WormMine: Gene WBGene00019339

• WormBase Gene ID: WBGene00019339
• Gene Name: K02F6.5
• Sequence Name: K02F6.5
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to be involved in protein homooligomerization. Is an ortholog of human TNFAIP1 (TNF alpha induced protein 1).
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 1567

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00019339

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K02F6.5.1	K02F6.5.1	1241	II: 2534759-2536316
Transcript:K02F6.5.2	K02F6.5.2	816	II: 2535375-2536325

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K02F6.5	K02F6.5	699	II: 2535417-2535518

6 RNAi Result

• WBRNAi00039073
• WBRNAi00049761
• WBRNAi00049762
• WBRNAi00003701
• WBRNAi00016493
• WBRNAi00092052

42 Allele

• WBVar02124326
• gk964317
• gk963801
• WBVar02122215
• WBVar02123657
• WBVar02123497
• WBVar02120780
• WBVar02121365
• WBVar02121366
• WBVar02123451
• WBVar02122300
• WBVar02123356
• WBVar02124156
• WBVar02121949
• WBVar02124670
• WBVar02120609
• WBVar01718578
• WBVar01718577
• WBVar01718576
• WBVar01764709
• WBVar01502957
• WBVar01502958
• gk781667
• gk666962
• WBVar02122777
• WBVar02114600
• WBVar02123881
• WBVar01625878
• otn7220
• WBVar02084493

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00019339
• Start: 2534759
• End: 2536325
• Strand: 1

3 Data Sets

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

0 Downstream Intergenic Region

28 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
	Single-cell RNA-Seq cell group 84_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:84_0
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 enriched in ASG according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ASG_enriched
	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
	Single-cell RNA-Seq cell group 71_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:71_0
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 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
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	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_M
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	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_SM
	Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage.	DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed.	WBPaper00048971:daf-16(mgDf50)_downregulated_L1
	Transcripts that showed significantly increased expression in pqm-1(ok485) animals after exposure to 5mM CoCl2 for 6hours, comparing to in N2 animals with the same exposure to CoCl2.	Significant differentially-expressed gene sets were identified using one or two-class SAM.	WBPaper00060399:pqm-1(ok485)_upregulated_CoCl2_6hr
	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 differential expression in dauer mir-34(gk437) vs dauer mir-34(OverExpression) animals at 20C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_dauer_20C
	Transcripts up regulated in daf-2(e1370) comparing to in N2 when animals were grown at 15 degree and then at 25 degree for 12 hours.	To select nuclear-hormone-receptor mutants for the cold-tolerance test, authors set the q-value threshold at q < 0.05, except that nhr-88, 113, 145, 172 and 207 were picked up from the genes with q < 0.25 in comparing between 15C-cultivated wild-type and wild-type cultivated at 25C for 12 h after cultivation at 15C.	WBPaper00049736:daf-2(e1370)_upregulated_15deg-then-25deg(12hr)
Bacteria diet: complex environmental microbiotas	Transcripts that showed significantly decreased expression after L1 larva grew on soil microbiota at 25C for 3 days.	N.A.	WBPaper00056139:soil-microbiota_downregulated
spaceflight-induced microgravity on the ISS (International Space Station).	Transcripts that showed significantly decreased expression in animals grew under spaceflight-induced microgravity on the ISS (International Space Station).	N.A.	WBPaper00061274:microgravity_downregulated
	Transcripts that showed significantly increased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_upregulated
	Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in normal growth condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_17
	Genes that showed significantly decreased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control.	Fold change > 1.2 or < 0.8.	WBPaper00042477:rsr-2(RNAi)_downregulated_TilingArray
	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 decreased expression in polyQ-expanded hungtingtin (HTT) 128Q touch receptor cells comparing to in 19Q touch receptor cells.	Authors performed the statistial analysis of the microarray data using the Varmixt tool of the R package, with VM parameters and FDR corrections of P-Values.	WBPaper00045417:128Q-huntingtin_downreglated
	Coexpression clique No. 90, ckr-1-T09B9.3, 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:ckr-1-T09B9.3
	Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 25C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_25C
	Transcripts that showed significantly increased expression in unc-4(e120) VA neurons comparing to in wild type VA neurons.	Differentially expressed transcripts were obtainedusing the RNA-Seq Differential Expression analysis pipeline in CLC, which utilizes a negative binomal GLM model. Genes were scored as differentially expressed > 2-fold difference and FDR p value < .05 compared to control.	WBPaper00062095:unc-4(e120)_upregulated_VA-neuron
	Single-cell RNA-Seq cell group 126 expressed in: ASG.	CellRanger, DecontX, Monocle3, Louvain algorithm.	WBPaper00065623:126
	Top 300 transcripts enriched in ASGL, ASGR 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:ASG

4 Expression Patterns

• Primary Identifier: Expr2022939
• 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: Expr1153475
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1017907
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2004715
• 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).

1 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00019339
• Start: 2534759
• End: 2536325
• Strand: 1

1 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1567

1 Sequence Ontology Term

• Name: gene

0 Strains

0 Upstream Intergenic Region