Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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DISCUSSION
0
null
null
17,459,890
null
One of the problems encountered with DNA array datasets is the unequal distribution of the variance, which is inversely proportional to the log of intensities, consequently affecting threshold settings for differential expression.
null
230
5,300
0
false
null
null
One of the problems encountered with DNA array datasets is the unequal distribution of the variance, which is inversely proportional to the log of intensities, consequently affecting threshold settings for differential expression.
true
true
true
true
true
881
0
DISCUSSION
0
null
null
17,459,890
null
In the analysis of expression profiling datasets, the central issue comes down to building confidence intervals that successfully fit the variability due to noise (experimental or technological).
null
195
5,301
0
false
null
null
In the analysis of expression profiling datasets, the central issue comes down to building confidence intervals that successfully fit the variability due to noise (experimental or technological).
true
true
true
true
true
881
0
DISCUSSION
0
null
null
17,459,890
null
One way to solve the problem is to mathematically transform the data in order to normalize the variance.
null
104
5,302
0
false
null
null
One way to solve the problem is to mathematically transform the data in order to normalize the variance.
true
true
true
true
true
881
1
DISCUSSION
1
28
[ "B28" ]
17,459,890
NA
Here, we propose the use of the normalized value of the expression level (EV), a model for micro-array data processing based on spline functions, which has proved its ability to provide models for complex phenomena (28) and curve fitting in data analysis of observations with random components.
[ "28" ]
294
5,303
1
false
Here, we propose the use of the normalized value of the expression level (EV), a model for micro-array data processing based on spline functions, which has proved its ability to provide models for complex phenomena and curve fitting in data analysis of observations with random components.
[ "28" ]
Here, we propose the use of the normalized value of the expression level (EV), a model for micro-array data processing based on spline functions, which has proved its ability to provide models for complex phenomena and curve fitting in data analysis of observations with random components.
true
true
true
true
true
882
1
DISCUSSION
1
28
[ "B28" ]
17,459,890
NA
The examples analyzed with EV show that, due to the Box–Cox spline transformation, the transformed data shows a normal distribution, and allows the definition of a continuous confidence band delineating the DS, the interval including all genes devoid of significant expression changes, which can be adjusted to a standar...
[ "28" ]
332
5,304
0
false
The examples analyzed with EV show that, due to the Box–Cox spline transformation, the transformed data shows a normal distribution, and allows the definition of a continuous confidence band delineating the DS, the interval including all genes devoid of significant expression changes, which can be adjusted to a standar...
[]
The examples analyzed with EV show that, due to the Box–Cox spline transformation, the transformed data shows a normal distribution, and allows the definition of a continuous confidence band delineating the DS, the interval including all genes devoid of significant expression changes, which can be adjusted to a standar...
true
true
true
true
true
882
1
DISCUSSION
1
28
[ "B28" ]
17,459,890
NA
The values (xi, yi) for each gene in the dataset not included in DS (located outside the upper or lower spline curves) is then associated with a P-value, which provides statistical support for the selection of outliers.
[ "28" ]
219
5,305
0
false
The values (xi, yi) for each gene in the dataset not included in DS (located outside the upper or lower spline curves) is then associated with a P-value, which provides statistical support for the selection of outliers.
[]
The values (xi, yi) for each gene in the dataset not included in DS (located outside the upper or lower spline curves) is then associated with a P-value, which provides statistical support for the selection of outliers.
true
true
true
true
true
882
2
DISCUSSION
0
null
null
17,459,890
NA|NA|pmid-12169537|pmid-12111897|pmid-12169536|pmid-11470887|pmid-10445855
The specificity and sensitivity of EV were determined analyzing the U133 Latin square dataset from Affymetrix.
null
110
5,306
0
false
null
null
The specificity and sensitivity of EV were determined analyzing the U133 Latin square dataset from Affymetrix.
true
true
true
true
true
883
2
DISCUSSION
0
null
null
17,459,890
NA|NA|pmid-12169537|pmid-12111897|pmid-12169536|pmid-11470887|pmid-10445855
The dataset was generated from the hybridization of 42 human genome chips with 3 technical replicates of 14 separate hybridizations, obtained from a human RNA containing 42 spiked transcripts at concentrations ranging from 0.125 to 512 pM.
