB, SDQR, HSN, and PQR.  
Picture: Fig 3.   Expr8844 Neuronal Expression: ASI, ASJ, AVB, AVE, PVC, AIB, AIN, DA, DB, M2, NSM. Non-neuronal Expression: pharynx, GLR cells.  
Picture: Figure 8. Reporter gene fusion type not specified.   Expr7972 Expressed in DA, VA, AS, chemosensory neuron in head. Also expressed in excretory cell, anal depressor, intestine.  
Picture: Fig 3.   Expr8671 Expression in the alimentary canal: Strong and consistent expression in pharyngeal epithelium, pm5, pm6, pm7, pm8, g2, rectal gland cells. Weak or rare expression in anterior arcades, posterior arcades, pm2, pm3, pm4, M3, MC, intestine, rectal epithelial cells. Expression in the nervous system: CEPsh, ALN, ASn, CAN, DAn, DBn, DDn, DVA, DVB, HSN, PDE, PLM, PVQ, PVR, PVT, URB, VAn, VBn, VDn, M3, MC. Expression in the reproductive system: In adult stage, expressed in spermatheca, vulval muscle, HSN. In developing larva stage, expressed in vulval muscle, uterine muscle, HSN. inx-3 was expressed broadly during early embryogenesis. After the beginning of morphogenesis, inx-3 expression becomes more restricted to the pharynx, hypodermis, and intestine. By three-fold stage inx-3 expression appears in ventral cord motor neurons (strongest in DA neurons) along with continued strong pharyngeal expression. By hatching, its hypodermal expression disappears, while postembryonically born ventral cord motor neurons express it at low levels. Its pharyngeal (strong) and neuronal (faint) expressions continue to adulthood.  
Picture: N.A.   Expr8675 Expression in the alimentary canal: Strong and consistent expression in pm5, MC. Weak or rare expression in pharyngeal epithelium, pm1, pm2, pm3, pm4 pm6, pm7, pm8, g1, g2, rectal gland cells. Expression in the nervous system: ADE, AIY, ALM, ALN, AVA, AVK, AVM, BDU, CAN, DAn, DVA, DVB, DVC, FLP, HSN, LUA, PLM, PLN, PVC, PVM, PVP, PVQ, PVT, PVW, RID, RIS, SDQ, URB, MC. Expression in the reproductive system: In adult stage, expressed in HSN. Faint hypodermal expression of inx-7 is seen around two-fold stage and becomes stronger by threefold stage.  
Neuronal gene expression pattern from collation by Shawn Lockery of neuron-specific promotors posted 20/04/98 (http://chinook.uoregon.edu). Since cell AS is listed under 'body' in the pattern, it presumably means the AS.1-11 ventral cord neurons rather than the AS amphid neurons.[sdm-curator]   Expr320 head: IL2 URA URB SAA SAB SIA SIB SMB SMD RMD AIY, sev more; phar: M1 M2 M5 I1f I6f, others; body: VA VB VC DA DB AS SDQ HSNf; tail: ALN PLN others [J. Duerr (personal communication to Shawn Lockery)], antibody  
Picture: Fig 3.   Expr8694 Expression in the alimentary canal: Strong and consistent expression in M5, I1, I3, I6, NSM. Weak or rare expression in posterior arcades. Expression in the nervous system: Phsh, ADA, ADE, ADL, AIN, AIY, ALM, AUA, AVA, AVD, AVH, AVJ, AVK, AVM, AWB, BDU, CAN, CEP, DAn, DBn, DDn, DVB, DVC, FLP, HSN, IL1, IL2, LUA, OLL, PDA, PDB, PDE, PHA, PHB, PHC, PLM, PLN, PVC, PVD, PVM, PVN, PVP, PVQ, PVR, PVT, PVW, RIB, RIC, RIF, RIP, RIS, RME, SDQ, SIA (early larva), SIB (early larva), SMB (early larva), SMD (early larva), URA, URB, VAn, VBn, VCn, VDn, M5, I1, I6, NSM. Expression in the reproductive system: In adult stage, expressed in vulval muscle, uterine muscle, HSN, VCn. In developing larva stage, expressed in HSN, VCn, and anchor cell.  

0 Life Stages

2 Parents

Definition Name Synonym Primary Identifier
neuron making synapse on an effector (muscle, gland). motor neuron motoneuron WBbt:0005409
neuron that uses vesicular acetylcholine as a neurotransmitter. cholinergic neuron ACh neuron WBbt:0006840