WormMine: Gene WBGene00014188

• WormBase Gene ID: WBGene00014188
• Gene Name: ZK1025.8
• Sequence Name: ZK1025.8
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable chondroitin 4-sulfotransferase activity. Predicted to be involved in chondroitin sulfate biosynthetic process and positive regulation of response to oxidative stress. Predicted to be located in membrane.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 2123

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00014188

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZK1025.8.1	ZK1025.8.1	906	I: 11469462-11471584

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZK1025.8	ZK1025.8	906	I: 11469462-11469531

3 RNAi Result

• WBRNAi00059043
• WBRNAi00004901
• WBRNAi00004906

6 Allele

• gk962858
• gk962706
• gk963849
• gk963906
• WBVar02124452
• WBVar01932623

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00014188
• Start: 11469462
• End: 11471584
• Strand: 1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_11471585..11473217
• Length (nt): 1633
• Chromosome Location: I: 11471585-11473217
• Organism: Caenorhabditis elegans

45 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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 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 increased expression in adr-1(tm668) and adr-1(gv6) comparing to in N2 at embryo stage.	DESeq FDR <= 0.05	WBPaper00056617:adr-1_upregulated_embryo_transcript
	Transcripts that showed significantly increased expression in mbl-1(syb4345), referred to as mbl-1long(ex7+), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4345)_upregulated
	Transcripts that showed significantly increased expression in ngn-1(ok2200) embryos comparing to in N2.	DESeq2 ver.3.4.1	WBPaper00059537:ngn-1(ok2200)_upregulated
	Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals.	DESeq2 v. 1.22.2, adjusted p-value <= 0.05.	WBPaper00059605:mut-16(pk710)_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
Bacteria infection: Serratia marcescens	Genes with increased 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_upregulated_TilingArray
	Transcripts that showed significantly increased expression in lin-22(ot269) comparing to in N2 at L3 larva.	Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1).	WBPaper00053295:lin-22(ot269)_upregulated
	Transcripts that showed significantly increased expression in lin-22(ot267) comparing to in N2 at L3 larva.	Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1).	WBPaper00053295:lin-22(ot267)_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
Bacteria infection: Photorhabdus luminescens	Genes with increased 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_upregulated_TilingArray
	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 tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_upregulated
	Transcripts that showed significantly increased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_downregulated
	Transcripts that showed significantly increased expression in eat-2(ad465) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:eat-2(ad465)_upregulated
	Transcripts that showed significantly increased expression in hpl-2(tm1489) comparing to in N2 animals.	DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.	WBPaper00054493:hpl-2(tm1489)_upregulated
	Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult.	Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed.	WBPaper00049377:MWCNT_downregulated
	Transcripts that showed significantly increased expression in N2 animals exposed to 30 uM CdCl2 for five days starting from L4.	edgeR, fold change > 2, p < 0.05.	WBPaper00066204:CdCl2_upregulated_mRNA
	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 sid-3(ok973) comparing to in N2 at 4 days post L4 adult hermaphrodite stage.	RNA-seq data were aligned to the C. elegans transcriptome WS190 using bowtie2. Counts were obtained from resulting BAM files using BEDTools, and these were used to generate normalized data tables using DESeq. A cutoff of mean 25 normalized reads (normalized according to DESeq negative binomial distribution) for at least one condition was used, and significantly altered genes were selected (DESeq Benjamini-Hochberg multiple-test correction q < 0.1).	WBPaper00053020:sid-3(ok973)_upregulated
	Transcripts uniquely expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_enriched
	Transcripts that showed more than 4 fold of expression in N2 comparing to in CB4856 animals.	DESeq2, fold change > 4.	WBPaper00053909:N2_vs_CB4856_upregulated
	Genes that showed increased mRNA expression in emr-1(RNAi);lem-2(tm1582) comparing to N2.	Library siggenes in R was applied to select the differentially expressed loci using the false discovery rate-based SAM method. Genes presenting a delta value > 4 were considered to be significantly altered.	WBPaper00044786:emr-1(RNAi);lem-2(tm1582)_upregulated
	Transcripts that showed significantly decreased expression in animals exposed to Camptothecin for 3 hours at 2C.	p < 0.01, logFC > 1 or p < 0.01, logFC < -1.	WBPaper00066610:Camptothecin_downregulated_2C_3h
	Transcripts that showed significantly decreased expression in animals exposed to Leptomycin B for 3 hours at 2C.	p < 0.01, logFC > 1 or p < 0.01, logFC < -1.	WBPaper00066610:Leptomycin-B_downregulated_2C_3h
	Transcripts that showed significantly increased expression in animals with pan-neuronal expression of both human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP) and human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals.	edgeR p-value < 0.01 and fold change > 4.	WBPaper00061613:human-amyloid-beta_alpha-Synuclein(A53T)_upregulated

1 Expression Patterns

• Primary Identifier: Expr1162478
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

5 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00014188
• Start: 11469462
• End: 11471584
• Strand: 1

5 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2123

1 Sequence Ontology Term

• Name: gene

0 Strains

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_11467613..11469461
• Length (nt): 1849
• Chromosome Location: I: 11467613-11469461
• Organism: Caenorhabditis elegans