Genomics
12 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:W03C9.4a.1 | W03C9.4a.1 |
2070
 |
II: 11917643-11933224 |
| Transcript:W03C9.4b.1 | W03C9.4b.1 |
2282
|
II: 11917649-11935340 |
| Transcript:W03C9.4c.1 | W03C9.4c.1 |
954
|
II: 11918339-11921438 |
| Transcript:W03C9.4j.1 | W03C9.4j.1 |
942
|
II: 11918339-11921438 |
| Transcript:W03C9.4k.1 | W03C9.4k.1 |
951
|
II: 11918339-11921438 |
| Transcript:W03C9.4l.1 | W03C9.4l.1 |
963
|
II: 11918339-11921438 |
| Transcript:W03C9.4d.1 | W03C9.4d.1 |
1356
|
II: 11918339-11933224 |
| Transcript:W03C9.4e.1 | W03C9.4e.1 |
1362
|
II: 11918339-11933224 |
| Transcript:W03C9.4f.1 | W03C9.4f.1 |
1365
|
II: 11918339-11933224 |
| Transcript:W03C9.4g.1 | W03C9.4g.1 |
1371
|
II: 11918339-11933224 |
| Transcript:W03C9.4h.1 | W03C9.4h.1 |
1377
|
II: 11918339-11933224 |
| Transcript:W03C9.4i.1 | W03C9.4i.1 |
1383
|
II: 11918339-11933224 |
Other
12 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:W03C9.4a | W03C9.4a |
1374
|
II: 11918339-11918546 |
| CDS:W03C9.4b | W03C9.4b |
1368
|
II: 11918339-11918546 |
| CDS:W03C9.4c | W03C9.4c |
954
|
II: 11918339-11918546 |
| CDS:W03C9.4j | W03C9.4j |
942
|
II: 11918339-11918546 |
| CDS:W03C9.4k | W03C9.4k |
951
|
II: 11918339-11918546 |
| CDS:W03C9.4l | W03C9.4l |
963
|
II: 11918339-11918546 |
| CDS:W03C9.4e | W03C9.4e |
1362
|
II: 11918339-11918546 |
| CDS:W03C9.4f | W03C9.4f |
1365
|
II: 11918339-11918546 |
| CDS:W03C9.4g | W03C9.4g |
1371
|
II: 11918339-11918546 |
| CDS:W03C9.4h | W03C9.4h |
1377
|
II: 11918339-11918546 |
| CDS:W03C9.4i | W03C9.4i |
1383
|
II: 11918339-11918546 |
| CDS:W03C9.4d | W03C9.4d |
1356
|
II: 11918339-11918546 |
54 RNAi Result
384 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| otn9593 |
| gk962684 |
| gk963539 |
| gk341509 |
| gk332927 |
| WBVar01312700 |
| WBVar02076580 |
| gk821603 |
| WBVar01935808 |
| WBVar01627335 |
| WBVar01627336 |
| WBVar01312709 |
| WBVar01627337 |
| WBVar01605197 |
| WBVar01605198 |
| WBVar01605199 |
| WBVar01605193 |
| WBVar01605194 |
| WBVar01605195 |
| WBVar01605196 |
| sy292 |
| WBVar00246595 |
| WBVar00246596 |
| WBVar00246594 |
| WBVar00246791 |
| WBVar00246792 |
| WBVar02069276 |
| sy531 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003015 | 11917643 | 11935340 | -1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
148 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| 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 showed expression levels higher than the corresponding reference sample (embryonic 24hr reference). | A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. | WBPaper00037950:bodywall-muscle_L1-larva_expressed | |
| Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. | Fold change > 2, FDR < 0.01. | WBPaper00065993:glp-1(e2141)_upregulated | |
| Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). | DESeq2, fold change >= 2, FDR <= 0.01. | WBPaper00056826:SGP_biased | |
| Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day5_vs_Day1_downregulated | |
| 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 | |
| Transcripts that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day11_vs_Day1_downregulated | |
| 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 | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age 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_age_regulated_developing | |
| 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) | |
| 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 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 | |
| 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 | |
| Expression Pattern Group C, enriched for genes involved in metabolic processes. | The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05. | WBPaper00036286:Pattern_C | |
| Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference). | A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. | WBPaper00037950:A-class-motor-neurons_L2-larva_expressed | |
| Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. | DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. | WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14 | |
| Genes that showed oscillating 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:oscillating_dev_expression | |
| Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2. | DESeq 2, fold change > 2, FDR < 0.05. | WBPaper00065581:hpk-1(pk1393)_upregulated | |
| Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:hda-1(ne4752)_upregulated | |
