Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C46A5.9.1 | C46A5.9.1 |
2790
 |
IV: 7770770-7774275 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C46A5.9 | C46A5.9 |
2349
|
IV: 7771206-7771346 |
41 Allele
| Public Name |
|---|
| gk964278 |
| gk964500 |
| gk963722 |
| gk963417 |
| gk963416 |
| WBVar00573529 |
| gk206085 |
| gk206086 |
| gk206083 |
| gk206084 |
| ok559 |
| WBVar01729947 |
| h4299 |
| WBVar01453172 |
| WBVar01453171 |
| WBVar01453173 |
| gk447031 |
| WBVar01908572 |
| ok5700 |
| tm11821 |
| gk909771 |
| gk605020 |
| gk691315 |
| gk851659 |
| gk344619 |
| gk746387 |
| gk347410 |
| gk824355 |
| gk830297 |
| gk481521 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00001827 | 7770770 | 7774275 | -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_chrIV_7770263..7770769 | 507 | IV: 7770263-7770769 | Caenorhabditis elegans |
153 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| oocyte proteins identified by two or more unique peptides during proteomics study. | In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide. | WBPaper00038289:oocyte_protein | |
| Genes with expression altered >= 3-fold in dpy-10(e128) mutants. | Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)). | WBPaper00035873:dpy-10_regulated | |
| 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 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 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 |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:hypodermis_expressed | |
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Maternal class (M): genes that are called present in at least one of the three PC6 replicates. | A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. | [cgc5767]:expression_class_M | |
| Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20) | |
| Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations. | Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50. | DESeq2 fold change > 2, p-value < 0.01. | WBPaper00061007:S.aquatilis_downregulated |
| Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines. | RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1. | WBPaper00035269:cde-1_regulated | |
| Genes down regulated by mir-243(n4759). | RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243. | WBPaper00036130:mir-243_down_regulated | |
| 25C vs. 20C | Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C. | CuffDiff, fold change > 2. | WBPaper00065096:25C_vs_20C_upregulated |
| Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. | CuffDiff, fold change > 2. | WBPaper00065096:Day10_vs_Day1_upregulated | |
| 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 decreased 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_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:all-neurons_L2-larva_expressed | |
| 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 | |
| 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:GABAergic-motor-neurons_L2-larva_expressed | |
| 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 | |
| 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:PVD-OLL-neurons_L3-L4-larva_expressed | |
| 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 | |
| Proteins interacting with HA-PPM-1.D. | N.A. | WBPaper00062498:PPM-1.D_interacting | |
| 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) |
| Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis. | To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. | WBPaper00045521:Gender_Neutral | |
| Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin. | N.A. | WBPaper00055862:antimycin_damt-1(gk961032)_regulated | |
| Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C. | EdgeR, FDR < 0.05, fold change < 0.5. | WBPaper00055971:nhl-2(ok818)_25C_upregulated |
11 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031072 | Tiling arrays expression graphs | |||
| Picture: Figure 4. The nuclear localization of native Ce HCF-1 is consistent with the nuclear localization of a recombinant Ce HCF-1-GFP protein observed in worms (Expr2780) upon heat shock-induced ectopic expression. | Expr7828 | Ce HCF-1 protein was detected in all embryonic cells, mainly in the nucleus. | nuclear localization | |
| Picture: Figure S3. | Expr8380 | Ubiquitous nuclear expression was observed in worms expressing a low-copy number of a functional hcf-1::gfp transgene. | ||
| Picture: Figure 2. The HCF-1 expression pattern detected in wild-type worms is highly specific because the hcf-1(pk924) and hcf-1(ok559) mutants only showed background fluorescence when they were examined using identical immunostaining conditions. | Expr8379 | Using an affinity-purified polyclonal HCF-1 antibody in immunostaining assays, prominent HCF-1 staining was observed in the nuclei of most, if not all, somatic and germline cells in wild-type worms. | The nuclear localization of HCF-1 was consistently observed from embryo through larval and adult stages. | |
| Expr2030611 | 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). | |||
| Expr2012375 | 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). | |||
| Expr2778 | The CeHCF protein accumulated in the cell nuclei during all stages of development and in a wide variety of adult cell types, independent of their lineage. The protein showed a diffuse nuclear pattern in early, late and later embryos. Nuclear accumulation showing nucleolar exclusion was evident in all larvae stages , as well as in adults. No expression was detected in oocytes, as expected for this promoter. These data indicated that CeHCF accumulates in the nuclei of C. elegans cells independently of their lineage, and also throughout worm development. | |||
| Type: mammalian cell transfection. Cells were transiently transfected with expression vectors for HCF-1 proteins containing an epitope tag at the N-terminus to facilitate detection and analysed by immunofluorescence. | Expr2779 | CeHCF showed a distinctly different and complex localisation whereby the typical pattern in ~75% cells showed a cytoplasmic threadlike pattern combined with a speckled distribution in the nucleus. To identify the very distinct cytoplasmic accumulation of CeHCF in mammalian cells, CeHCF distribution was examined in combination with a series of markers for different cytoplasmic compartments. The punctate localisation of CeHCF represented very specific and frequently quantitative colocalisation with mitochondria. This was observed with several independent mitochondrial markers for mitotracker, a mitochondrial specific dye. More diffuse cytoplasmic staining could sometimes be observed in addition to the cytoplasmic mitochondrial localisation, and in a significant fraction of cells (~25%) there was very little nuclear accumulation. | ||
