Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F59G1.6a | F59G1.6a |
21
 |
II: 5902269-5902289 |
| Transcript:F59G1.6b | F59G1.6b |
22
|
II: 5902308-5902329 |
Other
12 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk964349 |
| e912 |
| tm8370 |
| ma161 |
| gk757397 |
| bp238 |
| n408 |
| n410 |
| n409 |
| e92 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00002993 | 5902254 | 5902347 | 1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
19 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. | DESEQ2, fold change > 2 and FDR < 0.01. | WBPaper00062103:neuron_enriched | |
| Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066485:ogt-1(ok1474)_upregulated_neuron | |
| Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure. | Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours. | DESeq2, FDR < 0.05 | WBPaper00056868:P.aeruginosa_upregulated_smallRNA |
| Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. | Student's t-test, fold change > 2, p-value < 0.05. | WBPaper00055386:daf-2(e1370)_downregulated | |
| Transcripts that showed significantly increased expression in natural variant RC301(that showed resistance towards bacteria infection) vs. natural variant DA650, after 4 hour of infection by P. aeruginosa PA14. | Fold change > 2, p-value < 0.05. | WBPaper00050712:RC301_vs_DA650_4h-PA_upregulated | |
| Transcripts that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector. | Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. | WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA | |
| Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in hypodermis. | Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. | WBPaper00066447:Day8_vs_Day1_upregulated_hypodermis | |
| miRNAs that showed significantly increased expression in pry-1(mu38) comparing to in N2. | Fold change > 2, FDR < 0.05 | WBPaper00057033:pry-1(mu38)_upregulated | |
| MicroRNAs that showed significantly decreased expression in alg-1(gk214), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-1(gk214)_downregulated_miRNA | |
| MicroRNAs that showed significantly increased expression in alg-2(ok304), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-2(ok304)_upregulated_miRNA | |
| MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-5(tm1163)_downregulated_miRNA | |
| Heat Shock: 35C 4 hours at L4 larva stage. | Micro RNAs that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours | DESeq2 | WBPaper00057154:HeatShock_downregulated_miRNA |
| MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals. | Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. | WBPaper00053318:Aging_downregulated_miRNA_N2 | |
| MicroRNAs that showed significantly increased expression in alg-5(ram2), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-5(ram2)_upregulated_miRNA | |
| MicroRNAs that showed significantly increased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite. | Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. | WBPaper00053318:mir-71(n4115)_upregulated_miRNA | |
| Micro RNAs that showed significantly increased expression in hrpk-1(zen17) comparing to in N2 at embryo stage. | DESeq, fold change > 2, p-value <= 0.05. | WBPaper00058673:hrpk-1(zen17)_upregulated_miRNA_embryo | |
| MicroRNAs that showed significantly increased expression in alg-1(gk214), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-1(gk214)_upregulated_miRNA | |
| Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in neuron. | Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. | WBPaper00066447:Day8_vs_Day1_downregulated_neuron | |
| miRNA that showed decreased expression after 20mM nicotine treatment | Statistical analysis was based on t-test for independent samples via SPSS. The results were further narrowed based on two criteria. Only the genes whose expression changed with a P < 0.05 and a fold change > 0.5, when compared to control, were considered as differentially expressed. Fold change was calculated as 2**(DeltaCt(treatment)-DeltaCt(control))-1. DeltaCt = Ct(miRNA)-Ct(aveMRNA). | WBPaper00042480:20mM_nicotine_downregulated |
14 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr12254 | Expression of the Plin-4::GFP-pest reporter peaked in hyp7 and seam cells at the mid- and late-L3 stage and then again at the late-L4 stage. In addition, the majority of animals exhibited a cessation of hyp7 and seam cell Plin-4::GFP-pest expression immediately after L4 ecdysis. In contrast, Plin-4::GFP-pest expression in muscle cells displayed a different transcriptional profile. In the majority of animals, expression of GFP-pest in muscles peaked at L3 ecdysis, gradually diminished throughout the remainder of the L4 stage, and increased again at the young adult stage. These results suggest that, while lin-4 is dynamically expressed once each larval stage, its promoter activity may be differentially regulated in distinct tissues. | |||
| Expr11602 | plin-4::GFP was expressed in pharynx, neurons, and seam cells coincident with when mature lin-4 is detected at the end of the first larval stage. lin-4 primary transcripts start to be expressed towards the end of L1, coinciding with the accumulation of mature lin-4 miRNA. | |||
| Expr8409 | Expression seen from late L1 to adult stages. Weak expression detected ubiquitously (except germline). Stronger in pharynx, vulva, vulval muscle, body wall muscle. | |||
| Expr10057 | lin-4 is abundantly expressed in L1 larvae in many tissues, including muscles, hypodermal cells, and neurons in the head, the tail, the ventral nerve cord, the anterior body, and the mid-body. The lin-4 promoter reporter expression was broader and generally stronger during the L1 stage than in the embryonic stage. The lin-4 promoter reporter was expressed in lateral ganglion neurons (ADL, AWB, AWC, AFD), ventral nerve cord neurons (DA, DB, DD, VD), anterior-body region neurons (SDQR), tail neurons (PQR), touch neurons (AVM, PVM, ALM, PLM), and HSN neurons. | |||
| Expr12245 | In the zaIs1 (plin-4:GFP) line, GFP is driven by this region of the lin-4 promoter, and GFP expression in the stem cell-like hypodermal seam cells is detectable beginning in the early L2 stage, consistent with the timing of the appearance of mature lin-4, as detected by northern blot (Expr3738). | |||
