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TABLE 3. Ranking information and results for single nucleotide polymorphism description and location information for the selected variants in the DNA double-strand break repair pathway*
2005
Table 2 Information on all single nucleotide polymorphisms (SNPs) reported by name in this paper In the present study, in the control population, SNPs shown in bold were found to have the minor and major alleles opposite from what was reported in the database. References to genotypes in this paper use minor and major alleles as determined by the control population in the present study. For example, BCL6 homozygous variant refers to CC.
2004
"... In PAGE 3: ... From this distribution, it was inferred that each of 13 SNPs was individually significant at the P H11349 0.05 level (Table 1; see Table2 for full SNP information). Because the number of tests was high, a correction for multiple testing was applied so that the overall family of hypotheses has a reasonable false discovery rate.... ..."
Cited by 10
TABLE 1. Fully informed predicted numbers of nucleotide and protein signatures, and number of sequences required to approximate fully informed predictionsa
2004
Table II. Comparision between Promoter Scan and PromFD. Promoter Scan results for the training set* and test set* are from published data by Prestridge (1995) We have also tested Promoter Scan using our test set on the most recent version of Promoter Scan (version 1.7), which contains significant improvement over the published program. The result is shown in the last line. Note that the results from Prestridge apos;s original research are for single- stranded (ss) DNA, whereas our results are for double-stranded (ds) DNA. The result shows that PromFD also compares favorably against this version
Table 3. Influence of X-ray irradiation on the viability of F1 progeny from RNAi-treated animals
2007
"... In PAGE 12: ...5% due to embryonic lethality induced by RNAi alone; however, the viability of F1 progeny from irradiated drh-3(RNAi) animals markedly decreased to 0.6% ( Table3 ). A similar X-ray hypersensitivity was observed in rad-51(RNAi) animals, in which DNA double-strand break repair and meiotic homologous recombination were suppressed.... ..."
Table 8: Hyper-twist motif B7 and A0 strands. The SCOR description of these sites is mostly of stacked paired non- Watson/Crick double strand, or cross strand. At A3 the structure is considered to be a kink-turn motif. For the 7D VQ there is a clear preference for the r conformation to be in one of the complexes (AG BP BDBFBC).
2004
"... In PAGE 16: ... There is a G-A pair and an A-G pair. In Table8 we included both the B7 and the A0 strand.... ..."
Table 1: Summary table of the chromosome and plasmid sequences downloaded from GenBank. The number of individual DNA sequences examined includes plasmids and organelles for se- quenced genomes. The total number of bp reflects the count of A,T,G, and Cs within the se- quence, and does not include n or other ambiguous bases.
2002
"... In PAGE 6: ... This resulted in a total of 764 sequenced chromosomes from Prokaryotic and Eukaryotic organisms, as well as double-stranded DNA viruses. The totals can be seen in Table1 . Links to the individual chromosome sequences and references can be found on our Genome Atlas web page 1.... ..."
Cited by 1
Table 1. The goal was to estimate the minimum number of sequences required to approximate the number of TaqMan signature candidates predicted when all sequence data avail- able are used. That is, how much do we overestimate the number of conserved, unique signature candidates when we only have a fraction of the data compared to when we use all of the available data? Which are more valuable, target or near-neighbor sequences, for pruning the list of signature can- didates to those most likely to be conserved and unique, and thus likely to succeed in screening?
2004
"... In PAGE 3: ... Contour or topographic plots, traditionally used for complex data with two independent variables, were uninformative in preliminary analyses, since only one quantile point for each (t, n) pair, and not the entire range, could be displayed at once. RESULTS Analyses indicate that lack of conservation, more than lack of uniqueness, limits our ability to find species-specific, spe- cies-wide TaqMan signatures for most viruses, and thus more target than NN sequence data are required ( Table1 ). The range of the number of TaqMan signatures for random sub- samples of plum pox virus and NN genomes remains the same for a given target set size, regardless of the number of NNs, illustrated by the rectangular, stair-stepped pattern of horizon- tal lines in Fig.... In PAGE 4: ... Indeed, the variola and vaccinia genome sequences are an order of magnitude longer than those of the other viruses with sufficient sequence data for our Monte Carlo methods. Conservation does not depend on se- quence length alone, however, as illustrated by JC virus, the shortest of the double-stranded DNA viruses we examined at approximately 5,000 bp, and with a huge number of sequenced genomes ( Table1 ). Although no single signature was present in all genomes, other analyses (data not shown) indicate that there are 23 TaqMan signature candidates that are shared among at least 75% of the 187 JC genomes.... ..."
Cited by 5
Table 1. Recommended gel percentages for separation of linear DNA.
2006
"... In PAGE 5: ... As a result of this, only large alterations of the DNA will be visualized and complex electrophoresis system must be used to resolve the fragments into discrete bands. As a compromise, apos;six- cutter apos; enzymes are most often used for RFLP analysis because they are readily available, cheaper and they usually produce fragments in the size range of 200 to 20,000 bp, which can be separated conveniently on agarose gels ( Table1 ). After digestion by restriction enzymes, the DNA is present as a mixture of linear double-stranded molecules of various lengths.... ..."
Table 1 B. The truth table encoding using dinucleotide quot;bits quot;
1997
"... In PAGE 3: ... In this paper we show that this limitation can be overcome (in DNA), allowing a number of basic series and series-parallel bit operation sequences in solution. In an electronic computer an operator is succinctly represented by a truth table, a table of all possible combinations of the input bit values and their corresponding output values ( Table1 A). Our approach is to encode these truth tables in DNA using a three-level scheme.... In PAGE 4: ...combinations of the input and operand bits ( Table1 ). As a result of an operation the input strand hybridizes with its complementary operand strand to form a double stranded DNA complex.... In PAGE 4: ... This output is interpreted according to the truth table (level 3) of the operator applied. Table1 B shows our encoding scheme along with the truth tables for di erent boolean and arithmetic operations such as NAND, AND, XOR and ADD (addition). The truth table encoding can easily be extended to a number of other operators.... In PAGE 4: ... As a solution to the rst problem we attach, a priori, the corresponding output value to each of the operand strands in the form of a single stranded DNA. The DNA sequence of the output is constructed using the level 1 encoding ( Table1 B). Thus, each operand strand... In PAGE 11: ... Table1 A. The truth table for various binary operations Input 1 Input 2 NAND XOR ADD Output AND 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 0 0 0 0 0 1 1 0 10 1 1 1 1 1 1 0 0 0 0 0 0 1 1 0 10... ..."
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