WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00001069 Gene Name  dpy-7
Sequence Name  ? F46C8.6 Brief Description  dpy-7 encodes a cuticular collagen; DPY-7 functions as a structural constituent of the extracellular cuticle whose activity is required for normal cuticular morphology and hence, proper body form.
Organism  Caenorhabditis elegans Automated Description  A structural constituent of collagen and cuticulin-based cuticle. Involved in cuticle development involved in collagen and cuticulin-based cuticle molting cycle and post-embryonic body morphogenesis. Located in annular furrow extracellular matrix. Expressed in several structures, including P1; P12; P2; cuticle; and hypodermis. Used to study skin disease.
Biotype  SO:0001217 Genetic Position  X :-1.6004 ±0.006854
Length (nt)  ? 1326
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00001069

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F46C8.6.1 F46C8.6.1 1147   X: 7536467-7537792
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:F46C8.6 F46C8.6 957   X: 7536653-7537453

38 RNAi Result

WormBase ID
WBRNAi00115421
WBRNAi00025530
WBRNAi00082859
WBRNAi00114937
WBRNAi00087470
WBRNAi00087477
WBRNAi00087476
WBRNAi00030241
WBRNAi00008808
WBRNAi00087471
WBRNAi00087473
WBRNAi00087472
WBRNAi00087475
WBRNAi00087474
WBRNAi00067425
WBRNAi00067529
WBRNAi00068035
WBRNAi00068151
WBRNAi00047518
WBRNAi00114983
WBRNAi00087562
WBRNAi00115419
WBRNAi00115021
WBRNAi00112380
WBRNAi00064354
WBRNAi00115079
WBRNAi00115059
WBRNAi00110301
WBRNAi00115040
WBRNAi00114888

42 Allele

Public Name
gk964260
gk963732
WBVar01927321
gk963873
gk963874
gk964088
gk964087
gk964005
gk964003
qm63
tm12657
sc27
WBVar01883579
WBVar01883580
k128
chc1
gk906900
gk613378
gk362971
gk526529
gk580301
gk592914
WBVar01815997
WBVar01815996
WBVar00049686
WBVar02045064
e2076
m38
e88
gk610000

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00001069 7536467 7537792 -1

3 Data Sets

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

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrX_7534758..7536466   1709 X: 7534758-7536466 Caenorhabditis elegans

297 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
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
  Genes that were downregulated in lin-15B(n744). For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. WBPaper00038168:lin-15B(n744)_downregulated
  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
  Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rifampicin_upregulated
  Transcripts that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Psora-Allantoin_upregulated
  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 expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:GABAergic-neuron_expressed
  Genes that are significantly up regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2. DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1. WBPaper00046012:tdp-1(ok803)_upregulated
  Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:hypodermis_expressed
  Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. edgeR, fold change > 2, FDR < 0.05 WBPaper00060909:atfs-1(cmh15)_downregulated
  Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:intestine_expressed
  Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:NMDA-neuron_expressed
  Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade). For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). WBPaper00040858:eQTL_regulated_developing
  Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
  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
Bacteria infection: Bacillus thuringiensis Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304. N.A. WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated
  Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO. Fold change > 2. WBPaper00064306:Agaro-oligosaccharides_upregulated
  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 morc-1(tm6048) animals, comparing to in N2, after growing at 25C for five generations (late generation). CuffDiff2 WBPaper00051265:F4_morc-1(tm6048)_downregulated
  Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2. DEseq 1.18.0, adjusted p-value < 0.05. WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
  Transcripts that showed significantly increased expression in adr-1(tm668) and adr-1(gv6) comparing to in N2 at L4 larva stage. DESeq FDR <= 0.05 WBPaper00056617:adr-1_upregulated_L4_transcript
  Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684) To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
  Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2. To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. WBPaper00047131:daf-2(e1370)_upregulated_N2-background
  Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals. NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%. WBPaper00064727:daf-2(e1370)_upregulated
  Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. Sleuth WBPaper00051558:aging_regulated
  Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. DESeq WBPaper00053302:stavudine_24h_regulated
  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