| Transcripts that showed significantly increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:mep-1(ne4629)_upregulated | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference). | A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. | WBPaper00037950:hypodermis_L3-L4-larva_expressed | |
| Transcripts that showed significantly increased expression in npr-15(tm12539) comparing to in N2 at L4 larva stage. | Fold change > 2, FDR < 0.05. | WBPaper00066608:npr-15(tm12539)_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 decreased 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_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 |
21 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031408 | Tiling arrays expression graphs | |||
| Expr14800 | LIN-29 expression in probable neurons, including the tail region near DA9, is located has been noted and we verified this. | |||
| Clone: pUL#JRH/AA3 | Expr7697 | Quite generalised expression. However, there is also some particularly strong expression in the developing vulva or uterine connection to the vulva, and another gonadal component that may be very early spermatheca, and this stands out clearly above the weaker, more generalised expression. The more generalised expression is a bit stronger in late embryos. Can also see expression above the generalised expression in the nervous system and the grinder of adults. | ||
| Lineage expression: sexmyoblasts and descandents. | Expr1596 | LIN-29 was detected in many non-hypodermal cells in the head, tail and vulval region of the developing hermaphrodite. In the head, LIN-29 accumulates in cells of the pharynx and in a subset of neurons. In the tail, LIN-29 accumulates in the rectal cells B, F and U. LIN-29 also accumulates in the sex myoblasts and their progeny, in the distal tip cells, the anchor cell, and in many vulval cells. Although the accumulation of LIN-29 in the hypodermis is restricted to the L4 stage, accumulation in several of these other cell types is not. For example, the accumulation of LIN-29 in the anchor cell and the distal tip cells occurs during the L3 stage. In addition, many, if not all, of the cells that make up the pharynx contain low levels of LIN-29, beginning in the L1 stage and extending to the adult stage. The anti-LIN-29 antisera recognized a nuclear antigen in lateral hypodermal seam cells in wild-type C. elegans. The anti-LIN-29 antibodies revealed a differential pattern of lin-29 protein accumulation during development. LIN-29 was not detected in hermaphrodite hypodermal nuclei prior to the L4 stage. Although it is possible that LIN-29 is distributed diffusely throughout the hypodermal cytoplasm during the L3 and younger stages, there are no difference detected in hypodermal cell staining when these animals were incubated with secondary antibody alone, relative to animals incubated with both primary and secondary antibodies. The earliest LIN-29 accumulation in lateral seam cell nuclei was shortly after their final division, during the L3- to L4-molt. LIN-29 accumulated in these hypodermal nuclei during the L4 stage, and remained detectable in the adult animal. At approximately the same time, LIN-29 was detected in the hypodermal nuclei of the head (hyp1-hyp6), tail (hyp8-hyp12), and the large hypodermal syncytium covering most of the animal (hyp7). The accumulation of LIN-29 in hyp7 was typically observed following accumulation in the seam, and the signal was usually less intense. In summary, LIN-29 accumulates stage-specifically, beginning during the L4 stage and persisting into the adult stage, in all hypodermal cell nuclei of the worm. LIN-29 was also detectable in late stage gravid adults, at a time when lin-29 mRNAs are greatly reduced in abundance. | nuclei | |
| Expr14654 | The male-specific neuronal expression of lin-29a is not observed in male-specific neurons but is, interestingly, entirely restricted to sex-shared neurons (i.e. neurons that are generated in both sexes). Intriguingly, most of these neurons had not been previously reported to show sexually dimorphic gene expression patterns or functions. Specifically, 21 out of 116 sex-shared neuron classes express lin-29a, including seven sensory neuron classes in the head and tail (AWA, ASG, ASJ, ASK, ADF, PHB, PLM), seven interneuron classes (AVA, RIA, AIM, AVG, RIF, PVC, PVN), a few head and tail motor neurons (SAB, PDA, PDB) and most of the sex-shared ventral nerve cord motor neurons (dorsal and ventral A, B and D-type and AS neurons). Expression of lin-29a in all these neurons in the male nervous system is precisely temporally controlled; it is first observed in the early L4 stage and persists throughout adulthood. | |||
