WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00271606 Gene Name  F22F4.9
Sequence Name  ? F22F4.9 Organism  Caenorhabditis elegans
Automated Description  Enriched in several structures, including ABplppppaa; PVT; pharyngeal cell; rectal epithelial cell; and rectum based on single-cell RNA-seq studies. Is affected by several genes including etr-1; rrf-3; and ilc-17.1 based on RNA-seq studies. Is affected by Cisplatin and Doxorubicin based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1265
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00271606

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F22F4.9.1 F22F4.9.1 446   X: 5998240-5999504
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:F22F4.9 F22F4.9 246   X: 5998349-5998473

0 RNAi Result

24 Allele

Public Name
gk964260
gk963217
gk910941
gk693955
gk409891
gk357520
gk428348
gk679426
gk415203
gk326445
gk506744
WBVar01820032
ttTi13195
WBVar01550084
WBVar01550083
WBVar00027076
WBVar01526525
WBVar01526526
WBVar00027081
WBVar01880457
WBVar00027086
WBVar00027091
gk281854
gk281853

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00271606 5998240 5999504 -1

2 Data Sets

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

0 Downstream Intergenic Region

31 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
  Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
  Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage. DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
  Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:sin-3(tm1276)_upregulated
  Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. DESeq2, fold change > 2, adjusted p-value < 0.01 WBPaper00058598:sin-3(tm1276)_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
  Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals. Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed. WBPaper00062193:skn-1(RNAi)_upregulated
  Transcripts enriched in Rectal_gland according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:Rectal_gland_enriched
  Transcripts that showed significantly decreased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_downregulated_glp-1(e2141)
  Transcripts that showed significantly increased expression in diploid N2 animals after exposure to 5 uM doxorubicin for 72 hours at 15C from L1 to L4 larve stage. DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. WBPaper00066110:Doxorubicin_upregulated_diploid
  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 diploid N2 animals after exposure to 5uM cisplatin for 72 hours at 15C from L1 to L4 larve stage. DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. WBPaper00066110:Cisplatin_upregulated_diploid
  Single-cell RNA-Seq cell group 9_0 expressed in epithelium. scVI 0.6.0 WBPaper00065841:9_0
  Single-cell RNA-Seq cell group 9_1 expressed in epithelium. scVI 0.6.0 WBPaper00065841:9_1
  Single-cell RNA-Seq cell group 9_2 expressed in epithelium. scVI 0.6.0 WBPaper00065841:9_2
  Single-cell RNA-Seq cell group 24_0 expressed in epithelium. scVI 0.6.0 WBPaper00065841:24_0
  Single-cell RNA-Seq cell group 26_1 expressed in pharynx. scVI 0.6.0 WBPaper00065841:26_1
  Single-cell RNA-Seq cell group 27_0 expressed in epithelium. scVI 0.6.0 WBPaper00065841:27_0
  Top 300 transcripts enriched in mc1DL, mc1DR, mc1V 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:mc1
  Top 300 transcripts enriched in pm1, pm2 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:pm1_pm2
  Transcripts that showed significantly increased expression in sdc-3(ubs20);dpy-26(ubs4) comparing to in control animals. DESeq2 v.1.34, fold change > 2, FDR < 0.05. WBPaper00067078:sdc-3(ubs20);dpy-26(ubs4)_upregulated
  Transcripts that showed significantly increased expression in sdc-3(ubs20) comparing to in control animals. DESeq2 v.1.34, fold change > 2, FDR < 0.05. WBPaper00067078:sdc-3(ubs20)_upregulated
  Transcripts that showed significantly decreased 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_downregulated_neural
  Single-cell RNA-Seq cell group 62 expressed in: e2 (pharyngeal epithelium). CellRanger, DecontX, Monocle3, Louvain algorithm. WBPaper00065623:62
  Top 300 transcripts enriched in rectal gland cell 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:Rectal_gland
  Top 300 transcripts enriched in ABplppppaa, ABprppppaa 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:Parent_of_PVP_and_rect_V
  Single-cell RNA-Seq cell group 138_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:138_0
  Top 300 transcripts enriched in B cell, F cell, K cell, K' cell, U cell, Y cell 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:B_F_K_Kp_U_Y
  Top 300 transcripts enriched in pharyngeal-intestinal valve 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:Pharyngeal_intestinal_valve

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2021097 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).  
    Expr2002879 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).  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00271606 5998240 5999504 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1265

1 Sequence Ontology Term