null
239
5,307
0
false
null
null
The dataset was generated from the hybridization of 42 human genome chips with 3 technical replicates of 14 separate hybridizations, obtained from a human RNA containing 42 spiked transcripts at concentrations ranging from 0.125 to 512 pM.
true
true
true
true
true
883
2
DISCUSSION
0
null
null
17,459,890
NA|NA|pmid-12169537|pmid-12111897|pmid-12169536|pmid-11470887|pmid-10445855
These comparisons demonstrate that EV was more robust than MAS5 and VSN in this type of analysis.
null
97
5,308
0
false
null
null
These comparisons demonstrate that EV was more robust than MAS5 and VSN in this type of analysis.
true
true
true
true
true
883
2
DISCUSSION
0
null
null
17,459,890
NA|NA|pmid-12169537|pmid-12111897|pmid-12169536|pmid-11470887|pmid-10445855
Indeed, when analyzing experiments in which the spikes had a 2-fold change, for a fixed specificity EV showed a 1.27-fold and 6.32-fold higher sensitivity than MAS5 and VSN, respectively (see Figure 6B); and for a fixed sensitivity, EV was 2.3-fold and 58-fold higher specificity than MAS5 and VSN, respectively (see Fig...
null
328
5,309
0
false
null
null
Indeed, when analyzing experiments in which the spikes had a 2-fold change, for a fixed specificity EV showed a 1.27-fold and 6.32-fold higher sensitivity than MAS5 and VSN, respectively (see Figure 6B); and for a fixed sensitivity, EV was 2.3-fold and 58-fold higher specificity than MAS5 and VSN, respectively (see Fig...
true
true
true
true
true
883
2
DISCUSSION
0
null
null
17,459,890
NA|NA|pmid-12169537|pmid-12111897|pmid-12169536|pmid-11470887|pmid-10445855
Performance of EV was also directly compared to MAS5, Resolver, dChip and two types of t-test analyses, showing also a better performance than these tests (Figure 6D and E).
null
173
5,310
0
false
null
null
Performance of EV was also directly compared to MAS5, Resolver, dChip and two types of t-test analyses, showing also a better performance than these tests (Figure 6D and E).
true
true
true
true
true
883
2
DISCUSSION
0
null
null
17,459,890
NA|NA|pmid-12169537|pmid-12111897|pmid-12169536|pmid-11470887|pmid-10445855
The specificity of EV showed a large increase with the increase of FC in the spikes, concomitant with a moderate increase in specificity (not shown).
null
149
5,311
0
false
null
null
The specificity of EV showed a large increase with the increase of FC in the spikes, concomitant with a moderate increase in specificity (not shown).
true
true
true
true
true
883
3
DISCUSSION
0
null
null
17,459,890
pmid-1518992
The comparison of EV, VSN and MAS5 data analysis from a real expression profiling experiment (B6.1-arrays), comparing the profiles of exponentially growing and G1-arrested cells (Figures 3–5) gave a slightly different picture.
null
226
5,312
0
false
null
null
The comparison of EV, VSN and MAS5 data analysis from a real expression profiling experiment (B6.1-arrays), comparing the profiles of exponentially growing and G1-arrested cells (Figures 3–5) gave a slightly different picture.
true
true
true
true
true
884
3
DISCUSSION
0
null
null
17,459,890
pmid-1518992
In this experiment, EV leads to a more robust variance stabilization than VSN; in addition, EV leads to an increase in the homogeneity of the selected sets, and thus to an increased reproducibility on the selection of outliers.
null
227
5,313
0
false
null
null
In this experiment, EV leads to a more robust variance stabilization than VSN; in addition, EV leads to an increase in the homogeneity of the selected sets, and thus to an increased reproducibility on the selection of outliers.
