WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00044365 Gene Name  nspf-2
Sequence Name  ? F34D6.8 Organism  Caenorhabditis elegans
Automated Description  Enriched in male based on RNA-seq studies. Is affected by several genes including csr-1; rrf-3; and tph-1 based on microarray and RNA-seq studies. Is affected by six chemicals including Zidovudine; Psoralens; and allantoin based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 264
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00044365

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F34D6.8.1 F34D6.8.1 264   II: 2688916-2689179
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:F34D6.8 F34D6.8 264   II: 2688916-2689179

0 RNAi Result

9 Allele

Public Name
gk964317
gk963801
WBVar01364753
WBVar02076339
WBVar01764992
WBVar02028926
gk648081
WBVar01718720
gk555488

1 Chromosome

WormBase ID Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00044365 2688916 2689179 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_chrII_2689180..2689916   737 II: 2689180-2689916 Caenorhabditis elegans

27 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
  Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rapamycin-Metformin_upregulated
  Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline. Log2 Fold change > 2 or <-1, p-value < 0.05. WBPaper00053599:female_vs_male_downregulated
  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 decreased expression after animals were treated with 100uM Psora from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Psora_downregulated
Bacteria: B.thuringiensis Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. Cuffdiff WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
20C vs 25C Transcripts that showed differential expression in 20C vs 25C in N2 animals at adult stage. N.A. WBPaper00050488:20C_vs_25C_regulated_N2_adult
  Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 25C. DESeq2, fold change > 2, p-value < 0.05. WBPaper00061753:csr-1(tor159)_downregulated_25C
  Genes that showed flat mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. WBPaper00044736:flat_dev_expression
  Down-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2. Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off. WBPaper00045774:clk-1_downregulated
  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 enriched in male him-5(e1490 animals, comparing to in N2 hermaphrodite animals from L3 larva to young adult stages. DESeq FDR < 0.01. WBPaper00050231:male_enriched
  Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rapamycin-Allantoin_upregulated
  Transcripts that showed significantly decreased expression in flcn-1(ok975) comparing to in N2. Student's t-test. WBPaper00056471:flcn-1(ok975)_downregulated
  Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 20C. DESeq2, fold change > 2, p-value < 0.05. WBPaper00061753:csr-1(tor159)_downregulated_20C
  Transcripts that showed significantly altered expression after 24 hour exposure to zidovudine (AZT) starting at L1 lava stage. DESeq WBPaper00053302:zidovudine_72h_regulated
  Transcripts that showed significantly increased expression in uninfected nhr-42(tm1375) animals comparing to in uninfected N2 animals. Adjusted p-value (Padj) <= 0.01 was considered significant for differential gene expression. WBPaper00065225:nhr-42(tm1375)_upregulated_uninfected
  Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at young adult stage. DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. WBPaper00056169:rrf-3(pk1426)_upregulated_adult
  Transcripts that showed significantly decreased expression in N2 animals exposed to 30 uM CdCl2 for five days starting from L4. edgeR, fold change > 2, p < 0.05. WBPaper00066204:CdCl2_downregulated_mRNA
  Transcripts that showed significantly increased expression in adr-1(tm668) comparing to in N2. DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. WBPaper00055226:adr-1(tm668)_upregulated
  Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at L4 larva stage. DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. WBPaper00056169:rrf-3(pk1426)_upregulated_L4
  Transcripts that showed significantly decreased expression in nhr-8(hd117) comparing to in N2. Differentially expressed genes were identified using Sleuth (version 0.30.0). WBPaper00062446:nhr-8(hd117)_downregulated
  Transcripts that showed significantly decreased expression in spe-44(fx110) comparing to in control male animals. DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression. WBPaper00064502:spe-44(fx110)_downregulated
  Transcripts that showed significantly decreased expression in tph-1(mg280);odIs77 comparing to in odIs77 control animals. EdgeR, FDR<0.01 WBPaper00060921:tph-1(mg280)_downregulated
  Proteins expressed in activated sperm fraction after C. elegans spermatids were activated in vitro. N.A WBPaper00054996:activated_sperm_CE
  Proteins expressed in membranous oraganelle fraction after C. elegans spermatids were activated in vitro. N.A WBPaper00054996:membranous_oraganelle_CE
  Single-cell RNA-Seq cell group 170 expressed in: Seminal vesicle (male). CellRanger, DecontX, Monocle3, Louvain algorithm. WBPaper00065623:170

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2021497 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).  
    Expr1150147 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
WBGene00044365 2688916 2689179 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
264

1 Sequence Ontology Term