Genomics
3 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F11C1.6a.2 | F11C1.6a.2 |
2572
 |
X: 13008493-13013964 |
| Transcript:F11C1.6a.1 | F11C1.6a.1 |
2474
|
X: 13008886-13013962 |
| Transcript:F11C1.6b.1 | F11C1.6b.1 |
2353
|
X: 13009266-13013964 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F11C1.6a | F11C1.6a |
1719
|
X: 13008892-13009008 |
| CDS:F11C1.6b | F11C1.6b |
1479
|
X: 13009481-13009499 |
143 RNAi Result
95 Allele
| Public Name |
|---|
| gk964260 |
| gk964029 |
| gk962707 |
| gk964028 |
| gk963810 |
| gk963581 |
| WBVar01691274 |
| WBVar01691273 |
| WBVar01691275 |
| gk364153 |
| gk864691 |
| gk297666 |
| gk297665 |
| gk297670 |
| gk297669 |
| gk297668 |
| gk297667 |
| gk297674 |
| gk297673 |
| gk297672 |
| gk297671 |
| gk297675 |
| WBVar01602359 |
| WBVar01602361 |
| WBVar01602360 |
| kry6 |
| h17041 |
| WBVar01817152 |
| gk887523 |
| WBVar01471893 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003623 | 13008493 | 13013964 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_13013965..13014449 | 485 | X: 13013965-13014449 | Caenorhabditis elegans |
217 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts of coding genes that showed significantly decreased expression in muscle. | DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. | WBPaper00062325:muscle_depleted_coding-RNA | |
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| adult vs dauer larva | Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. | N.A. | WBPaper00050488:adult_vs_dauer_regulated_N2_20C |
| Osmotic stress | Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:OsmoticStress_regulated_Food |
| Osmotic stress | Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:OsmoticStress_regulated_NoFood |
| Bacteria infection: Enterococcus faecalis | Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50. | For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. | WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray |
| Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin_upregulated | |
| Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). | DESeq2, fold change >= 2, FDR <= 0.01. | WBPaper00056826:SGP_biased | |
| Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Metformin_upregulated | |
| Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq. | DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison. | WBPaper00045934:wrn-1(gk99)_upregulated | |
| Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:body-muscle_expressed | |
| Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day5_vs_Day1_downregulated | |
| Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:hypodermis_expressed | |
| Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00060909:atfs-1(cmh15)_downregulated | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade). | For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). | WBPaper00040858:eQTL_age_regulated_aging | |
| Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 hours at 24 centigrade). | For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). | WBPaper00040858:eQTL_regulated_aging | |
| Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141) | |
| Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141) | |
| Bacteria infection: Bacillus thuringiensis | mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h |
| Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO. | Fold change > 2. | WBPaper00064306:Agaro-oligosaccharides_upregulated | |
| Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
| Bacteria infection: Bacillus thuringiensis | mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h |
| Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2. | DEseq 1.18.0, adjusted p-value < 0.05. | WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated | |
| Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-1(gk214)_upregulated | |
| Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. | DESeq2, fold change > 2, adjusted p-value < 0.01 | WBPaper00058598:sin-3(tm1276)_downregulated | |
| Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition. | Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed. | WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose | |
| Transcripts that showed significantly increased expression in xrep-4(lax137). | DESeq2. Genes were selected if their p value < 0.01. | WBPaper00066062:xrep-4(lax137)_upregulated | |
| Gamma irradiation 100 mGY per hour for 72 hours since L1 larva. | Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage. | DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3. | WBPaper00058958:100mGy-irradiation-72h_upregulated |
| Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. | The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. | WBPaper00044736:oscillating_dev_expression | |
| Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2. | DESeq 2, fold change > 2, FDR < 0.05. | WBPaper00065581:hpk-1(pk1393)_upregulated |
27 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2871 | The mRNAs for lin-42, nhr-23, and nhr-41a exhibit a low-high (peak)-low profile during the L1 intermolt that is precisely reiterated at later stages. The mRNAs for nhr-25a, nhr-25b, and nhr-41b have a high-low-high (peak) expression profile during the L1 stage (and into early L2) that is also reiterated. nhr-25a and nhr-41b also show a downward trend in baseline expression as development proceeds. For all six mRNAs, there are peaks of expression that occur at precise intervals relative to the molt at all larval stages: nhr-25b and nhr-41b peak at the beginning of the intermolt; nhr-23 peaks at mid-intermolt, slightly preceding the intermolt peak in lin-42 expression; and nhr-25a and nhr-41a peak at the time the larval molts occur. Two mRNAs, nhr-6 and nhr-85a, show a more irregular expression pattern with respect to the molt; however, it should be noted that nhr-6 mRNA has consistent relatively lower expression values at the times the molt takes place. nhr-67 also does not display a reiterated, oscillating expression pattern, although two early peaks are observed at the end of the L1 stage and at the beginning of L2. | |||
| Expr1031669 | Tiling arrays expression graphs | |||
| Data observed from, atIs13, atEx32 and atEx35. | Expr970 | In comma to 1.5-fold stage embryos, the nhr-25::GFP are expressed in the V cells, P cells and hyp7. Expression also observed in the head and tail hypodermal cells of embryos. The earliest expression is at ~250-300 min post fertilization. atEx32 and atEx35 L1 animals exhibited consistent reporter expression in the hyp7 and P cell nuclei. The P cell expression was very strong at hatching. GFP expression in the P cell and hyp7 decreased during mid-L1, but frequently increased late L1. At hatching no expression in observed in the V cells. In mid L1 the V cells divided and the anterior daughters begin to express GFP as they join the syncytium. Strong expression is also seen in the head and tail hypodermal nuclei of L1 larva. Expression in the hypodermal nuclei of older larva stages is similar to that in the L1. GFP expression decreases markedly in adults. GFP is also observed in other ectodermal cells. In L1, expression is observed in the G2(excretory pore) cell and in a cell tentatively identified as the W neuroblast. In older larva, expression continues in G2 but disappears in the W lineage once the cells divides to generate neurons. Beginning in L2, GFP is expressed in the region around the rectum. Expression is also occasionally observed in the anterior pharynx, in the nuclei with positions consistent with those of the pharyngeal epithelial cells. | nuclei | |
| Expr7322 | Click the movie links below for interactive 4D movies of a fluorescence reporter. http://glowormnotes.blogspot.com/2009/11/nhr-25yfp-transcriptional-fusion.html | |||
| Expr1132 | maternal mRNA was evenly distributed in the early embryo. By about 120min, zygotic mRNA expression began in the progeny of E cell. then progressed into the posterior hypodermal precursor cells. Starting from the comma stage, the mRNA expression localized to the hypodermis and intestine, where it continued during early larva stages. Strong expression in the developing and adult germ line. The mRNA appeared in the primordial gonads of L2-L3 larvae and continued to accumulate in the gonadal loops as they expanded in L4. The adult gonad was loaded with transcript. mRNA expressed declined in the rest of the body after L2. | |||
| Expr11328 | NHR-25 was first observed in major epidermal cells of embryo with approximately 200 cells and continuously expressed throughout embryogenesis and larval stages as judged by a combination of cell morphology and position. It was also observed in precursor/blast cells of neuron and epidermis which are called Pnp cells in embryo and in seam cells during early larval stages. Despite its expression in precursors of neurons and epidermal cells, NHR-25 appears not to be expressed in the neurons of larval stage. | |||
| Expr11461 | NHR-25::GFP was evenly distributed prior to the first division in all VPCs, whereas after the first division the pattern became graded: highest in 1 P6.p daughters, lower in 2 P5.p and P7.p daughters, and lowest in 3 P(3,4,8).px. After the third round of cell divisions NHR-25::GFP expression continued in all 22 P(5-7).pxxx cells and remained high during early vulva morphogenesis until it temporarily disappeared by the ''Christmas tree stage''. In wild type animals, NHR-25::GFP was normally expressed in the anchor cell at the time of the first VPC divisions, and subsequently decreased. NHR-25::GFP is expressed in nuclei of seam cells and hyp7. | |||