true
true
true
true
true
884
3
DISCUSSION
0
null
null
17,459,890
pmid-1518992
In this experiment, however, the direct comparison of the three methods, clearly shows that EV and VSN are closer (71%) than MAS5, whereas the coincidences between EV and MAS5, or VSN and MAS5 are 33 and 38% respectively.
null
221
5,314
0
false
null
null
In this experiment, however, the direct comparison of the three methods, clearly shows that EV and VSN are closer (71%) than MAS5, whereas the coincidences between EV and MAS5, or VSN and MAS5 are 33 and 38% respectively.
true
true
true
true
true
884
3
DISCUSSION
0
null
null
17,459,890
pmid-1518992
The differences between EV and VSN are mainly due to the fact that EV takes into account the shape of the diagonal in the form of concave or convex distortions.
null
160
5,315
0
false
null
null
The differences between EV and VSN are mainly due to the fact that EV takes into account the shape of the diagonal in the form of concave or convex distortions.
true
true
true
true
true
884
3
DISCUSSION
0
null
null
17,459,890
pmid-1518992
In the small fraction of datasets devoid of such distortions, there are virtually no differences in the set of selected genes (not shown), and VSN performs definitively better in this experiment than in the Latin square data analysis.
null
234
5,316
0
false
null
null
In the small fraction of datasets devoid of such distortions, there are virtually no differences in the set of selected genes (not shown), and VSN performs definitively better in this experiment than in the Latin square data analysis.
true
true
true
true
true
884
3
DISCUSSION
0
null
null
17,459,890
pmid-1518992
The data reported here also demonstrate that, unlike classical approaches such as MAS5, EV does not encounter any difficulty on selecting regulated genes with either high- or low-expression levels.
null
197
5,317
0
false
null
null
The data reported here also demonstrate that, unlike classical approaches such as MAS5, EV does not encounter any difficulty on selecting regulated genes with either high- or low-expression levels.
true
true
true
true
true
884
4
DISCUSSION
0
null
null
17,459,890
null
Furthermore, in two analyses in which chips hybridized with RNAs obtained from cells grown in two different conditions (A and B), and the set of selected genes was compared with another dataset in which the datasets compared were 10xA and B.
null
241
5,318
0
false
null
null
Furthermore, in two analyses in which chips hybridized with RNAs obtained from cells grown in two different conditions (A and B), and the set of selected genes was compared with another dataset in which the datasets compared were 10xA and B.
true
true
true
true
true
885
4
DISCUSSION
0
null
null
17,459,890
null
It is relevant that in both comparisons, the set of identified genes was rigorously the same (>98% identities) (not shown).
null
123
5,319
0
false
null
null
It is relevant that in both comparisons, the set of identified genes was rigorously the same (>98% identities) (not shown).
true
true
true
true
true
885
4
DISCUSSION
0
null
null
17,459,890
null
This demonstrates, not only the strength and robustness of EV on variance stabilization, and might allow to compare data obtained under different conditions, and even datasets generated with chips from different origins.
null
220
5,320
0
false
null
null
This demonstrates, not only the strength and robustness of EV on variance stabilization, and might allow to compare data obtained under different conditions, and even datasets generated with chips from different origins.
true
true
true
true
true
885
5
DISCUSSION
0
null
null
17,459,890
null
For physiological and pathological processes, in general there is no a priori evidence for a higher number of up-regulated or down-regulated genes.
null
147
5,321
0
false
null
null
For physiological and pathological processes, in general there is no a priori evidence for a higher number of up-regulated or down-regulated genes.
true
true
true
true
true
886
5
DISCUSSION
0
null
null
17,459,890
null
Normalization of the distribution by the Box–Cox transformation makes globally a symmetric distribution of expression datasets, although at the extremes of this distribution, asymmetries are often detected.
null
206
5,322
0
false
null
null
Normalization of the distribution by the Box–Cox transformation makes globally a symmetric distribution of expression datasets, although at the extremes of this distribution, asymmetries are often detected.
true
true
true
true
true
886
5
DISCUSSION
0
null
null
17,459,890
null
Moreover, it is possible to force an asymmetric selection, by using different sets of tuning parameters (EV thresholds), when there is information suggesting that the ‘treatment’ will lead to a larger number of either up-regulated or down-regulated genes.
