Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F21H11.3.1 | F21H11.3.1 |
1829
 |
III: 5130923-5136319 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F21H11.3 | F21H11.3 |
1272
|
III: 5131337-5131930 |
61 Allele
| Public Name |
|---|
| WBVar01263436 |
| tm282 |
| WBVar01656665 |
| ut192 |
| ut180 |
| WBVar00056066 |
| WBVar01701743 |
| WBVar00059916 |
| ttTi26817 |
| WBVar01408576 |
| ok5088 |
| gm111 |
| WBVar01445604 |
| ok529 |
| gk606311 |
| gk405076 |
| gk591641 |
| gk376400 |
| gk612990 |
| gk491511 |
| gk903093 |
| WBVar01938991 |
| gk360995 |
| gk856869 |
| WBVar00563199 |
| gk494610 |
| WBVar01644535 |
| gk401004 |
| WBVar01644536 |
| gk477943 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006543 | 5130923 | 5136319 | -1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_5130677..5130922 | 246 | III: 5130677-5130922 | Caenorhabditis elegans |
207 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 | |
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| 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:all-neurons_L1-larva_expressed | |
| adult vs dauer larva | Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. | N.A. | WBPaper00050488:adult_vs_dauer_regulated_N2_20C |
| 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 |
| Genes that showed increased expression in wdr-5(ok1417) comparing with in N2. | Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated. | WBPaper00045861:wdr-5(ok1417)_upregulated | |
| 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 | |
| Bacteria infection: Enterococcus faecalis | Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50. | For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. | WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray |
| 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 that showed significantly increased expression in eif-2alpha(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2 | |
| Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:body-muscle_expressed | |
| 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 | |
| Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
| Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:seam_expressed | |
| 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 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 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 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 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 sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage. | DESeq2, fold change > 2 | WBPaper00058725:sftb-1(cer6)_downregulated | |
| 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 | |
| Reduced humidity (98% relative humidity). | Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis. | Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001. | WBPaper00044578:reduced-humidity_downregulated_microarray |
| 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:all-neurons_L2-larva_expressed | |
| Transcripts that showed significantly increased expression in pie-1(ne4443[PIE-1-Degron-GFP]) | DESeq2. Differentially expressed genes were defined as twofold change and adjusted p-value less than 0.05. | WBPaper00061478:pie-1(ne4433)_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:dopaminergic-neurons_L3-L4-larva_expressed | |
| 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 |
16 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr4283 | TBX-2::GFP expression was present in the both MS- and ABa-derived pharynx cells. TBX-2::GFP expression initiated at the 8E stage (staging by the number of endodermal, or E, cells), in 11 - 12 anteriorly localized pharyngeal cells. Based on position, these cells are likely to be the ABa descendants that will give rise to pharyngeal muscle cells (i.e., ABalpaaa a/p, ABalpapp a/p, ABaraaaaa, ABaraapa a/p, ABarapaa a/p, ARarapapp and ABaraapp a/p). By the 1.5-fold stage, TBX-2::GFP was expressed in pm3, pm5 and variably pm4, with expression persisting throughout the larval and adult stages. Surprisingly, expression extended beyond the ABa lineage after the 1.5-fold stage. For example, only 2/6 pm5 nuclei derive from ABa but authors often observed all pm5 cells expressing TBX-2::GFP in larvae. By the 3-fold stage authors also observed expression in pharyngeal neurons, occasionally in the posterior muscle pm8 and in cells outside of the pharynx such as body wall muscles. Thus, TBX-2::GFP expression initiated within the ABa lineage but ultimately appeared in both ABa and MS-derived muscle cells. | While TBX-2::GFP was initially localized to nuclei, it was detected in the cytoplasm as well as the nucleus in pm4 and pm5 cells by the 1.5-fold stage. Cytoplasmic expression was not homogeneous. Rather, TBX-2::GFP appeared filamentous, as though it was associated with the cytoskeleton. Cytoplasmic expression was observed even in lines expressing very low levels of TBX-2::GFP, suggesting that cytoplasmic TBX-2::GFP did not reflect over-expression from transgenes. The same pattern was observed in tbx-2(ok529); tbx-2::GFP embryos. This localization pattern suggests that the timing of tbx-2 transcriptional function likely initiates before the 1.5-fold stage, when TBX-2 appears completely nuclear. | ||
| Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http: | Expr4284 | tbx-2 transcripts was detected starting at the 4E stage (~102 cell stage, 143 min after the 4-cell stage), and with mid-gastrula expression observed by in situ hybridization (Shin-i and Kohara, http://nematode.lab.nig.ac.jp/). | ||