| Expr14655 | In addition to the male-specific neuronal expression of the lin-29a isoform [Expr14655], we also found that the lin- 29b isoform is expressed in three postembryonically generated touch neurons (AVM, PVM, PDE), where its expression is not temporally regulated, that is, its expression is induced right after the neurons are born in the first two larval stages and expression is observed in both sexes. | |||
| No detailed description on cellular expression pattern at hermaphrodites. | Expr1300 | LIN-29 accumulates in B cell progeny. In contrast to the LIN-29 accumulation pattern observed in wild-type hermaphrodites, LIN-29 is not detectable in the F, U, Y, or M blast cell nuclei, or in their progeny, in males. LIN-29 is detected in the progeny of B. LIN-29 is first detectable in B cell progeny during the L3 stage. Although all B.a and B.p progeny accumulate LIN-29, the LIN-29 accumulation signals appear weaker and transient in B.p progeny. The identification of these LIN-29-accumulating cells as B progeny is based on their size, shape, and relative position within the male tail and is further supported by laser microsurgery experiments and the examination of LIN-29-accumulation patterns in a mutant with defects in B cell specification. Elimination of the B cell by laser micro-surgery during the L1 stage reduced the number of LIN-29-accumulating nuclei in the male tail by 1015. LIN-29 appears to persist in B.a progeny in the adult stage. LIN-29 accumulates in the linker cell. The first male-specific LIN-29 accumulation is detected in the nucleus of the linker cell (LC) positioned at the tip of the growing end of the gonad. LIN-29 accumulates in the LC during the L3 stage, after the gonad arm has completed the 180 turn. LIN-29 remains detectable until the late L4 stage when its disappearance is presumably due to LC destruction. LIN-29 accumulates in the male tail seam. LIN-29 accumulates in the lateral body seam cell nuclei and in the SET nuclei in L4 stage wild-type males. LIN-29 accumulates in ventral cord nuclei. During the late L3 stage, five to seven nuclei that belong to the preanal ganglion accumulate LIN-29. Four preanal ganglion nuclei accumulates LIN-29 and were identified by position as the CA9, CP9, AS11, and VA11 neurons which are descended from P11.a. LIN-29 accumulation in the preanal ganglion cluster persists through adulthood. In late L4 stage and adult males, additional ventral cord nuclei anterior to the preanal ganglion accumulate LIN-29. The accumulation of LIN-29 in ventral cord neurons is not observed in hermaphrodites. Also in contrast to hermaphrodites, the ventral hypodermal nuclei positioned within the ventral cord do not contain detectable levels of LIN-29 in adult males. | nuclei | |
| Since we could not create a LIN-29b-specific tag due to lack of isoform-specific sequence, we used a C-terminal fusion that tags both isoforms and mutated the lin-29a isoform in this background. | Expr15022 | LIN- 29b was first detectable in lateral seam cell nuclei of late L3 worms. Subsequently, in mid-L4 stage animals, it also accumulated, weakly, in the major hypodermal syncytium hyp7. | ||
| Expr15023 | By contrast, LIN-29a was not detected in either seam cells or the major hypodermal syncytium hyp7 during the L3 stage. Instead, LIN-29a accumulation began in both cell types in mid-L4 stage worms. Finally, protein levels of both LIN-29a and LIN- 29b peaked in lateral seam cells and hyp7 in late L4 stage animals and persisted into adulthood. | |||
| Expr15021 | Using live imaging of the GFP-tagged proteins, we observed LIN-29 isoform accumulation. In agreement with immunofluorescence-based analysis (Bettinger et al., 1996), we detected signal in the epidermis and in other regions such as the head, the tail and the vulva. In most sites, patterns of the two LIN-29 isoforms appeared to differ. | |||
| Expr12983 | LIN-29 antibody staining of L4 stage animals demonstrated that LIN-29 is absent in the intestine but is found throughout the hypodermis. | |||