13 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1030677 Tiling arrays expression graphs  
Picture: Fig. 3A.   Expr7814 Throughout development DPY-7 localises to the furrows that define the annuli in the wild type cuticle.  
    Expr1151357 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
Transgenic Marker: rol-6(su1006)   Expr516 Hypodermal cells in embryo; ventral hypodermal cells, hyp5, hyp6, hyp7 in head, and hyp7, hyp10 in tail at L1. Low, mosaic expression in seam cells. Staining in hypodermal cells of the body, head and tail of the embryo from late comma stage onwards in each of the four larval stages and in adults. Staining observed in the cytoplasm. With nuclear localization signal, first detected at comma-stage in nuclei of hypodermal cells. L1 anti-lacZ antibodies hyp7 and P-cell nuclei, hyp5, hyp6 and hyp7 in the head and hyp7 and hyp10 nuclei in the tail with similar level of expression. High level of expression in hyp7, P-cells and particularly hypodermal cells of the head and tail but show much lower level of expression in hypodermal seam cells. Expression was seen in increasing number of nuclei at each developmental stage, including the adult, corresponding to the increase in hypodermal syncytial cell nuclei. Staining in other hypodermal cells of the head and tail but was mosaic, less intense and took longer time to develop. Minority of animals (20%) show staining in seam cells. This was very mosaic. GFP pattern entirely consistent with lacZ.  
    Expr3167 The fluorescence of transgenic animals carrying pdpy-7/GFP was observed in hypodermal cells. The expression of pdpy-7/GFP was observed from embryo to adult and the intensity of fluorescence decreased gradually from L4 to adult.  
    Expr2553 Intracellular localization of DPY-7 is first observed at the comma stage of embryogenesis, which corresponds to ~4 h before secretion of the L1 cuticle, concurring with the known temporal pattern of expression of dpy-7. The staining remains intracellular through the later stages of embryogenesis, and the first evidence of secretion of DPY-7 is at the threefold stage. Extracellular staining within the secreted cuticle is seen at the late threefold stage of embryogenesis just before hatch. DPY-7 location within the cells is detected as a halo surrounding the nucleus. To assist in the identification of cells, the antibodies MH27 and anti-LIN-26 were used to visualize hypodermal cell junctions and nuclei of hypodermal cells, respectively. The DPY-7 protein is detected during embryogenesis in most and probably all hypodermal cells, and certainly within the hyp-7 cells that form the major body hypodermal syncytium, the P cells that form the ventral hypodermis, and the V cells that constitute the lateral seam. Although DPY-7 is synthesized in all major hypodermal cells, the mature secreted collagen is only detected on the apical surfaces of the dorsal and ventral hypodermal cells and not on the lateral surface above the seam cells of developmental stages that have alae. This absence was shown by costaining with the MH27 antibody to delineate the boundaries of the seam cells. The DPY-7 protein is detected in circumferential bands within the cuticle of each larval stage and the adult. The DPY-7 bands locate within the furrows that delineate the annuli. The DPY-7 bands are not continuous around the entire worm body. In the adult and the L1 larva, longitudinal ridges termed alae exist within the cuticle above the seam cells. DPY-7 was not detected within these ridges or the matrix region immediately surrounding them. In larval stages with no alae, the DPY-7 bands start and end above the lateral seam cells where they partly interdigitate. When a partial reduction step is included during fixation for immunostaining, the DPY-7containing bands dissociate from other ECM material and adopt a discrete thread-like appearance. The DPY-7 bands seem to be more resistant to reduction than the ECM material that lies between the bands. DPY-7 collagen probably assembled into tight band or thread-like structures that run circumferentially around the body of the animal, located within the furrows that delineate the annuli.
    Expr1934 Immunostaining patterns in the hypodermal cells were observed at pre-elongated 1.5-fold embryo stage. The nuclear-excluded pattern observed probably represents an endoplasmic reticulum (ER) location. In elongated embryos the first larval cuticle has been synthesized, the cuticle collagen DPY-7 has already been secreted from the ER and has been fully incorporated into the developing cuticle2. endoplasmic reticulum (ER)
    Expr2011077 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).  
See Expr614 for expression pattern for the same locus. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).   Expr613 Fluorescence is first observed at around the comma stage. Level of fluorescence decreases gradually after L4 to adult-molt. Expression is detected throughout late embryonic and larval development with no change in intensity.  
See Expr614 for expression pattern for the same locus. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).   Expr614 Postembryonic worms assayed showed rapid reduction of mRNA between 2 and 3 h prior to the L4/adult molt and no expression in adults. Four separate peaks of mRNA abundance of the dpy-7 transcript are detected, one peak during each intermolt period.  
    Expr1026499 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr10274 Inferred expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/  
    Expr2029314 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).  

8 GO Annotation

Annotation Extension Qualifier
  enables
  enables
  enables
  part_of
  located_in
  located_in
  involved_in
happens_during(WBls:0000050) involved_in

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00001069 7536467 7537792 -1

8 Ontology Annotations

Annotation Extension Qualifier
  enables
  enables
  enables
  part_of
  located_in
  located_in
  involved_in
happens_during(WBls:0000050) involved_in

2 Regulates Expr Cluster

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in dpy-7(e88) animals comparing to N2 animals. Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1. WBPaper00053771:up_at_dpy-7(e88)
  Transcripts that showed significantly decreased expression in skn-1(RNAi);dpy-7(e88) animals comparing to dpy-7(e88) vector controls. Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1. WBPaper00053771:down_by_skn-1(RNAi)_at_dpy-7(e88)

1 Sequence

Length
1326

1 Sequence Ontology Term