WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Anatomy Term :

Definition  Major cell type of nervous tissue, specialized for transmission of information in the form of patterns of impulses. Name  neuron
Primary Identifier  WBbt:0003679 Synonym  neurone

20 Children

Definition Name Synonym Primary Identifier
neuron with its cell body situated in the head, excluding the pharynx. head neuron   WBbt:0006751
neuron with its cell body situated in the tail, posterior to rectum. tail neuron   WBbt:0006759
neuron of the pharyngeal nervous system. pharyngeal neuron   WBbt:0005439
neuron making synapse on an effector (muscle, gland). motor neuron motoneuron WBbt:0005409
neuron that uses serotonin as a vesicular neurotransmitter. serotonergic neuron 5-HT neuron WBbt:0006837
Neuron that uses dopamine (DA) as a neurotransmitter. dopaminergic neuron   WBbt:0006746
neuron that uses GABA as a vesicular neurotransmitter. GABAergic neuron   WBbt:0005190
neuron that uses vesicular acetylcholine as a neurotransmitter. cholinergic neuron ACh neuron WBbt:0006840
neuron that senses external stimuli and transduce them to signals internal to the organism. sensory neuron   WBbt:0005759
  interneuron   WBbt:0005113
neuron type, neurons that have ciliated nerve endings. ciliated neuron   WBbt:0006816
neuron of the somatic nervous system. somatic neuron body neuron WBbt:0006752
neuron with cell body in the preanal ganglion. preanal ganglion neuron preanal ganglion neurons WBbt:0005447
neuron whose cell body is in the retrovesicular ganglion. retrovesicular ganglion neuron retrovesicular ganglion WBbt:0005403
neuron that uses glutamate as a vesicular neurotransmitter. glutamatergic neuron   WBbt:0006829
Neuron class of two neurons with cell bodies situated in the lateral ganglia. AUA   WBbt:0006817
Neuron class of two neurons that are closely associated with the excretory canal. CAN   WBbt:0006827
Male-specific neuron whose cell body is in the cloacal ganglion. cloacal neuron   WBbt:0005807
neuron type, cell body located in left lateral ganglion. lateral ganglion left neuron   WBbt:0005102
neuron type, cell body located in right lateral ganglion. lateral ganglion right neuron   WBbt:0005100

39 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_upregulated_neural
  Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. DESeq. False discovry rate (FDR) < 0.1. WBPaper00048988:neuron_expressed
  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:all-neurons_L1-larva_expressed
  Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. DESEQ2, fold change > 2 and FDR < 0.01. WBPaper00062103:neuron_enriched
  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
  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:all-neurons_L2-larva_expressed
  Transcripts that showed significantly decreased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6. DESeq2, log2 fold change > 2, adjusted p-value < 0.005. WBPaper00055103:thoc-5(wy822)_downregulated
  Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. DESeq2. FDR < 0.05. WBPaper00060459:bcat-1(RNAi)_downregulated
  WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups). To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. WBPaper00031532:Larva_Pan_Neuronal_Depleted
  Embryonic Pan-neural 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_Pan_Neuronal
  Transcripts enriched at neuron synapses by comparing presynaptic and somatic cell fragments labeled with different protein markers and sorted by FACS. DESeq2, FDR < 0.05 WBPaper00059027:neuron-synapses_enriched
  Transcripts up regulated in the FACS isolated neurons from daf-16(mu86);daf-2(e1370), comparing to daf-2(e1370). DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05. WBPaper00048988:daf-16(mu86)_upregulated_neuron
  Larval Pan-neural 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_Pan_Neuronal
  Transcripts that showed significantly increased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. DESeq2. FDR < 0.05. WBPaper00060459:bcat-1(RNAi)_upregulated
  Transcripts that showed significantly decreased 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)_downregulated_neuron
  Transcripts that showed significantly decreased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_downregulated_neural
  WT-Pico Pan-neural Enriched Genes, with genes found multiple times in a single dataset removed (without dups). To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. WBPaper00031532:Larva_Pan_Neuronal_Enriched
  Transcripts enriched in neuronal cells, by comparing fluorescence-activated cell sorted (FACS) neurons with whole worm expression. DESeq. False discovry rate (FDR) < 0.1. WBPaper00048988:neuron_enriched
Olfactory long term associative memory (LTAM). Neuronal mRNAs that showed significantly increased expression by an olfactory long term associative memory (LTAM). Fold change > 1.8. p-value < 0.05. WBPaper00051352:Long-Term-Association-Memory_upregulated
  Transcripts depleted at neuron synapses (enriched at the somatic fragments) by comparing presynaptic and somatic cell fragments labeled with different protein markers and sorted by FACS. DESeq2, FDR < 0.05 WBPaper00059027:neuron-synapses_depleted
  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:all-neurons_larva_enriched
Olfactory long term associative memory (LTAM). Neuronal mRNAs that showed significantly decreased expression by an olfactory long term associative memory (LTAM). Fold change > 1.8. p-value < 0.05. WBPaper00051352:Long-Term-Association-Memory_downregulated
  Genes enriched in neuronal miRNA-induced silencing complexes (miRISC) as detected by immunoprecipitations and microarray analysis. Testable genes were defined as having reliable signals in two different biological replicates using the Agilent microarray chip. Multiple probes for the same gene were removed, keeping the probe with the lowest p-value as defined by a one-tailed t-test comparing all testable probes versus probes towards a designated gene. The testable data was then supplemented with the enrichment values (as percent ranks) of a fifth replicate, from another microarray platform GPL5883 (which had a single probe for each gene), and statistical significance was re-calculate. p < 0.001 was the final cutoff. WBPaper00042548:miRISC_enriched
  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:all-neurons_embryo_enriched
  Transcripts that showed significantly increased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6. DESeq2, log2 fold change > 2, adjusted p-value < 0.005. WBPaper00055103:thoc-5(wy822)_upregulated
  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:all-neurons_larva_SelectivelyEnriched
  Transcripts expressed in neuronal cells in wild type background during neuron-specic RNASeq analysis via FACS of Pacr-2::gfp reporter juIs14. DESeq2, p-value < 0.05. Identification of expressed genes in wildtype was determined using Cufflinks. Expressed genes were selected by filtering for genes with an FPKM>10 in both replicates. WBPaper00059763:neuron_expressed
  Transcripts up regulated in the FACS isolated neurons from daf-16(mu86);daf-2(e1370), comparing to N2. DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05. WBPaper00048988:daf-2(e1370)_daf-16(mu86)_upregulated_neuron
  Genes whose transcripts exhibited <= 2 fold change in expression between wild-type and adr-2(ok735) neural cells. DESeq2. Genes with a greater than 2-fold change in expression were reported. WBPaper00053094:adr-2(ok735)_neuron_downregulated
  Transcripts that showed significantly altered expression in acr-2(n2420) gain-of-function animals comparing to in wild type background during neuron-specic RNASeq analysis via FACS of Pacr-2::gfp reporter juIs14. DESeq2, p-value < 0.05. Identification of expressed genes in wildtype was determined using Cufflinks. Expressed genes were selected by filtering for genes with an FPKM>10 in both replicates. WBPaper00059763:neuron_acr-2(n2420gf)_regulated

