Genomics
1 Transcripts
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
Transcript:B0218.3.1 | B0218.3.1 | 1671 | IV: 8148794-8151266 |
Other
1 CDSs
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
CDS:B0218.3 | B0218.3 | 1134 | IV: 8148806-8148954 |
46 RNAi Result
63 Allele
Public Name |
---|
gk964278 |
gk964500 |
gk963722 |
gk963417 |
gk963416 |
pkP672 |
tm676 |
gk946388 |
qd15 |
qd20 |
qd11 |
qd13 |
qd47 |
qd49 |
qd9 |
gk398314 |
gk375887 |
gk527233 |
gk332180 |
gk406245 |
gk475187 |
gk896162 |
gk793804 |
gk676969 |
gk359757 |
gk371859 |
WBVar02057882 |
ku54 |
gk348144 |
gk359756 |
1 Chromosome Location
Feature . Primary Identifier |
Start | End | Strand |
---|---|---|---|
WBGene00004055 | 8148794 | 8151266 | 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_chrIV_8151267..8152444 | 1178 | IV: 8151267-8152444 | Caenorhabditis elegans |
112 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 | |
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 |
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 | |
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 | |
Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
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 | |
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 | |
Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines. | RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1. | WBPaper00035269:cde-1_regulated | |
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 xrep-4(lax137). | DESeq2. Genes were selected if their p value < 0.01. | WBPaper00066062:xrep-4(lax137)_upregulated | |
Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult | |
Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult | |
Transcripts that showed significantly increased expression after N2 animals were exposed to BL21 bacteria carrying pET28a-cry5B, comparing to animals exposed to BL21 control bacteria. | Differentially expressed genes were identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05. | WBPaper00065732:Cry5Ba_upregulated_N2 | |
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours. | Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50. | Cuffcompare and Cuffdiff | WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047) |
Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. | N.A. | WBPaper00026929:sir-2.1_overexpression_regulated | |
Genes expressed in N2. | Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0. | WBPaper00025141:N2_Expressed_Genes | |
Strictly embryonic class (SE): genes that are the subset of embryonic genes that are not also classified as maternal. | A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. | [cgc5767]:expression_class_SE | |
Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:spr-1(ok2144)_upregulated | |
24 hours of AgNPs exposure. | Genes downregulated more than 2 fold after 24 hours of AgNPs exposure. | Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL). | WBPaper00034661:AgNPs_downregulated |
Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2. | DESeq2 Benjamini-Hochberg adjusted p-value < 0.05. | WBPaper00049545:jmjd-3.1(+)_upregulated | |
Transcripts with significantly increased expression in isp-1(qm150) vs. N2, and in isp-1(qm150) ced-4(n1162) vs. ced-4(n1162). | Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. | WBPaper00045263:isp-1(qm150)_upregulated | |
Transcripts that showed significantly increased expression in plp-1(ok2155) adult animals comparing to in wild type. | DESeq2. Genes with at least 2-fold upregulation with a raw P value <= 0.05 only are listed. | WBPaper00060526:plp-1(ok2155)_upregulated | |
Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis. | A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. | [cgc5767]:expression_class_E | |
Bacteria infection: Xenorhabdus nematophila | Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila. | Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. | WBPaper00041606:CE_X.nematophila_regulated |
Genes that showed significant differential expressed between control and 150 mg\/L Atrazine treatment. | t-test, p < 0.05. | WBPaper00036123:Atrazine_regulated | |
Transcripts that showed significantly decreased expression in oocyte germline cells comparing to in mitosis germline cells. | Log2 Fold change > 2 or <-1, p-value < 0.05. | WBPaper00053599:oocyte_vs_mitosis_downregulated |
11 Expression Patterns
Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
---|---|---|---|---|
Expr1031953 | Tiling arrays expression graphs | |||
Expr16025 | Consistent with previous reports, our immunofluorescence result confirmed that the p-PMK-1 is expressed exclusively in somatic cells, particularly the anterior end of the intestine, while this signal is completely abolished in the pmk-1 mutant. | |||
Expr10582 | pmk-1::gfp is expressed in the cytoplasm of anterior and posterior intestinal cells as well as in some neurons of the head region. | pmk-1 is localized in the cytoplasm. | ||
Expr15772 | PMK-1-p38 MAPK protein is nuclearly localized throughout the germline in wild type. | |||