null
255
5,323
0
false
null
null
Moreover, it is possible to force an asymmetric selection, by using different sets of tuning parameters (EV thresholds), when there is information suggesting that the ‘treatment’ will lead to a larger number of either up-regulated or down-regulated genes.
true
true
true
true
true
886
5
DISCUSSION
0
null
null
17,459,890
null
It should also be noted that the selection of genes is only one of the steps in the process of data analysis, the data should be strengthened by replicated analysis with other biological samples, and subsequently validated by northern, western, Q-PCR, etc.
null
256
5,324
0
false
null
null
It should also be noted that the selection of genes is only one of the steps in the process of data analysis, the data should be strengthened by replicated analysis with other biological samples, and subsequently validated by northern, western, Q-PCR, etc.
true
true
true
true
true
886
6
DISCUSSION
0
null
null
17,459,890
null
In conclusion, splines seem to be well adapted for micro-array analyses since, (i) the transformed data shows a normal distribution and the median axis overlaps the first diagonal; (ii) it results in a robust variance stabilization; (iii) its usage is independent of the number of genes present on each dataset and the t...
null
664
5,325
0
false
null
null
In conclusion, splines seem to be well adapted for micro-array analyses since, (i) the transformed data shows a normal distribution and the median axis overlaps the first diagonal; (ii) it results in a robust variance stabilization; (iii) its usage is independent of the number of genes present on each dataset and the t...
true
true
true
true
true
887
6
DISCUSSION
0
null
null
17,459,890
null
We, thus, propose that EV could play a pivotal role in expression profiling data analysis, since it overcomes many of the difficulties shown by other methods on selecting differentially expressed genes.
null
202
5,326
0
false
null
null
We, thus, propose that EV could play a pivotal role in expression profiling data analysis, since it overcomes many of the difficulties shown by other methods on selecting differentially expressed genes.
true
true
true
true
true
887
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5" ]
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
Antiretroviral resistance is a major threat to successful anti-HIV treatment.
[ "1", "2", "3–5" ]
77
5,327
0
false
Antiretroviral resistance is a major threat to successful anti-HIV treatment.
[]
Antiretroviral resistance is a major threat to successful anti-HIV treatment.
true
true
true
true
true
888
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5" ]
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
This problem is more frequent among individuals that started therapy in the 1990s, who were treated sequentially with single antiviral agents (1), allowing sequential development of resistance to each treatment.
[ "1", "2", "3–5" ]
211
5,328
1
false
This problem is more frequent among individuals that started therapy in the 1990s, who were treated sequentially with single antiviral agents, allowing sequential development of resistance to each treatment.
[ "1" ]
This problem is more frequent among individuals that started therapy in the 1990s, who were treated sequentially with single antiviral agents, allowing sequential development of resistance to each treatment.
true
true
true
true
true
888
0
INTRODUCTION
1
2
[ "B1", "B2", "B3 B4 B5" ]
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
Therapy with combinations of antiretroviral drugs is more effective, but nevertheless up to 50% of individuals currently in care in the US harbor HIV-resistant viruses (2).
[ "1", "2", "3–5" ]
172
5,329
1
false
Therapy with combinations of antiretroviral drugs is more effective, but nevertheless up to 50% of individuals currently in care in the US harbor HIV-resistant viruses.
[ "2" ]
Therapy with combinations of antiretroviral drugs is more effective, but nevertheless up to 50% of individuals currently in care in the US harbor HIV-resistant viruses.
true
true
true
true
true
888
0
INTRODUCTION
1
3–5
[ "B1", "B2", "B3 B4 B5" ]
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
These resistant strains can also be transmitted—more than 15% of recently infected individuals have acquired viruses that are resistant to at least one of the major antiretroviral classes (3–5).
[ "1", "2", "3–5" ]
194
5,330
1
false
These resistant strains can also be transmitted—more than 15% of recently infected individuals have acquired viruses that are resistant to at least one of the major antiretroviral classes.