1205 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr4855 A-class motor neuron: enriched in embryo (1.9) and larva (1.6). Neuronal expression include: All neurons.. Pan-neuronal: expressed in embryo; enriched in larva (3.2).  
Picture: Fig. 6A Reporter gene fusion type not specified.   Expr4828 The unc-33::gfp reporter is expressed in dividing neuroblasts at pre-comma embryonic stages. unc-33::gfp expression can be observed outside the nervous system in two amphid socket cells and weakly in non-neuronal pharyngeal cells.  
    Expr4698 Expressed in muscle cells and neurons.  
    Expr4699 Expressed in pharyngeal muscle and neuron.  
    Expr4792 TAX-6::GFP was expressed in neurons and in the cytoplasm and nucleus of intestinal cells. Expressed in the cytoplasm and nucleus of intestinal cells.
    Expr4781 Confocal analysis of strains containing the Punc-31::GFP transcriptional reporter revealed expression in the nerve ring, ventral nerve cord motor neurons, preanal ganglion, and head ganglion. Counts of cell bodies in the ventral nerve cord and preanal ganglion revealed an average of 65 +/- 2 (n = 4) GFP-positive cells, indicating that essentially all of the neurons of the ventral nerve cord and preanal ganglion express unc-31. Additional positive identifications were made for SDQ, PDE, BDU, ALM, DVA, DVB, DVC, HSN, and CAN neurons. Because these encompass most of the identifiable neurons in the background of a pan-neuronal expression pattern, authors infer that unc-31 may be expressed in essentially all neurons. All reporter strains also displayed expression in the vulval muscles VM1 and VM2 and occasional expression in what is likely VulE and VulF. Consistent expression was also noted in the UV1 cells and the spermatheca. In summary, CAPS/UNC-31 is expressed throughout the nervous system and in other secretory cells.  
    Expr4768 vps-45::EGFP is ubiquitously expressed in all major tissues, such as neuron, muscle, hypodermis and intestine. vps-45::EGFP is also expressed in coelomocytes.  
    Expr4762 CAV-1::GFP was expressed in most, if not all, cells in embryos. It was predominantly localised to, or close to, the membrane in these cells although some small intracellular bodies were also visible. This widespread expression continued into the early larval stages, but with maturation, CAV-1::GFP became restricted to most, but not all, neurons. Staining was seen in the ventral nerve cord (VNC), and was also frequently observed in the commissures. Of particular interest was the punctate nature of labelling which is most obvious in the VNC, this staining suggests possible localisation to synapses.  
    Expr4763   No substantial co-localisation was detected with pre-synaptic markers. Thus cav-1 is unlikely to be presynaptic within the VNC. Confocal images of worms carrying both cav-1::YFP and unc-63::CFP revealed that CAV-1::YFP and UNC-63::CFP co-localise in some parts of the nervous system and in structures that are either part of, or close to, the VNC. The latter localisation suggests that CAV-1 and UNC-63 co-localise in muscle arms. This pattern may include localisation to the post-synaptic regions of NMJs and extrasynaptic positioning. Within the nervous system as a whole, obvious area without co-localisation also exist, these are particularly evident in neurons that express only unc-63 and not cav-1 or vice versa, confirming that cav-1 is not expressed in all neurons.
    Expr4701 Expressed exclusively in neurons.  
    Expr4704 Expressed in head muscle, pharyngeal muscle, vulva muscle and neurons.  
    Expr4705 Expressed in pharyngeal muscle and neuron.  
