WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00194664 Gene Name  K09E9.7
Sequence Name  ? K09E9.7 Organism  Caenorhabditis elegans
Automated Description  Enriched in several structures, including amphid neurons; germ line; hermaphrodite somatic gonadal cell; somatic gonad precursor; and vulval cell based on RNA-seq and single-cell RNA-seq studies. Is affected by several genes including etr-1; hsp-6; and csr-1 based on RNA-seq and microarray studies. Is affected by five chemicals including rifampin; antimycin; and cholesterol based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1955
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00194664

Genomics

4 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:K09E9.7.1 K09E9.7.1 612   X: 15640903-15642853
Transcript:K09E9.7.2 K09E9.7.2 644   X: 15641217-15642854
Transcript:K09E9.7.3 K09E9.7.3 601   X: 15641233-15642857
Transcript:K09E9.7.4 K09E9.7.4 538   X: 15641414-15642854
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:K09E9.7 K09E9.7 309   X: 15641423-15641501

1 RNAi Result

WormBase ID
WBRNAi00016217

32 Allele

Public Name
gk964260
gk962707
gk963810
gk691654
gk672804
gk699823
gk933544
gk964354
gk633105
gk656405
gk469554
WBVar01553640
WBVar01929102
WBVar01553639
WBVar01553638
WBVar01553637
WBVar01760835
WBVar01760836
gk640827
gk638985
h12538
WBVar01760833
WBVar01760834
WBVar00086690
WBVar01528606
WBVar02027827
WBVar01473012
WBVar02027828
WBVar01901872
gk303872

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00194664 15640903 15642857 1

2 Data Sets

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

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrX_15642858..15642937   80 X: 15642858-15642937 Caenorhabditis elegans

34 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
Bacteria: E.faecalis strain OG1RF Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. WBPaper00059754:E.faecalis_OG1RF_upregulated
  Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. Fold change > 2, FDR < 0.01. WBPaper00065993:glp-1(e2141)_upregulated
  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 decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. DESeq2 version 1.22.2, p < 0.05 WBPaper00064716:paraquat_downregulated
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_upregulated
  Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. WBPaper00062159:hda-2(ok1479)_upregulated
  Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin. N.A. WBPaper00055862:antimycin_damt-1(gk961032)_regulated
  Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector. Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples. WBPaper00051039:germline_enriched
  Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage, comparing to N2 animals. Genes exhibiting at least two-fold change were considered differentially expressed. WBPaper00061439:unc-30(ok613)_upregulated
  Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage after 4 hours of Pseudomonas aeruginosa infection, comparing to infected N2 animals. Genes exhibiting at least two-fold change were considered differentially expressed. WBPaper00061439:unc-30(ok613)_upregulated_P.aeruginosa-infection
moderate static magnetic field Transcripts that showed significantly decreased expression after exposure to moderate static magnetic field. N.A. WBPaper00064509:static-magnetic-field_downregulated
  Transcripts that showed significantly decreased expression in ash-2(RNAi) comparing to in wild type animals injected with vector. Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed. WBPaper00066232:ash-2(RNAi)_downregulated_WT
  Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite npr-8(ok1439) animals grown at 25C, comparing to in N2 animals. CuffDiff, fold change > 2. WBPaper00065096:npr-8(ok1439)_upregulated_Day1_25C
25C vs. 20C Transcripts that showed significantly decreased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C. CuffDiff, fold change > 2. WBPaper00065096:25C_vs_20C_downregulated
  Transcripts that showed significantly increased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage. EdgeR, fold change > 2, FDR < 0.001. WBPaper00056290:hsp-6(mg585)_upregulated
  Transcripts that showed significantly increased expression in bcf-1(ylf1) comparing to in N2 adult animals. DESeq2 WBPaper00064933:bcf-1(ylf1)_upregulated_transcript
  Transcripts that showed significantly increased expression in nhr-8(hd117) comparing to in N2. Differentially expressed genes were identified using Sleuth (version 0.30.0). WBPaper00062446:nhr-8(hd117)_upregulated
  Transcripts that showed significantly increased expression in mrps-5(RNAi) comparing to in control animals. Fold change > 4, p-value < 0.01 WBPaper00056330:mrps-5(RNAi)_upregulated
  Transcripts that showed significantly decreased expression after 24 hours of treatment by 50 uM atracurium. Differential expression was assessed using an empirical Bayes moderated t test within limma's linear model framework including the precision weights estimated by voom. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Fold change > 2, p-value < 0.05. WBPaper00061636:atracurium_downregulated
  Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. CuffDiff, fold change > 2. WBPaper00065096:Day10_vs_Day1_downregulated
  Transcripts that showed significantly increased expression when grown with 20ug per ml cholesterol supplementation, comparing to animals grown with 5ug per ml supplementation. DESeq2 WBPaper00059728:20ug_cholesterol_upregulated
  Transcripts that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector. Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA
  Single-cell RNA-Seq cell group 12_0 expressed in various. scVI 0.6.0 WBPaper00065841:12_0
  Transcripts significantly enriched in AVK neurons comparing to all cell types at L1 larva stage. edgeR, FDR < 0.001, fold change > 2. WBPaper00055565:AVK_enriched
  Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 20C. DESeq2, fold change > 2, p-value < 0.05. WBPaper00061753:csr-1(tor159)_upregulated_20C
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure. Transcripts that showed significantly decreased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2). DEseq 1.18.0, adjusted p-value < 0.05. WBPaper00056471:S.aureus-4h_downregulated_N2
  Transcripts that showed significantly increased expression in nhl-2(ok818) comparing to in N2 at 20C. EdgeR, FDR < 0.05, fold change < 0.5. WBPaper00055971:nhl-2(ok818)_20C_downregulated
  Single-cell RNA-Seq cell group 31_0 expressed in gonad. scVI 0.6.0 WBPaper00065841:31_0
  Top 300 transcripts enriched in ASJL, ASJR 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:ASJ

3 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2023205 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).  
    Expr2004984 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).  
    Expr1154144 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00194664 15640903 15642857 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1955

1 Sequence Ontology Term