WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00018192 Gene Name  F39B3.3
Sequence Name  ? F39B3.3 Organism  Caenorhabditis elegans
Automated Description  Enriched in germ line and sensory neurons based on RNA-seq studies. Is affected by several genes including cyc-1; jmjd-3.1; and mir-243 based on microarray and RNA-seq studies. Is affected by hydrogen sulfide and cadmium based on microarray studies. Biotype  SO:0001217
Genetic Position  Length (nt)  ? 420
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00018192

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F39B3.3.1 F39B3.3.1 420   X: 17578692-17579111
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:F39B3.3 F39B3.3 420   X: 17578692-17579111

4 RNAi Result

WormBase ID
WBRNAi00041609
WBRNAi00046764
WBRNAi00011437
WBRNAi00031984

19 Allele

Public Name
gk964260
gk963810
gk963581
gk964446
gk964447
gk655151
gk865764
gk822004
gk351734
gk645086
gk520755
gk931899
gk705046
gk731240
gk774310
gk308292
gk308293
WBVar00603780
WBVar01529421

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00018192 17578692 17579111 -1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

0 Downstream Intergenic Region

24 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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 increased expression in daf-2(e1370) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:daf-2(e1370)_upregulated
  Transcripts that showed significantly decreased expression in nhr-114(gk849) comparing to wild type animals at L4 larva. DESeq2 1.26.0, fold change > 2, FDR < 0.05. WBPaper00064539:nhr-114(gk849)_downregulated
  Significantly downregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. SAM algorithm with an FDR < 0.1. WBPaper00033065:cyc-1(RNAi)_downregulated
  Genes that showed significant differential expressed between control and 20 mg\/L Cadmium treatment. t-test, p < 0.05. WBPaper00036123:Cadmium_regulated
  Transcripts that showed significantly decreased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2. DESeq2 Benjamini-Hochberg adjusted p-value < 0.05. WBPaper00049545:jmjd-3.1(+)_downregulated
  siRNAs that showed significantly lower expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine). DESeq2 v1.13.8, fold change > 2, FDR < 0.01. WBPaper00056161:male_enriched_siRNA
  Genes up regulated by mir-243(n4759). RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243. WBPaper00036130:mir-243_up_regulated
  Genes that are significantly down regulated after 24 hour exposure to H2S. Data were RMA normalized and probe-level data were Summarized with the NimbleScan software. Genes with weak signal intensity across all groups and those with low variability across samples were excluded from further analysis. Each H2S-treated sample was statistically compared to a matched untreated control using the Bioconductor package limma. The false discovery rate (FDR) method of Benjamini and Hochberg was used to adjust p-values for multiple testing. An adjusted p-value <= 0.05 was used to define differential expression. WBPaper00040285:H2S_24hr_downregulated
Fungi infection: Drechmeria coniospora Genes with decreased expression after 12 hours of infection by D.coniospora 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:D.coniospora_12hr_downregulated_RNAseq
  Transcripts that showed significantly increased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. DESeq2. FDR < 0.05. WBPaper00060459:bcat-1(RNAi)_upregulated
  Coexpression clique No. 1, Y40H4A.2-ZK1053.2, on the genome-wide coexpression clique map for the nematode GPL200 platform. All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. WBPaper00061527:Y40H4A.2-ZK1053.2
  Genes that showed rising 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:rising_dev_expression
  Genes that were enriched in spermatogenic fem-3(q96gf) gonads comparing to in oogenic fog-2(q71), according to RNAseq analysis. To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. WBPaper00045521:Spermatogenic
Bacteria infection: Serratia marcescens Genes with decreased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_downregulated_TilingArray
  Genes that are significantly down regulated after 12 hour exposure to H2S. Data were RMA normalized and probe-level data were Summarized with the NimbleScan software. Genes with weak signal intensity across all groups and those with low variability across samples were excluded from further analysis. Each H2S-treated sample was statistically compared to a matched untreated control using the Bioconductor package limma. The false discovery rate (FDR) method of Benjamini and Hochberg was used to adjust p-values for multiple testing. An adjusted p-value <= 0.05 was used to define differential expression. WBPaper00040285:H2S_12hr_downregulated
  Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm. Fold change > 2, p-value < 0.05. WBPaper00060661:sensory-neuron_enriched
Bacteria infection: Enterococcus faecalis Genes with decreased 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_downregulated_TilingArray
  Genes that showed decreased expression in bar-1(ga80) animal comparing to in N2. All statistical analyses were performed using the statistical programming language R (version 2.13.1 x 64). A linear model was used to determine the effect and significance of the genotype on the expression levels (probe intensity + genotype + error). Using permutations of the original data in the same linear model, authors determined thresholds adjusted for multiple testing (FDR 0.05: -log10(p) > 2; FDR 0.01: -log10(p) > 3). To correct for the developmental difference between bar-1(ga80) and N2 authors used the developmental gene expression data from Snoek et al. (2014) together with the gene expression data generated for this study (bar-1(ga80) vs. N2) in one linear model (probe intensity, sample age + genotype + error). The intensities were corrected for batch effect and for sample age authors used an age of 44 hours for the bar-1(ga80) samples (as estimated), and 48 hours for the N2 samples. WBPaper00045257:bar-1(ga80)_downregulated
  Transcripts that showed significantly altered expression at AFD neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain. RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis. WBPaper00061902:camt-1(ok515)_regulated_AFD
Bacteria infection: Photorhabdus luminescens Genes with decreased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_downregulated_TilingArray
  Transcripts that showed significantly decreased expression in ifg-1(RNAi) animals comparing to in control RNAi animals Benjamini and Hochbergs method of false detection rate was used to etermine adjusted q-values (< 0.05) based on four biological replicates. WBPaper00050015:ifg-1(RNAi)_downregulated
  Genes specifically expressed in germline when comparing RNAseq data of N2 to glp-4(bn2ts). Authors extracted all genes with more than 25 mapped reads and computed fold changes for all gene loci between wild type and mutants. The group of genes with 4-fold up-regulation in wild type was considered to be specifically expressed in the germline, while genes with 4-fold down-regulation in wild type where assumed to be specific to somatic cell lineages. WBPaper00044760:germline_specific

4 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2021711 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).  
    Expr1150638 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr1023426 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr2003496 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).  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00018192 17578692 17579111 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
420

1 Sequence Ontology Term