Picture: Fig. 5, Fig 6.   Expr4956 NAB-1::GFP expression is restricted to epithelia and neurons. The earliest expression was observed in the hypodermis of 2-fold-stage early embryos. Immediately prior to hatching, this expression became restricted to the epithelial excretory canal and the nervous system, including the central nervous system and the motoneurons (dorsal and ventral nerve cords. In L3 and L4 larvae, NAB-1::GFP also localized transiently at the membranes of the developing vulva epithelia. Also expressed in distal tip cell (pers. comm. from Wesley Hung 11-17-07.) NAB-1::GFP puncta partially co-localized with the synaptic-vesicle protein SNT-1 and the active-zone protein UNC-10, suggesting that NAB-1 is present in presynaptic regions that are associated with vesicle pools and active zones. Similar to NAB-1, SAD-1 also showed co-localization with SNT-1. NAB-1::GFP and SAD-1 also showed partial co-localization, where each NAB-1::GFP punctum was associated with SAD-1 staining.
    Expr4930 strong bwm, vul, anal, rare ant pharynx, bwm precursors, tail hyp, neurons; early embryonic bwm at least by horseshoe stage  
    Expr4926 strong pan neuronal; spermatheca; faint vulval mu; rare and faint bwm in adult; neuronal starts at bean with strong at 3-fold.  
    Expr4383 The eps-8p::nls::gfp reporter is expressed in a variety of cell types including neurons, gut, muscle and seam cells as well as in the VPCs and their descendants. A time course analysis revealed a dynamic expression pattern of eps-8::nls:.gfp in the vulval cells. In mid-L2 larvae, eps-8p::nls::gfp is weakly expressed in all VPCs except for P3.p. Around 6 h later in early L3 larvae, before the first round of vulval cell divisions, expression is strongest in P6.p, lowest in P5.p and P7.p and intermediate in P3.p, P4.p and P8.p.  
Reporter gene fusion type not specified.   Expr4324 Pan-neuronal GFP expression.  
    Expr4236 Expressed in neurons and muscles. Whole-mount staining with SYD-9 antibodies showed specific staining in the nuclei of neurons and muscles in WT animals, whereas in ju49 and ok1110 animals, the staining either disappeared completely or was drastically reduced. Both antibodies revealed staining patterns enriched at specific subdomains within the nuclei. The C-terminal antibody detected a speckle-like pattern exclusively in the nuclei. The N-terminal antibody stained a broader region but also included the speckle-like pattern in the nuclei, suggesting that SYD-9 isoforms may have slightly different subcellular distribution.
Speckle-like patterns at the interchromatin regions are hallmarks for many RNA-binding proteins and proteins regulating pre-mRNA processing, suggesting that SYD-9 is likely involved in pre-mRNA processing.   Expr4235 GFP expression was observed throughout the nervous system and muscle cells. SYD-9::GFP accumulates in speckle-like patterns. SYD-9B::GFP preferentially accumulates at interchromatin regions.
ace-3 and ace-4 are transcribed together from an operon.   Expr4203 The construct was expressed in many cells outside the pharynx, including body wall muscle and neurons, and in several muscle cells within the pharynx, including pm3, pm4, pm5 and pm7.  
    Expr4310 Some neuronal expression.  
    Expr4311 Some neuronal expression.  
    Expr4312 Some neuronal expression.  
    Expr4302 Detected primarily in neurons.  
    Expr4303 Detected primarily in neurons.  
    Expr4304 Detected primarily in neurons.  
    Expr4305 Detected primarily in neurons.  
    Expr4306 Detected primarily in neurons.  
    Expr4307 Some neuronal expression.  
    Expr4308 Some neuronal expression.  

3 Life Stages

Remark Definition Other Name Public Name Primary Identifier
  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 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
Complement of nervous tissue (neurones, nerves, receptors and support cells) serving to detect, relay and coordinate information about an animal`s internal and external environments and to initiate and integrate its effector responses and activities. nervous system   WBbt:0005735
a cellular object that consists of subcellular components, expresses genes or functions. Cell Cell type WBbt:0004017