WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00194679 Gene Name  T26C11.9
Sequence Name  ? T26C11.9 Organism  Caenorhabditis elegans
Automated Description  Enriched in AFD based on RNA-seq studies. Is affected by several genes including etr-1; mrpl-2; and fog-3 based on microarray and RNA-seq studies. Is affected by bisphenol A; rifampin; and allantoin based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1012
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00194679

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T26C11.9.1 T26C11.9.1 893   X: 1852838-1853849
Transcript:T26C11.9.2 T26C11.9.2 596   X: 1852941-1853584
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:T26C11.9 T26C11.9 279   X: 1852941-1853098

1 RNAi Result

WormBase ID
WBRNAi00054185

34 Allele

Public Name
gk963725
gk963864
WBVar01467756
WBVar01467757
WBVar01467754
gk964444
gk964445
WBVar02080083
WBVar00075535
WBVar00075537
WBVar00075536
gk272288
gk272287
gk272286
tm10733
tm13033
gk666231
gk963977
ttTi22987
gk496220
gk343185
gk669286
WBVar01467758
gk362499
gk810451
gk347571
gk925563
gk512899
gk648808
gk676616

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00194679 1852838 1853849 -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_1852737..1852837   101 X: 1852737-1852837 Caenorhabditis elegans

32 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_upregulated_neural
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
  Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rifampicin-Allantoin_upregulated
25C vs. 20C Transcripts that showed significantly increased 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_upregulated
  Transcripts that showed significantly increased 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_upregulated
  Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:eat-2(ad1116)_downregulated
  Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067044:hda-1(RNAi)_upregulated
  Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. All three experiments have CPM >= 1. WBPaper00067147:germline_expressed
  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
Starvation 48 hours at L1 arrest Transcripts that showed significantly increased expression in starved N2 animals (48 hours at L1 arrest) Fold change > 2. WBPaper00064005:starvation_upregulated_N2_mRNA
  Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
  Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage. DESeq2, FDR < 0.05 WBPaper00058691:cfp-1(tm6369)_upregulated
  Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals. DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. WBPaper00060014:set-2(tm1630)_upregulated
  Transcripts that showed significantly increased expression in emb-4(hc60) comparing to in N2. DESeq2 WBPaper00052884:emb-4(hc60)_upregulated
  Transcripts that interact with both BAZ-2 and SET-6 in Chip-Seq analysis. N.A. WBPaper00059356:BAZ-2_SET-6_interacting
  siRNAs that showed significantly higher 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:hermaphrodite_enriched_siRNA
  Transcripts that showed significantly increased expression in mes-3(bn199) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mes-3(bn199)_upregulated_PGCs
  Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:daf-2(e1370)_downregulated
  Transcripts that showed significantly increased expression in lin-53(RNAi) embryos comparing to control animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067044:lin-53(RNAi)_upregulated
  Transcripts that showed significantly increased expression in mes-4(bn73) comparing to in control animals in early germ cells (EGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mes-4(bn73)_upregulated_EGCs
Starvation 48 hours at L1 arrest Transcripts that showed significantly increased expression in starved aptf-1(gk794) animals (48 hours at L1 arrest) Fold change > 2. WBPaper00064005:starvation_upregulated_aptf-1(gk794)_mRNA
  Transcripts that showed significantly increased expression in AFD neuron cells comparing to in whole animal, according to dissected single neuron RNASeq analysis. Fold change >= 4. WBPaper00050344:AFD-neuron_enriched
  Genes regulated by unc-39(hp701). Authors compared genes enriched in FACS sorted GFP+ cells (RID, ALA, AIY, CAN and a sheath cell) vs. whole animal in WT hpIs202[Pceh-10GFP] (WT enriched sets), and genes enriched in FACS sorted GFP+ cells (ALA, AIY, CAN and a sheath cell) vs. whole animal in unc-39(hp701) hpIs202[Pceh-10GFP] (unc-39 enriched sets) at L2 larva stage. This set of genes are WT enriched but not unc-39 enriched, suggesting they are enriched in RID neurons. DESeq WBPaper00050496:unc-39(hp701)_regulated
  FOG-1associated mRNAs identified by RIP-ChIP To identify transcripts enriched in RIP samples, background corrected and normalized data were analyzed with the Bioconductor package Siggenes (siggenes 1.38.0) using two-class significance analysis of microarrays (SAM function). WBPaper00048762:FOG-3_associated
  Transcripts that showed significantly increased expression in 24-cell stage embryo of chd-3(eh4) animals, comparing to in N2 animals, both fed 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)_upregulated_24-cell-embryo
  Transcripts that showed increased expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, and their mRNAs co-purify with SMG-2. edgeR WBPaper00053308:SMG-2_associated_NMD(-)_upregulated_ClassI
  Transcripts that showed significantly increased expression in mes-3(bn199) comparing to in control animals in early germ cells (EGCs) at L1 larva stage. DESeq2(v1.32.0), FDR < 0.05. WBPaper00064315:mes-3(bn199)_upregulated_EGCs
  Transcripts that showed significantly increased expression in mrpl-2(osa3) comparing to wild-type animals. Differential expression analysis was performed using DESeq2R package(v.1.10.1).Relative expression of genes with Benjamini-Hochberg corrected P-values (Padj)<0.05 were considered to be differentially expressed. WBPaper00060951:mrpl-2(osa3)_upregulated
Human amyloid beta peptide and pro or anti aggregating tau protein. Transcripts that showed differential expression between N2 and animals expressing human amyloid beta peptide (strain CL2355) and pro-aggregating tau (strain BR5270) or anti-aggregating tau protein (BR5271), at L4 larva stage. To identify differential gene expression, analysis was performed using CuffLinks 2.2.1 with false discovery rate corrected P values (q values) of < 0.05 and log2 (fold change) > 1 or < 1. WBPaper00053154:human-amyloid-beta_tau_regulated

4 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1040454 Tiling arrays expression graphs  
    Expr2024745 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).  
    Expr2006526 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).  
    Expr1157730 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
WBGene00194679 1852838 1853849 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1012

1 Sequence Ontology Term