| To address the possibility that the accumulation pattern of CeHCF in mammalian cells was the result of overexpression in transient transfection assay, a HeLa cell line stably expressing CeHCF-GFP was established . The cells expressed the protein in lower but readily detectable amounts. Strikingly, when stably expressed the CeHCF-GFP protein accumulated mainly in mitochondria, showing very little if any nuclear accumulation. These results suggested that the CeHCF is targeted very effectively to mitochondria in mammalian cells, with nuclear accumulation probably resulting from higher expression levels (for example saturating the mitochondrial association). Type: mammalian cell transfection. A mammalian expression vector for CeHCF-GFP was constructed. A mutant lacking the C1 tail was also constructed in this context (CeHCFDC1-GFP). | Expr2780 | CeHCF-GFP showed strong mitochondrial and nuclear localisation in mammalian cells, both live and after fixation. CeHCFDC1-GFP accumulated diffusely in the cytoplasm with little if any nuclear or mitochondrial localisation. | ||
| Expr1016045 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1146565 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
30 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| part_of(GO:0006979) | involved_in |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| part_of(GO:0006979) | enables |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| has_input(WB:WBGene00004804) | involved_in |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| part_of | |
| part_of | |
| enables | |
| enables | |
| part_of(GO:0098542) | acts_upstream_of_or_within |
| acts_upstream_of_or_within |
9 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
30 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| part_of(GO:0006979) | involved_in |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| part_of(GO:0006979) | enables |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| has_input(WB:WBGene00004804) | involved_in |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| part_of | |
| part_of | |
| enables | |
| enables | |
| part_of(GO:0098542) | acts_upstream_of_or_within |
| acts_upstream_of_or_within |
17 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Genes downregulated in hcf-1(-), downregulated in sir-2.1(O/E) and downregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1down_sir-2.1down_daf-2down | |
| Genes upregulated in hcf-1(-), upregulated in sir-2.1(O/E) and upregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1up_daf-2up | |
| Genes upregulated in hcf-1(-), upregulated in sir-2.1(O/E) and no change in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1up_daf-2nc | |
| Genes down regulated in hcf-1(-), downregulated in sir-2.1(O/E) and no change in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1down_sir-2.1down_daf-2nc | |
| Genes downregulated in hcf-1(-), downregulated in sir-2.1(O/E) and upregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1down_sir-2.1down_daf-2up | |
| Genes upregulated in hcf-1(-), downregulated in sir-2.1(O/E) and no change in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1down_daf-2nc | |
| Genes downregulated in hcf-1(-), upregulated in sir-2.1(O/E) and downregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1down_sir-2.1up_daf-2down | |
| Genes that were up regulated in the absence of hcf-1 and the presence of skn-1. | N.A. Reanalyzing previously published data.Authors compared the genes differentially expressed in hcf-1(pk924) mutant worms relative to N2 wild-type worms (referred to as hcf-1(-) profile) (Rizki et al., 2011) to those changed in wild-type worms treated with control RNAi relative to skn-1 RNAi (referred to as skn-1 (+) profile) (Oliveira et al., 2009). | WBPaper00041075:hcf-1(-)_skn-1(+)_upregulated | |
| Genes downregulated in hcf-1(-), upregulated in sir-2.1(O/E) and upregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1down_sir-2.1up_daf-2up | |
| Genes that were down regulated in the absence of hcf-1 and the presence of skn-1. | N.A. Reanalyzing previously published data.Authors compared the genes differentially expressed in hcf-1(pk924) mutant worms relative to N2 wild-type worms (referred to as hcf-1(-) profile) (Rizki et al., 2011) to those changed in wild-type worms treated with control RNAi relative to skn-1 RNAi (referred to as skn-1 (+) profile) (Oliveira et al., 2009). | WBPaper00041075:hcf-1(-)_skn-1(+)_downregulated | |
| Genes upregulated in hcf-1(-), no change in sir-2.1(O/E) and upregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1nc_daf-2up | |
| Genes downregulated in hcf-1(-), upregulated in sir-2.1(O/E) and no change in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1down_sir-2.1up_daf-2nc | |
| Genes upregulated in hcf-1(-), downregulated in sir-2.1(O/E) and upregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1down_daf-2up | |
| Genes upregulated in hcf-1(-), no change in sir-2.1(O/E) and no change in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1nc_daf-2nc | |
| Genes downregulated in hcf-1(-), no change in sir-2.1(O/E) and no change in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1down_sir-2.1nc_daf-2nc | |
| Genes upregulated in hcf-1(-), upregulated in sir-2.1(O/E) and downregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1up_daf-2down | |
| Genes upregulated in hcf-1(-), downregulated in sir-2.1(O/E) and downregulated in daf-2(-). | To identify the genes that show consistent and significant expression changes across the independent biological replicates of hcf-1(-) or sir-2.1(O/E), authors used Significance Analysis of Microarrays (SAM) with a stringent criteria of expected false discovery rate (FDR) set at 0%. | WBPaper00040184:hcf-1up_sir-2.1down_daf-2down |