[ "3–5" ]
These resistant strains can also be transmitted—more than 15% of recently infected individuals have acquired viruses that are resistant to at least one of the major antiretroviral classes.
true
true
true
true
true
888
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5" ]
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
Current treatment guidelines in the United States recommend resistance testing before beginning or changing antiretroviral therapy.
[ "1", "2", "3–5" ]
131
5,331
0
false
Current treatment guidelines in the United States recommend resistance testing before beginning or changing antiretroviral therapy.
[]
Current treatment guidelines in the United States recommend resistance testing before beginning or changing antiretroviral therapy.
true
true
true
true
true
888
1
INTRODUCTION
0
null
null
17,576,693
pmid-16825395|pmid-17206150
In the developing world, where much of the burden of HIV infection is concentrated, combination therapy is increasingly available.
null
130
5,332
0
false
null
null
In the developing world, where much of the burden of HIV infection is concentrated, combination therapy is increasingly available.
true
true
true
true
true
889
1
INTRODUCTION
0
null
null
17,576,693
pmid-16825395|pmid-17206150
A sharp increase in drug resistance is expected as patients become more treatment experienced.
null
94
5,333
0
false
null
null
A sharp increase in drug resistance is expected as patients become more treatment experienced.
true
true
true
true
true
889
1
INTRODUCTION
0
null
null
17,576,693
pmid-16825395|pmid-17206150
Unfortunately, resistance genotyping is generally unavailable in the developing world due to the prohibitive expense.
null
117
5,334
0
false
null
null
Unfortunately, resistance genotyping is generally unavailable in the developing world due to the prohibitive expense.
true
true
true
true
true
889
2
INTRODUCTION
1
1
[ "B1" ]
17,576,693
pmid-14999114
Genotypic and phenotypic methods are commonly used to detect antiviral resistance in clinical specimens.
[ "1" ]
104
5,335
0
false
Genotypic and phenotypic methods are commonly used to detect antiviral resistance in clinical specimens.
[]
Genotypic and phenotypic methods are commonly used to detect antiviral resistance in clinical specimens.
true
true
true
true
true
890
2
INTRODUCTION
1
1
[ "B1" ]
17,576,693
pmid-14999114
Genotypic methods use bulk sequencing of the protease (PR) and reverse transcriptase (RT) coding regions, which reports the sequence of the predominant circulating HIV variants.
[ "1" ]
177
5,336
0
false
Genotypic methods use bulk sequencing of the protease (PR) and reverse transcriptase (RT) coding regions, which reports the sequence of the predominant circulating HIV variants.
[]
Genotypic methods use bulk sequencing of the protease (PR) and reverse transcriptase (RT) coding regions, which reports the sequence of the predominant circulating HIV variants.
true
true
true
true
true
890
2
INTRODUCTION
1
1
[ "B1" ]
17,576,693
pmid-14999114
Resistance mutations conferring reduced sensitivity to the three most widely used drug classes (nucleoside and non-nucleoside RT inhibitors and PR inhibitors) are well characterized, allowing probable resistance patterns to be inferred from sequence information.
[ "1" ]
262
5,337
0
false
Resistance mutations conferring reduced sensitivity to the three most widely used drug classes (nucleoside and non-nucleoside RT inhibitors and PR inhibitors) are well characterized, allowing probable resistance patterns to be inferred from sequence information.
[]
Resistance mutations conferring reduced sensitivity to the three most widely used drug classes (nucleoside and non-nucleoside RT inhibitors and PR inhibitors) are well characterized, allowing probable resistance patterns to be inferred from sequence information.
true
true
true
true
true
890
2
INTRODUCTION
1
1
[ "B1" ]
17,576,693
pmid-14999114
Phenotypic methods rely on cloning the RT and PR-coding regions from patient samples into a standard HIV plasmid backbone, allowing generation of viral stocks and functional analysis of viral drug sensitivity in short-term culture (1).
