3 Children
| Definition | Name | Synonym | Primary Identifier |
|---|---|---|---|
| intestinal muscle cell, attach to intestine and body wall anterior to anus | intestinal muscle | stomato-intestinal muscle | WBbt:0005796 |
| intestinal lumen | WBbt:0005791 | ||
| any of 20 large epithelial cells which form a tube and are mostly situated as bilaterally symmetric pairs around the tubular lumen. Each of these cell pairs forms an intestinal ring ( II-IX int rings). The most anterior intestinal ring (int ring I), however, is made of four cells. Intestinal cells contain large nuclei with large nucleoli and numerous autofluorescent granules in their cytoplasm. | intestinal cell | WBbt:0005792 |
49 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Transcripts that showed significantly increased expression at the intestine cells of daf-2(e1370) comparing to the intestine cells of N2 animals at L2 larva stage. | DESeq2 (version 1.24.0), fold change >= 2, FDR < 0.05 | WBPaper00064632:daf-2(e1370)_upregulated_intestine | |
| 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 unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_enriched | |
| Single-cell RNA-Seq cell group 3_4 expressed in intestine. | scVI 0.6.0 | WBPaper00065841:3_4 | |
| Single-cell RNA-Seq cell group 3_5 expressed in intestine. | scVI 0.6.0 | WBPaper00065841:3_5 | |
| Transcripts enriched in intestine by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector. | Genes were determined intestine-enriched if the lowest expression value (log2(FPKM+1)) observed in the intestine empty vector samples was at least 2-fold higher than the highest expression value observed in the germline empty vector samples. | WBPaper00051039:intestine_enriched | |
| Top 300 transcripts enriched in intestine 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:Intestine | |
| 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:intestine_embryo_enriched | |
| 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 | |
| Proteins expressed in intestine cytoplasm, according to tissue specific APX enzyme expression using spp-5 promoter driven NES(cytoplasm)-GFP-APX, followed with mass spectrometry. | Fold change > 2. | WBPaper00051245:intestine_cytoplasm_expressed | |
| Genes enriched in intestine. | To identify genes that are significantly enriched by mRNA tagging, we first normalized the total amount of Cy3 and Cy5 signal to each other in each hybridization. We measured the ratio of the signals from the co-immunoprecipitated mRNA (Cy5) to total RNA in the cell extract (Cy3), and calculated the percentile rank for each gene relative to all genes in each hybridization. The mean percentile rank was determined from eight repeats of the mRNA-tagging experiment. Student's t-test was used to determine which genes showed a mean enrichment significantly greater than the median enrichment for all genes (P<0.001). | WBPaper00026980:intestine_enriched | |
| P.pacificus genes enriched in intestine. | Cuffdiff (version v2.0.1) | WBPaper00049334:PE_intestine_enriched | |
| Transcripts that showed significantly decreased expression in ifo-1(kc2) comparing to in N2 animals. | ANOVA, p-value < 0.05. | WBPaper00056167:ifo-1(kc2)_downregulated | |
| Genes enriched in L4 larva intestinal AIN-2 miRISCs, potentially involved in non-development processes. Pges-1-ain-2-gfp IP was performed in synchronized L4 larva. | Enrichment values are expressed as mean percent rank. The p value was computed by comparing all enrichment values for a given transcript to all enrichment values of all transcripts by a one-tailed t test. Significantly enriched genes are those with p value < 0.01. | WBPaper00040985:AIN-2_L4_intestine | |
| Proteins expressed in intestine nucleus, according to tissue specific APX enzyme expression using spp-5 promoter driven NLS(nucleus)-GFP-APX, followed with mass spectrometry. | Fold change > 2. | WBPaper00051245:intestine_nucleus_expressed | |
| 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:intestine_larva_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:intestine_embryo_SelectivelyEnriched | |
| Enriched in intestinal (adult). | WBPaper00029359_1217 | ||
| Enriched in intestinal (adult). | WBPaper00029359_1280 | ||
| Enriched in intestinal (adult). | WBPaper00029359_1353 | ||
| Enriched in intestinal (adult). | WBPaper00029359_1444 | ||
| Enriched in intestinal (adult). | WBPaper00029359_1504 | ||
| Enriched in intestinal (adult). | WBPaper00029359_1548 | ||
| Enriched in intestinal (adult). | WBPaper00029359_1604 | ||
| C.elegans genes enriched in intestine. | Cuffdiff (version v2.0.1) | WBPaper00049334:CE_intestine_enriched | |
| Genes enriched in intestinal AIN-2 miRISCs. Pges-1-ain-2-gfp IP was performed in mixed stage worms. | Enrichment values are expressed as mean percent rank. The p value was computed by comparing all enrichment values for a given transcript to all enrichment values of all transcripts by a one-tailed t test. Significantly enriched genes are those with p value < 0.01. | WBPaper00040985:AIN-2_asynchronous_intestine | |
| Enriched in intestinal (adult), body wall muscle (adult), pharynx). | WBPaper00029359_1578 | ||