| Embryos at the ~200 cell stage contain 24 clonally committed pharyngeal precursors located in the anterior of the embryo (13 ABa-derived and 11 MS-derived), and the location of the 12 tbx-2::gfp expressing cells at this stage suggests that they are included among these precursors. To determine if these early tbx-2::gfp expressing cells were indeed pharyngeal precursors and to characterize their lineal origin, athors examined expression of a tbx-2::gfp promoter fusion containing the same tbx-2 5'-flanking sequences characterized above fused to gfp just downstream of the tbx-2 translation initiation codon (pOK206.30). Previous studies demonstrated that such promoter fusions can produce a longer lived GFP signal than full-length protein fusions. This tbx-2::gfp promoter fusion produced cytoplasmic GFP first detected in premorphogenetic embryos in the same pattern as full-length fusion protein, but GFP perdured in the pharynx until near hatching. GFP expression was observed in 3-fold embryos and early larvae in a reproducible subset of pharyngeal muscles, with occasional expression in body wall muscles and head neurons. GFP was observed predominantly in pharyngeal muscle types derived solely from ABa or from mixed lineages, and the number of these GFP-positive cells was generally consistent with those containing ABa-derived cells. However, exceptions to this generalization were found. Most notably, GFP was reproducibly observed in one MS-derived m7 muscle and all three m4 muscles (of which 2 contain only MS-derived cells). Taken together, these results strongly suggest that tbx-2::gfp expression in premorphogenetic embryos is limited to pharyngeal precursors, and most of these are ABa-derived, although expression is also likely in a small number of MS-derived pharyngeal precursors. | Expr4285 | In transgenic embryos, this larger tbx-2::gfp reporter was expressed in a dynamic pattern, including in a subset of pharyngeal precursors in the premorphogenetic embryo, as well as body wall muscle and pharyngeal neurons. tbx-2::gfp expression initiated in 2 anterior cells in approximately 100 cell embryos and increased to 12 cells by approximately the 200 cell stage. The increasing number of GFP expressing cells was not due to cell divisions; rather tbx-2::gfp expression appeared to initiate asynchronously in individual cells. Expression in these cells was transient and was undetectable by the bean stage. Prior to the bean stage, tbx-2::gfp expression was also observed in body wall muscles, and later, in 2- to 3-fold embryos, expression was observed in a number of pharyngeal neurons. Expression in both of these tissues continued in larvae. | This full-length fusion protein is nuclear localized. | |
| Reporter gene fusion type not specified. | Expr4286 | Expression initiated in the pharyngeal neurons in late embryogenesis, but earlier expression was not observed. | ||
| Expr2035483 | 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). | |||
| The whole-mount in situ hybridization database by the Kohara Lab [NEXTDB Ver. 3.0 beta (July 07, 2001), yk112c4, shows that the gene is expressed transiently in the midembryonic stage. | Expr2890 | Expression was detected in some neurons in the head and pharynx of larvae and adult animals. The neurons expressing Ce-TBX-2 was identified in adult animals: they were amphid sensory neurons AWB, AWC, ASJ, and pharyngeal neurons I1, I3, I5, M1, M2, M5, NSM. | Most Ce-TBX-2 protein molecules were localized in the cytoplasm and not in the nuclei of all the neurons that express this protein. The mutations ut180 and ut192 did not change the localization. | |
| Expr12335 | In wild-type animals, Ptbx-2::gfp is expressed in the developing pharynx of embryos and becomes restricted to several neurons in the head near hatching, where expression persists through adulthood. Occasional GFP expression was also observed in tail neurons, but no expression was detected elsewhere. | |||
| Expr1032691 | Tiling arrays expression graphs | |||
| Expr1200028 | Data from the TransgeneOme project | |||
| Expr11215 | In embryos, Ptbx-2::gfp was expressed in pharyngeal precursors beginning at the 100-200 cell stage, and GFP remained detectable in the pharynx until near hatching. During larval and adult stages Ptbx-2::gfp was strongly expressed in several neurons in the head and occasionally neurons in the tail, but it was not expressed in the pharynx or other tissues. In embryos, Ptbx-2::gfp was expressed in pharyngeal precursors beginning at the 100-200 cell stage, and GFP remained detectable in the pharynx until near hatching. During larval and adult stages Ptbx-2::gfp was strongly expressed in several neurons in the head and occasionally neurons in the tail, but it was not expressed in the pharynx or other tissues. | |||
| Reporter gene fusion type not specified. | Expr2891 | This GFP fusion showed very weak fluorescence in pharyngeal neurons I5 and M2. Although the intensity of fluorescence was not enough for detailed expression studies, this expression is not in contradiction to the results obtained with the antibody. | ||
| Original chronogram file: chronogram.1753.xml | [F21H11.3:gfp] transcriptional fusion. | Chronogram722 | ||
| Expr1010921 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2017347 | 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). | |||
| Expr1170043 | Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191 | |||
| Expr1149173 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
37 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in |
10 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
37 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in |
2 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Genes with increased expression in tbx-2(bx59) comparing to N2. | The limma package was used to calculate differential expression using the limma linear model fit, eBayes smoothing of standard errors, and Benjamini-hochberg(Bh) multiple test correction with a false discovery rate of 5%. | WBPaper00042274:tbx-2(bx59)_upregulated | |
| Genes with decreased expression in tbx-2(bx59) comparing to N2. | The limma package was used to calculate differential expression using the limma linear model fit, eBayes smoothing of standard errors, and Benjamini-hochberg(Bh) multiple test correction with a false discovery rate of 5%. | WBPaper00042274:tbx-2(bx59)_downregulated |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_5136320..5137357 | 1038 | III: 5136320-5137357 | Caenorhabditis elegans |