| Expr12246 | lin-4 was temporally expressed in the hypodermal seam cells at the early L2 stage and expression persisted in adulthood. Furthermore, the spatial patterning of lin-4 in the hypodermal seam cells correlated with the requirement of this gene at the L1/L2 transition to direct normal seam cell development.lin-4 expression was first observed within the developing gonad at the beginning of L3, specifically in the distal tip cells and the anchor cell of the somatic gonad and expression in the distal tip cells continued in the adult. lin-4 and let-7 were weakly expressed in the anchor cell, which is required for proper vulval patterning, and in the P5.p, P6.p, and P7.p cells that will later differentiate into the mature vulva. | |||
| Expr12251 | For each of the mir::GFP-pest reporters (Plin-4::GFP-pest, Plet-7::GFP-pest, mir-1::GFP-pest) post-embryonic GFP-pest expression was first detected at approximately 14 hours post L1 arrest. Once transcriptionally activated, Plin-4::GFP-pest and Plet-7::GFP-pest reporters peak in expression by 18-20 hours and diminish with similar kinetics. For animals expressing the Plet-7::GFP-pest reporter GFP-pest expression was monitored for longer periods after release from L1 arrest. Consistent with the highly pulsatile nature of this expression pattern, GFP-pest expression was reinitiated at 30 hours, which correlates with the later portions of the L2 stage. While transcriptional activation of the Pmir-1::GFP-pest reporter was also initiated at 14 hours post-L1 arrest, the peak of Pmir-1::GFPpest expression occurred at a later time point, and diminished with slower kinetics, as compared to Plin-4::GFP-pest and Plet-7::GFP-pest expression.The majority of animals which harbor the Plin-4::GFP-pest transgene cease GFP-pest expression by L3 ecdysis and resume expression by the mid-L4 stage. The pulse of Plin-4::GFP-pest expression at the L4 stage extends through the early portion of young adulthood and completely overlaps with the lethargus period in all animals. Plet-7::GFP-pest expression followed a similar pattern. However, GFP-pest expression was more variable at the L3-to-L4 transition and L4-specific induction of this transgene was primarily restricted to the lethargus period. In contrast to the expression profiles of the lin-4 and let-7 reporters, induction of Pmir-1::GFP-pest expression began during, or immediately after, L3 ecdysis and persisted into the L4 stage. A second pulse of Pmir-1::GFP-pest expression completely overlapped with the L4 lethargus period and continued into early adulthood. Collectively, these results suggest that the expression patterns of lin-4, let-7 and mir-1 are dynamic throughout development and that the cyclical transcription of these miRNAs is mediated by their cognate promoter sequences. | |||
| Expr10890 | ||||
| Expr3738 | The lin-4 miRNA is highly expressed during the late L1/eL2 transition through to adulthood with peak expression noted in mid-L3. | |||
| Expr2519 | No signal detected in embryos and L1 larva. Intense signals detected in L2, L3, L4 larva, adults, and glp-4(bn2) adults. | |||
| Gene_regulation: Because the lin-4::YFP reporter gene contains only genomic regulatory sequence fused to the YFP coding sequence, this result demonstrates that lin-4 transcription is repressed by starvation and/or activated by nutrition, as opposed to a posttranscriptional regulatory mechanism. Consistent with other aspects of the L1-arrest-defective phenotype of daf-16(mgDf50), lin-4::YFP is expressed in starved daf-16(mgDf50) L1s. However, the penetrance of lin-4::YFP expression is relatively low, visible in only 3% and 8% of larvae after 3 and 7 days of starvation, respectively [0% in wild-type and hsf-1(sy441) L1s]. It is intriguing to speculate that nutritional control of developmental timing could be mediated by direct transcriptional regulation of lin-4 by DAF-16. However, given the low penetrance of the lin-4::YFP-expression phenotype together with the presumption that DAF-16 function likely results in global repression of gene expression during starvation, the simplest interpretation is that DAF-16 represses lin-4 transcription indirectly. Thus, the low penetrance of the lin-4::YFP-expression phenotype in starved daf-16(mgDf50) L1s likely reflects the proportion of individuals that develop to the relatively late period in the L1 stage when lin-4::YFP expression becomes visible. Alternatively, DAF-16 could regulate lin-4 directly, but initial expression levels could be too low for detection by reporter gene. | Expr3869 | A lin-4::YFP reporter gene is robustly expressed in all somatic cells of the L1 within 12 hr of hatching in the presence of food, but it is not expressed during L1 arrest. | ||
| Expr1332 | lin-4S RNA was not detected in embryos, or early L1 larvae, and was first detected during the latter half of the L1 larval stage, 12 h after larval development began. lin-4S levels continued to increase through the L1 and during subsequent stages of development (lin-4S RNA is also present in high levels in adult worms). lin-4L is expressed at very low levels and was difficult to detect by these Northern blots. | |||
| Expr3845 | lin-4::GFP in the zaIs1 strain continues to be widely expressed in the aging adult. | |||
| Expr12020 |
15 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00003003) | enables |
15 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00003003) | enables |
8 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Class F gene expression showed no change in lin-14(lf) in L1, down regulation in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_F | |
| Class A gene expression showed down regulation in lin-14(lf) in L1, no change in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_A | |
| Class B gene expression showed up regulation in lin-14(lf) in L1, no change in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_B | |
| Class E gene expression showed no change in lin-14(lf) in L1, up regulation in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_E | |
| Class H gene expression showed up regulation in lin-14(lf) in L1, up regulation in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_H | |
| Class C gene expression showed down regulation in lin-14(lf) in L1, up regulation in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_C | |
| Class D gene expression showed up regulation in lin-14(lf) in L1, down regulation in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_D | |
| Class G gene expression showed down regulation in lin-14(lf) in L1, down regulation in lin-4(lf) in L2. | Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control). | WBPaper00026952:class_G |