| Expr3137 | Antibody stained the same nuclei lit by the scm::gfp seam-cell-specific marker at L1 and later stages. A weaker signal was observed in the nuclei of hyp7 cells produced by the first asymmetric division of the V cells. A transgenic nhr-25::gfp construct confirmed that nhr-25 was expressed in the seam cells from L1 until adulthood; consistent with the antibody staining, this construct was less active in the hyp7 daughters. | nuclei | ||
| Reporter gene fusion type not specified. nhr-25::gfp-C causes early embryonic developing arrest, thus none of the embryos showing GFP expression hatched. | Expr1133 | Expression first appeared in the four descendants of the E cell and later in derivatives of AB.p and C blastomeres. The expression continued in the hypodermis but not gut throughout the remainder of the embryogenesis. In L1, the strongest GFP was signals were observed in the seam cells and the pharyngeal and tail hypodermis. Also noted expression in the excretory duct cell. | Regardless of NLS, localized to nuclei. | |
| Expr11078 | NHR-25::YFP is expressed in the nuclei and cytoplasm of epidermal cells during morphogenesis. | |||
| Expr3035 | An nhr-25::gfp reporter was found to be expressed in the nuclei of many epidermal cells, including the epidermal syncytial cells, the seam cells, and all the Pn.p cells and their progeny. Many cells in the head and tail also showed nhr-25::gfp expression. nhr-25 expression was first observed during embryogenesis around the 100-cell stage and continued to be expressed throughout development in the epidermal and seam cells. In the Pn.p-derived vulval cells, when vulval morphogenesis (including cell division, fusion, and migration) was almost complete during the L4-to-adult transition, nhr-25::gfp expression significantly decreased, whereas in other Pn.p cells that fused with hyp7, nhr-25::gfp expression remained largely unchanged. | Expressed in the nuclei of many epidermal cells | ||
| Expr1200106 | Data from the TransgeneOme project | |||
| Expr10510 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr10511 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr10513 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr3975 | nhr-25 mRNA is present in the early gonad primordium. | |||
| Expr11054 | nhr-25 transcriptional reporter shows a dynamic expression pattern in which expression in hyp8-11 is intense prior to and at the beginning of tail tip morphogenesis, rapidly shuts off in late L4, and is never on in adult animals. | |||
| Expr3976 | The NHR-25 protein can be detected in the nuclei of Z1 and Z4 as well as in the nuclei of their daughter cells, but not in the Z2 and Z3 precursors of the germline. | nuclei | ||
| Expr13677 | The 3' nhr-25 enhancer specifically drives GFP expression in approximately 20 hypodermal cells in the head and tail of the worm during larval development. | |||
| Expr12800 | nhr-25 was expressed in V seam cells, in the posterior seam-cell T and its daughters (T.a, T.p), and in the hyp cells of wild-type animals. | |||
| Expr969 | Both nhr-25a and nhr-25b transcripts were detected in all stages. Furthur more, based on detection in serial dilutions relative to ama-1 mRNA levels, both nhr-25 transcripts are more highly expressed in embryos and L1 - L3 stages than in the L4 and adult stages. | |||
| Expr2014151 | Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans). | |||
| Expr2032394 | Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans). | |||
| Expr1148306 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1014976 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr10512 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr1200241 | Data from the TransgeneOme project |
23 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| part_of | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00000039),occurs_in(WBbt:0005753) | acts_upstream_of_or_within |
| involved_in | |
| involved_in | |
| enables | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables |
12 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| orthologue |
| least diverged orthologue |
23 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| part_of | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00000039),occurs_in(WBbt:0005753) | acts_upstream_of_or_within |
| involved_in | |
| involved_in | |
| enables | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables |
2 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Genes down-regulated following nhr-25(RNAi). | Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. | WBPaper00045015:nhr-25(RNAi)_downregulated | |
| Genes up-regulated following nhr-25(RNAi). | Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. | WBPaper00045015:nhr-25(RNAi)_upregulated |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_13008420..13008492 | 73 | X: 13008420-13008492 | Caenorhabditis elegans |