| Transcription factors expressed exclusively in intestine, according to mRNA-tagging and RNAseq studies. | Cuffdiff algorithm was used. FPKM >= 1 was used as threshold across all tissues profiled for defining expressed genes. | WBPaper00046338:intestine_unique | |
| 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:intestine_larva_SelectivelyEnriched |
3539 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr16505 | We examined the expression of pals-17p::GFP and pals-20p:: wrmScarlet transcriptional reporters at the L4 stage. Both transgenes were expressed in intestinal tissue, especially in the anterior-most and posterior-most intestinal cells. Furthermore, we found that both reporters were expressed in the head region. pals-17p::GFP signal was present in head neurons, whereas pals-20p::wrmScarlet was sporadically and weakly expressed in the head region. | |||
| Picture: Figure S2. | Expr4898 | SRP-6::GFP was expressed in the socket cells, the pharyngeal-intestinal valve, vulval hypoderm, the spermatheca and spermathecal-uterine junction and the intestine. Corresponding expression was seen in the srp-6::lacZ fusions. | ||
| Picture: FIG. 1D-G. | Expr4885 | Expressed in a relatively broad range of tissues. Robustly expressed in vulval muscles, and modestly expressed in body wall muscles and in the pharynx. Expression of was also observed in the intestine and expression of asd-1 was observed in the nervous system. Widely expressed in the early embryos before morphogenesis. | ||
| Picture: FIG. 1D-G. | Expr4886 | Expressed in a relatively broad range of tissues. Robustly expressed in vulval muscles, and modestly expressed in body wall muscles and in the pharynx. Expression of was also observed in the intestine. Widely expressed in the early embryos before morphogenesis. | ||
| Picture: Fig. 4A. | Expr4883 | Low GFP signals were detected exclusively in the intestinal cells of late embryos, L1L4, and adult hermaphrodites. | ||
| Picture: Fig. 4C. | Expr4884 | Immunolocalization by electron microscopy of GSTO-1 using wild-type worms confirmed expression of GSTO-1 in intestinal cells. | ||
| Picture: Figure 4H, 4I. | Expr4876 | The expression of nfya-2 was restricted to few tissues, including the spermatheca, some neurons in the head and other body regions. Notably, it was highly expressed in intestine cells at all developmental stages. | NFYA-2 localized to the nucleus. | |
| Expr4870 | A-class motor neuron: expressed in embryo; enriched in larva (1.6). Neuronal expression include: All ventral cord motor neurons, head neurons, touch neurons. Also expressed in other cells: Intestine, anal depressor, head muscle. Pan-neuronal: expressed in embryo and larva. | |||
| 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). | |||
| Expr4861 | A-class motor neuron: enriched in embryo (6.3) and larva (2.5). Neuronal expression include: VA, head neurons. Also expressed in other cells: Intestine. Pan-neuronal: expressed in embryo; enriched in larva (3.1). | |||
| 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). | |||
| Expr4843 | 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). | |||
| Expr4840 | 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. | |||
| Picture: Figure 1D, I and II. | Expr4833 | The promoter extracted from B0336.3 is able to drive GFP expression in hypodermis, pharyngeal gland cell, gut, and nerve ring. | ||
| Picture: Figure 1D III and IV. | Expr4834 | B0336.2 is able to drive GFP expression in the pharynx, gut, and head neurons. | ||
| Picture: Figure 5. | Expr4837 | Fluorescence started to be visible in two cells of young embryos at around the 64 AB cell stage. Towards the end of gastrulation expression was visible in about 40 cells throughout the embryo including neuronal precursors, ventral hypodermal cells, and pharyngeal precursor cells. At the 1 to 2 fold stages fluorescence was observed in IL1 neurons (the identity was determined post-embryonically), the nine buccal epidermal cells, and additional cells in the head, most likely arcade cells. Transient expression was also observed in embryonic motoneurons (no longer visible in 3 fold stage embryos) and in a few apoptotic cells in the head. Based on their position they could be the sister cells of some of the IL1 neurons, which are known to undergo programmed cell death at this developmental stage. At the 3 fold stage expression was restricted to the buccal epidermal cells, most of the arcade cells (3 anterior and the DL and DR posterior arcade cells), and the six IL1 neurons. The two lateral IL1 neurons expressed the marker only weakly also in the L1 larval stage (but not later during development), whereas the dorsal and ventral IL1 neurons expressed GFP strongly throughout all larval stages and in the adults. Starting from the L1 larval stage expression could also be observed in the posterior cells of the gut. Starting from the L2 stage, when gonad development and migration begins, fluorescence became also visible in the distal tip cells of the gonad. | ||
| Picture: Fig. 10 H. | Expr4823 | The hex-3 construct was expressed in gut granules. Expressed throughout the life-cycle. | ||