[ "1" ]
235
5,338
1
false
Phenotypic methods rely on cloning the RT and PR-coding regions from patient samples into a standard HIV plasmid backbone, allowing generation of viral stocks and functional analysis of viral drug sensitivity in short-term culture.
[ "1" ]
Phenotypic methods rely on cloning the RT and PR-coding regions from patient samples into a standard HIV plasmid backbone, allowing generation of viral stocks and functional analysis of viral drug sensitivity in short-term culture.
true
true
true
true
true
890
3
INTRODUCTION
1
6
[ "B6", "B7", "B8", "B9" ]
17,576,693
NA|pmid-15635002|pmid-15247339|pmid-17215531
Several studies have demonstrated that minor drug-resistant HIV populations that are not detectable in the standard assays can impair the response to therapy (6,7).
[ "6", "7", "8", "9" ]
164
5,339
0
false
Several studies have demonstrated that minor drug-resistant HIV populations that are not detectable in the standard assays can impair the response to therapy.
[ "6,7" ]
Several studies have demonstrated that minor drug-resistant HIV populations that are not detectable in the standard assays can impair the response to therapy.
true
true
true
true
true
891
3
INTRODUCTION
1
6
[ "B6", "B7", "B8", "B9" ]
17,576,693
NA|pmid-15635002|pmid-15247339|pmid-17215531
This problem is particularly apparent in studies of pregnant women that received single doses of nevirapine, a non-nucleoside reverse transcriptase inhibitor (NNRTI), at the time of delivery to prevent vertical transmission of HIV.
[ "6", "7", "8", "9" ]
231
5,340
0
false
This problem is particularly apparent in studies of pregnant women that received single doses of nevirapine, a non-nucleoside reverse transcriptase inhibitor (NNRTI), at the time of delivery to prevent vertical transmission of HIV.
[]
This problem is particularly apparent in studies of pregnant women that received single doses of nevirapine, a non-nucleoside reverse transcriptase inhibitor (NNRTI), at the time of delivery to prevent vertical transmission of HIV.
true
true
true
true
true
891
3
INTRODUCTION
1
6
[ "B6", "B7", "B8", "B9" ]
17,576,693
NA|pmid-15635002|pmid-15247339|pmid-17215531
In these patients, the presence of minor populations with resistance to nevirapine—which were often undetectable by conventional sequencing—compromised the response to subsequent NNRTI therapy (8,9).
[ "6", "7", "8", "9" ]
199
5,341
0
false
In these patients, the presence of minor populations with resistance to nevirapine—which were often undetectable by conventional sequencing—compromised the response to subsequent NNRTI therapy.
[ "8,9" ]
In these patients, the presence of minor populations with resistance to nevirapine—which were often undetectable by conventional sequencing—compromised the response to subsequent NNRTI therapy.
true
true
true
true
true
891
4
INTRODUCTION
1
7
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
A variety of technologies have been devised to allow characterization of minor HIV drug-resistant populations (7,10,11).
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
120
5,342
0
false
A variety of technologies have been devised to allow characterization of minor HIV drug-resistant populations.
[ "7,10,11" ]
A variety of technologies have been devised to allow characterization of minor HIV drug-resistant populations.
true
true
true
true
true
892
4
INTRODUCTION
1
12
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
In one method, microarrays were designed to interrogate positions of drug resistance mutations (12).
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
100
5,343
1
false
In one method, microarrays were designed to interrogate positions of drug resistance mutations.
[ "12" ]
In one method, microarrays were designed to interrogate positions of drug resistance mutations.
true
true
true
true
true
892
4
INTRODUCTION
1
7
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
This technique allows analysis of many genomic positions in a single experiment, but the method has not been widely used, in part due to the high cost of each test.
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
164
5,344
0
false
This technique allows analysis of many genomic positions in a single experiment, but the method has not been widely used, in part due to the high cost of each test.
[]
This technique allows analysis of many genomic positions in a single experiment, but the method has not been widely used, in part due to the high cost of each test.
true
true
true
true
true
892
4
INTRODUCTION
1
10
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
Another method involves allele-specific RT-PCR, which allows sensitive detection of single drug resistance mutations (10).
