WormMine: Gene WBGene00194870

• WormBase Gene ID: WBGene00194870
• Gene Name: F53A2.11
• Sequence Name: F53A2.11
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable alpha-(1->3)-fucosyltransferase activity. Predicted to be involved in fucosylation.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 3620

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00194870

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F53A2.11.1	F53A2.11.1	2354	III: 13319059-13322678

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F53A2.11	F53A2.11	1362	III: 13319265-13320060

2 RNAi Result

• WBRNAi00048039
• WBRNAi00006116

58 Allele

• gk963887
• gk963904
• gk963552
• gk547478
• gk400702
• gk330181
• gk400703
• gk566905
• gk891703
• h8946
• WBVar01964178
• gk490169
• WBVar01794204
• gk472194
• WBVar01794203
• gk489654
• WBVar01794202
• gk539465
• WBVar01794201
• gk712714
• gk485111
• gk563001
• gk507405
• WBVar01794205
• gk762457
• gk341120
• gk736583
• gk791374
• gk484393
• WBVar01794200

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00194870
• Start: 13319059
• End: 13322678
• Strand: -1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_13318604..13319058
• Length (nt): 455
• Chromosome Location: III: 13318604-13319058
• Organism: Caenorhabditis elegans

23 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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
	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
Heat shock: 34C 30min.	Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min.	DESeq2 v 1.18.1, fold change > 2, FDR < 0.01.	WBPaper00058955:heatshock_upregulated_CE
	Genes that showed significant differential expressed between control and 20 mg\/L Cadmium treatment.	t-test, p < 0.05.	WBPaper00036123:Cadmium_regulated
	Genes with differential expression under 0.5mg/l Chlorpyrifos (CPF) and 0.5mg/l Diazinon (DZN) treatment at 24 centigrade.	To identify the differentially expressed genes in each treatment authors used linear models per toxicant and temperature (gene expression = Toxicant (effect) + error). The lm function in R stats package was used to implement the linear models analysis with recommended default options. For threshold determination authors used a permutation approach. For each of the 23,232 permutations used authors randomly picked a transcript (array spot), which could only be picked once. Authors combined all the expression values of this transcript and randomly distributed them over the replicates and used them in the linear model. In this way authors obtained a threshold for each of the toxicants. Authors used a -log10 p-value 2 as common threshold for the analysis, which resembles to the following FDR per toxicant: 0.0155 for CPF at 24 centigrade, 0.0148 for DZN at 24 centigrade, 0.0168 for CPF+DZN at 24 centigrade, 0.0142 for CPF at 16 centigrade, 0.0151 for DZN at 16 centigrade, and 0.0148 for CPF+DZN, at 16 centigrade.	WBPaper00040210:Chlorpyrifos_Diazinon_24C_regulated
	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
Bacteria: B.subtilis	Transcripts that showed significantly increased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult.	edgeR 3.16.5, FDR < 0.05, fold change > 2.	WBPaper00059117:B.subtilis_upregulated
	Transcripts that showed significantly decreased expression in daf-2(e1370); daf-18(yh1) comparing to in daf-2(e1370) animals.	Differentially expressed genes (fold change > 2 and adjusted p value < 0.05) were identified by using DESeq2 (v.1.22.2).	WBPaper00061952:daf-18(yh1)_downregulated
Bacteria infection: Enterococcus faecalis	Genes down-regulated in animals infected with Enterococcus faecalis compared to the E. coli OP50 control after 24h of infection.	MAANOVA and BRB-Array-Tools.	WBPaper00030985:Enterococcus_faecalis_downregulated
	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 alg-1(gk204) comparing to in N2 at 5-days post L4 adult hermaphrodites.	DESeq, fold change > 2, adjusted p-value < 0.05.	WBPaper00054758:alg-1(gk204)_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin-Psora_downregulated
	Transcripts that showed significantly increased expression in let-418(n3536);dcp-66(RNAi) comparing to control.	DESeq, fold change > 2.	WBPaper00062672:let-418(n3536)dcp-66(RNAi)_upregulated
	Transcripts that showed significantly increased expression in 24-cell stage embryo of chd-3(eh4)let-418(RNAi) animals, comparing to in N2 animals injected with gfp control RNAi vector.	DESeq and EdgeR were used. A threshold of 1.5 log2 fold change and a p value <10 % were applied. let-418: wild-type; let-418(RNAi)-treated embryos; chd-3: chd-3(eh4);controlGFP(RNAi)-treated embryos; chd-3_let-418: chd-3(eh4); let-418(RNAi)-treated embryos. All fold changes are calculated versus wild-type;control(RNAi)-treated embryos. 1h and 3h correspond to the 24- and 100-cell stages, respectively.	WBPaper00050163:chd-3(eh4);let-418(RNAi)_upregulated_100-cell-embryo
	Transcripts that showed significantly increased expression in 100-cell stage embryo of let-418(RNAi) animals, comparing to in control RNAi (with gfp control vector) animals.	DESeq and EdgeR were used. A threshold of 1.5 log2 fold change and a p value <10 % were applied. let-418: wild-type; let-418(RNAi)-treated embryos; chd-3: chd-3(eh4);controlGFP(RNAi)-treated embryos; chd-3_let-418: chd-3(eh4); let-418(RNAi)-treated embryos. All fold changes are calculated versus wild-type;control(RNAi)-treated embryos. 1h and 3h correspond to the 24- and 100-cell stages, respectively.	WBPaper00050163:let-418(RNAi)_upregulated_100-cell-embryo
Bacteria infection: P. aerugi-nosa PA14	Transcripts differentially expressed between AWA neurons of adult hermaphrodite worms exposed to PA14 and AWA neurons of adult hermaphrodite worms exposed to OP50 for 4-6 hours.	P values are derived from two-sided exact test used in the R package edgeR and the FDR values are BenjaminiHochberg adjusted P values. FDR < 0.05 (set by WormBase Curator).	WBPaper00064871:PA14_downregulated_AWA
	Transcripts that showed significantly increased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6.	DESeq2, log2 fold change > 2, adjusted p-value < 0.005.	WBPaper00055103:thoc-5(wy822)_upregulated
	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 let-418(n3536) comparing to control.	DESeq, fold change > 2.	WBPaper00062672:let-418(n3536)_upregulated
	Top 300 transcripts enriched in AVAL, AVAR 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:AVA
	Coexpression clique No. 144, 183712_at-srbc-74_8864, 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.	WBPaper00061527:183712_at-srbc-74_8864

3 Expression Patterns

• Primary Identifier: Expr1151855
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2022240
• Pattern: 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).

• Primary Identifier: Expr2004018
• Pattern: 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).

2 GO Annotation

21 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00194870
• Start: 13319059
• End: 13322678
• Strand: -1

2 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3620

1 Sequence Ontology Term

• Name: gene

0 Strains

0 Upstream Intergenic Region