Expr14762 | We tagged the endogenous pmk-1 gene with mNG::3Flag at the 3' end. We observed PMK-1::mNG expression in vulval lineages and throughout the rest of the animal, with the exception of the germline; germline expression appeared to be silenced, an established phenomenon with certain foreign DNA insertions. | |||
Expr2014969 | 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). | |||
Expr1142956 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
Expr1028519 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
Expr12210 | PMK-1 was found to be broadly expressed in multiple tissue types. | |||
Expr2033204 | 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). | |||
Expr14763 | We N-terminally tagged PMK-1 expressed from lin-31 promoter in VPCs, using the mini- Mos system, and with mKate2 rather than mNG. We observed localization to both nuclei and cytosol of VPCs. |
53 GO Annotation
Annotation Extension | Qualifier |
---|---|
enables | |
has_input(WB:WBGene00004804) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
has_input(WB:WBGene00004393),occurs_in(WBbt:0005772) | involved_in |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
part_of(GO:0050832) | involved_in |
involved_in | |
involved_in |
22 Homologues
Type |
---|
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
53 Ontology Annotations
Annotation Extension | Qualifier |
---|---|
enables | |
has_input(WB:WBGene00004804) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
has_input(WB:WBGene00004393),occurs_in(WBbt:0005772) | involved_in |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
part_of(GO:0050832) | involved_in |
involved_in | |
involved_in |
10 Regulates Expr Cluster
Regulated By Treatment | Description | Algorithm | Primary Identifier |
---|---|---|---|
Genes that showed more than 2 fold increased expression in pmk-1(km25) comparing to in N2 when fed with OP50. | The significantly expressed genes were selected based on ANOVA analysis by Partek Genomics Suite software. Genes with a p-value of <0.05 and a 2-fold or greater fold change were considered differentially expressed. | WBPaper00046083:pmk-1(km25)_OP50_upregulated | |
Genes that showed more than 2 fold increased expression in pmk-1(km25) comparing to in N2 when fed with OP50. | The significantly expressed genes were selected based on ANOVA analysis by Partek Genomics Suite software. Genes with a p-value of <0.05 and a 2-fold or greater fold change were considered differentially expressed. | WBPaper00046083:pmk-1(km25)_OP50_downregulated | |
Transcripts that showed significantly increased expression in pmk-1(km25) BPW156 animals comparing to in BPW158 wild type animals | fold change > 2, p-value < 0.05 | WBPaper00065823:pmk-1(km25)_upregulated | |
Bacteria infection: Pseudomonas aeruginosa PA14. 4 hours at 25C. | Transcripts that showed significantly increased expression after N2 L4 animals were infected by P. aeruginosa (PA14) bacteria for 4 hours at 25C, but pmk-1(km25) animals showed reduced fold change after they went through the same infection. | DESeq2 | WBPaper00056275:P.aeruginosa_upregulated_pmk-1(km25)_dependent |
Bacteria infection: Pseudomonas aeruginosa PA14. 4 hours at 25C. | Transcripts that showed significantly decreased expression after N2 L4 animals were infected by P. aeruginosa (PA14) bacteria for 4 hours at 25C, but pmk-1(km25) animals showed reduced fold change after they went through the same infection. | DESeq2 | WBPaper00056275:P.aeruginosa_downregulated_pmk-1(km25)_dependent |
Transcripts that showed significantly decreased expression in pmk-1(km25) BPW156 animals comparing to in BPW158 wild type animals | fold change > 2, p-value < 0.05 | WBPaper00065823:pmk-1(km25)_downregulated | |
Genes upregulated by wild-type pmk-1 (downregulated in daf-2(e1368);pmk-1(km25) strain as compared to daf-2(e1368) strain) by at least 2 fold and P < 0.01, as determined by a t-test. | At least 2 fold and P < 0.01, as determined by a t-test. | WBPaper00028789:pmk-1_upregulated | |
Genes downregulated by wild-type pmk-1 (upregulated in daf-2(e1368);pmk-1(km25) strain as compared to daf-2(e1368) strain) by at least 2 fold and P < 0.01, as determined by a t-test. | At least 2 fold and P < 0.01, as determined by a t-test. | WBPaper00028789:pmk-1_downregulated | |
Transcripts that showed significantly decreased expression in pmk-1(km25) comparing to in N2. | Differentially regulated transcripts were determined by edgeR. For the microarray and NanoString analyses, genes were considered differentially regulated at FDR < 0.05 and log2 (Fold Change) > 1 or < 1. | WBPaper00050515:pmk-1(km25)_downregulated | |
Transcripts that showed significantly increased expression in pmk-1(km25) comparing to in N2. | Differentially regulated transcripts were determined by edgeR. For the microarray and NanoString analyses, genes were considered differentially regulated at FDR < 0.05 and log2 (Fold Change) > 1 or < 1. | WBPaper00050515:pmk-1(km25)_upregulated |