| Picture: fig. S3 A. | Expr4826 | A transgene containing the sel-10 promoter driving green fluorescent protein (GFP) labeled a subset of neurons including the HSNL, which suggests that sel-10 is expressed in the HSNL. sel-10 promoter driven GFP is widely expressed in body wall muscles (not consistent though), intestine(not consistent), pharynx, distal tip cell, spermatheca, and within nervous system, it is expressed in HSNs, some ventral cord neurons, a bunch of unidentified head neurons and a few tail neurons. --Pers. Comm. from Mei Ding 11-20-07. | ||
| Expr4687 | Embryonic expression of pgp-2::gfp was first seen in the daughters of the E blastomere (E2 stage), which generate the intestine. Intestinal expression persisted through embryogenesis and into adulthood. Rarely, weak expression of pgp-2::gfp was detected in embryonic and adult hypodermal cells. Pharyngeal or AWA expression of the pgp-2::gfp reporter were never detected. | |||
| Expr4688 | Intestinally expressed PGP-2::GFP was localized to prominent vesicular structures and the plasma membrane in embryos and adults. Similar organelles were stained by anti-PGP-2 antibodies. Anti-PGP-2 antibodies only stained intracellular compartments in embryos and adults, suggesting that the PGP-2::GFP might be partially mislocalized to the plasma membrane. PGP-2::GFP colocalized with birefringent material and the V-ATPase subunit FUS-1 in embryos, and in adults PGP-2::GFP colocalized with autofluorescent compartments. PGP-2 antibodies stained compartments containing GLO-1::GFP. These results indicate that PGP-2 and PGP-2::GFP are associated with the gut granule membrane. | |||
| Expr4684 | GFP expression was detected at most developmental stages, with the spatial expression depending on the developmental stage of the animal. Neuronal expression of hlh-29 was detected in larvae and adults in both amphid and phasmid sockets, in the ALA and PVT neurons, in the chemosensory and mechanosensory neurons, ASI, ASK, PHA, and PQR, and in neurons of the anterior pharyngeal bulb. Weaker expression was also detected in the ASG chemosensory neurons in some transgenic lines. L1 animals show strong expression of hlh-29 in intestinal cells, and weaker expression in the rectal glands and the pharyngeal muscle cell PM1. By L3 stage, intestinal expression of the hlh-29::GFP is limited to the posterior intestinal cells, and PM1 expression is no longer detected. Expression is also detected in the ventral posterior coelomocytes in the later L3-stage larvae, and in the spermatheca and vulval muscles of L4 and adult animals. | |||
| 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. | ||
| The subcellular patterns observed in experiments using anti-HAF-6 antibody were similar to the patterns of GFP expression observed in transgenic animals expressing the HAF-6::GFP fusion protein. | Expr4795 | HAF-6 was predominantly expressed in intestinal and germline tissue. | In double-labeling experiments, the anti-HAF-6 antibody did not decorate the same cellular compartment as a mitochondrial antibody (anti-Complex IV). Authors did observe co-compartmentalization using anti-HAF-6 and anti-Calreticulin antibodies, indicating that HAF-6 likely resides in the endoplasmic reticulum and not in mitochondria. HAF-6 localization extended to perinuclear regions in germline tissue, which is consistent with an endoplasmic reticulum (ER) localization. However, localization of HAF-6 to the nuclear periphery was not prominent in intestinal tissue. | |
| Expr4783 | Prominent expression of ORAI-1::GFP was detected in the spermatheca, intestine and hypodermis. In the intact animal, it was unclear whether gonadal sheath cells expressed ORAI-1::GFP, due to the intense fluorescence from the intestine and spermatheca. To examine sheath cell expression further, authors imaged gonads dissected free from a worm strain expressing an orai-1 transcriptional GFP reporter. orai-1 is also expressed in both proximal and distal gonadal sheath cells. | Intestinal expression appeared to be localized to both apical and basolateral membrane regions. The circumferential ORAI-1::GFP localization pattern is consistent with expression in the basal plasma membrane. Non-circumferential localization is probably due to membrane folding and/or expression at lateral cell borders. The complicated morphology of the spermatheca precluded definitive localization of ORAI-1::GFP to the apical cell membrane. | ||
| Expr4779 | The fkb-6 transcript was temporally expressed in all stages from embryo to adult with predominant spatial expression being noted in the adult dorsal and ventral nerve cords. In addition, weaker spatial expression was noted in the pharynx, hypodermis, body wall muscle cells and some somatic and gut cells. | |||
| Expr4771 | Expressed in pharynx, intestine (basolateral membrane). | Expressed in basolateral membrane of intestine. | ||
| Expr4773 | Expressed in intestine, excretory cell, seminal vesicle/vas deferens. | |||
| Expr4774 | Expressed in intestine (apical membrane). | Expressed in apical membrane of intestine. | ||
| 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. |
4 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 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 |
3 Parents
| Definition | Name | Synonym | Primary Identifier |
|---|---|---|---|
| inner tube of two concentric tubes that make up the body | digestive tract | WBbt:0005743 | |
| alimentary system | WBbt:0005748 | ||
| a collection of cells or cell groups that collectively perform a function | organ | WBbt:0003760 |