| Expr13142 | Expression of lin-29 was observed in the AC throughout the course of uterine-vulval connection but was not observed in the other cells in contact with or bordering the basement membrane boundary. | |||
| Expr14653 | The expression pattern of the gfp allele that tags both isoforms of lin-29 (lin-29a and lin-29b), matches the expression pattern reported using an antibody directed against both LIN-29 isoforms (Bettinger et al., 1996; Euling et al., 1999). As previously reported, we observed expression in head neurons and the ventral nerve cord. However, we found that this neuronal expression is almost completely restricted to the male and this male-specific expression can be entirely ascribed to the a-isoform. | |||
| Expr2013172 | 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). | |||
| Expr11856 | The transcription of lin-29 starts at approximately mid L3 stage and continues during L4. | |||
| Expr1158206 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr15019 | lin-29b isoform. The levels of the LIN-29b protein agreed with its previously reported pattern of mRNA accumulation, with detectable accumulation throughout larval stages and an increase in levels in the L3 and L4 stages. By contrast, although the lin-29a transcript is detectable in L1 and abundant in L2 (Rougvie and Ambros, 1995), LIN-29a protein was undetectable in L1 or L2 stage worms, accumulated weakly in L3 stage, and peaked in L4 stage worms. | |||
| Expr15020 | lin-29a isoform. The levels of the LIN-29b protein agreed with its previously reported pattern of mRNA accumulation, with detectable accumulation throughout larval stages and an increase in levels in the L3 and L4 stages. By contrast, although the lin-29a transcript is detectable in L1 and abundant in L2 (Rougvie and Ambros, 1995), LIN-29a protein was undetectable in L1 or L2 stage worms, accumulated weakly in L3 stage, and peaked in L4 stage worms. | |||
| Expr1586 | A probe generated from the 1.1 kb EcoRI fragment of the lin-29 cDNA detects both the 2.4 and 1.8 kb transcripts beginning in the L1 stage. These transcripts increase in abundance as development proceeds to the L4 stage, and then decrease at least 5-fold relative to the L4 levels in adults. The abundance of the 1.8 kb transcript increases slightly relative to the 2.4 kb transcript during larval development. | |||
| Expr2031404 | 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). | |||
| Expr1011509 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 |
36 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00000626)|has_input(WB:WBGene00000647)|has_input(WB:WBGene00000615) | enables |
| enables | |
| has_input(WB:WBGene00000615)|has_input(WB:WBGene00000626)|has_input(WB:WBGene00000647) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| occurs_in(WBbt:0005062) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(GO:0009408) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in |
36 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00000626)|has_input(WB:WBGene00000647)|has_input(WB:WBGene00000615) | enables |
| enables | |
| has_input(WB:WBGene00000615)|has_input(WB:WBGene00000626)|has_input(WB:WBGene00000647) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| occurs_in(WBbt:0005062) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(GO:0009408) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in |
4 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly decreased expression in animals carrying hsp-16.2p-LIN-29 (induced at early L3 larva stage), comparing to animals carrying empty vectors. | DESeq2 v.1.12.3, FDR < 0.05, fold change > 1.7. | WBPaper00059191:hsp-16.2p-LIN-29_downregulated | |
| Transcripts that showed significantly increased expression in lin-29(n333) comparing to in N2 at day 1 adult stage. | DESeq2, FDR < 0.01, fold change > 2. | WBPaper00066970:lin-29(n333)_upregulated | |
| Transcripts that showed significantly increased expression in animals carrying hsp-16.2p-LIN-29 (induced at early L3 larva stage), comparing to animals carrying empty vectors. | DESeq2 v.1.12.3, FDR < 0.05, fold change > 1.7. | WBPaper00059191:hsp-16.2p-LIN-29_upregulated | |
| Transcripts that showed significantly decreased expression in lin-29(n333) comparing to in N2 at day 1 adult stage. | DESeq2, FDR < 0.01, fold change > 2. | WBPaper00066970:lin-29(n333)_downregulated |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_11935341..11947578 | 12238 | II: 11935341-11947578 | Caenorhabditis elegans |
