WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00004055 Gene Name  pmk-1
Sequence Name  ? B0218.3 Brief Description  pmk-1 encodes a mitogen-activated protein kinase (MAPK), orthologous to human p38 MAPK (OMIM:600289); PMK-1 is an essential component of the MAPK pathway that regulates the innate immune response; PMK-1 is required, upstream of CED-9, for eliciting gonadal programmed cell death in response to Salmonella enterica infection; PMK-1 physically interacts with the ATF-7 transcription factor to regulate the transcriptional innate immune response and phosphorylation of ATF-7 is dependent upon PMK-1 and SEK-1.
Organism  Caenorhabditis elegans Automated Description  Enables MAP kinase activity and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in several processes, including behavioral response to nicotine; positive regulation of macromolecule biosynthetic process; and response to stress. Located in cytosol and nucleus. Expressed in several structures, including germ line; head neurons; intestine; and vulval precursor cell. Used to study Parkinson's disease. Human ortholog(s) of this gene implicated in gastrointestinal system cancer (multiple). Is an ortholog of human MAPK11 (mitogen-activated protein kinase 11) and MAPK14 (mitogen-activated protein kinase 14).
Biotype  SO:0001217 Genetic Position  IV :3.64389 ±0.001545
Length (nt)  ? 2473
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00004055

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

WormBase ID
WBRNAi00113180
WBRNAi00038745
WBRNAi00027999
WBRNAi00062839
WBRNAi00077210
WBRNAi00077216
WBRNAi00077208
WBRNAi00095259
WBRNAi00112950
WBRNAi00113095
WBRNAi00113149
WBRNAi00093371
WBRNAi00093372
WBRNAi00087938
WBRNAi00069165
WBRNAi00064194
WBRNAi00084568
WBRNAi00112551
WBRNAi00097088
WBRNAi00097089
WBRNAi00097092
WBRNAi00084155
WBRNAi00095109
WBRNAi00097054
WBRNAi00097057
WBRNAi00022792
WBRNAi00038577
WBRNAi00022861
WBRNAi00038578
WBRNAi00038579

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

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

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

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00004055 8148794 8151266 1

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

1 Sequence

Length
2473

1 Sequence Ontology Term