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
122
5,345
1
false
Another method involves allele-specific RT-PCR, which allows sensitive detection of single drug resistance mutations.
[ "10" ]
Another method involves allele-specific RT-PCR, which allows sensitive detection of single drug resistance mutations.
true
true
true
true
true
892
4
INTRODUCTION
1
11
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
A third approach takes advantage of the massively parallel polony sequencing method (11), and a fourth uses an early version of pyrosequencing to query single nucleotide positions for possible mutations (13).
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
208
5,346
1
false
A third approach takes advantage of the massively parallel polony sequencing method, and a fourth uses an early version of pyrosequencing to query single nucleotide positions for possible mutations.
[ "11", "13" ]
A third approach takes advantage of the massively parallel polony sequencing method, and a fourth uses an early version of pyrosequencing to query single nucleotide positions for possible mutations.
true
true
true
true
true
892
4
INTRODUCTION
1
10
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
However, except for the microarray method, all of the above methods queried individual base pairs at a time (10).
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
113
5,347
1
false
However, except for the microarray method, all of the above methods queried individual base pairs at a time.
[ "10" ]
However, except for the microarray method, all of the above methods queried individual base pairs at a time.
true
true
true
true
true
892
4
INTRODUCTION
1
7
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
Given that there are over 60 amino acid positions just in PR and RT that can affect resistance to the three widely used drug classes, these methods are time consuming and difficult to use for comprehensive analysis.
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
215
5,348
0
false
Given that there are over 60 amino acid positions just in PR and RT that can affect resistance to the three widely used drug classes, these methods are time consuming and difficult to use for comprehensive analysis.
[]
Given that there are over 60 amino acid positions just in PR and RT that can affect resistance to the three widely used drug classes, these methods are time consuming and difficult to use for comprehensive analysis.
true
true
true
true
true
892
4
INTRODUCTION
1
7
[ "B7", "B10", "B11", "B12", "B10", "B11", "B13", "B10" ]
17,576,693
pmid-15635002|pmid-16825395|pmid-17206150|pmid-8673920|pmid-16825395|pmid-17206150|pmid-11158091|pmid-16825395
An ideal method for investigating drug resistance mutations would yield many complete sequences of HIV genomic regions at risk for mutations for each viral population, and allow analysis of many samples of HIV populations in a single experiment.
[ "7", "10", "11", "12", "10", "11", "13", "10" ]
245
5,349
0
false
An ideal method for investigating drug resistance mutations would yield many complete sequences of HIV genomic regions at risk for mutations for each viral population, and allow analysis of many samples of HIV populations in a single experiment.
[]
An ideal method for investigating drug resistance mutations would yield many complete sequences of HIV genomic regions at risk for mutations for each viral population, and allow analysis of many samples of HIV populations in a single experiment.
true
true
true
true
true
892
5
INTRODUCTION
1
14
[ "B14", "B15", "B16" ]
17,576,693
pmid-16056220|pmid-17299583|pmid-8944025
We have adapted pyrosequencing (14), combined with a DNA bar coding system (15,16), to characterize rare drug-resistant HIV variants in many samples in parallel.
[ "14", "15", "16" ]
161
5,350
1
false
We have adapted pyrosequencing, combined with a DNA bar coding system, to characterize rare drug-resistant HIV variants in many samples in parallel.
[ "14", "15,16" ]
We have adapted pyrosequencing, combined with a DNA bar coding system, to characterize rare drug-resistant HIV variants in many samples in parallel.
true
true
true
true
true
893
5
INTRODUCTION
1
14
[ "B14", "B15", "B16" ]
17,576,693
pmid-16056220|pmid-17299583|pmid-8944025
In a single experiment, we determined 118 093 sequences from ∼100 bp segments of the PR and RT-coding regions for seven samples of viral populations (Table 1).
[ "14", "15", "16" ]
159
5,351
0
false
In a single experiment, we determined 118 093 sequences from ∼100 bp segments of the PR and RT-coding regions for seven samples of viral populations (Table 1).
[]
In a single experiment, we determined 118 093 sequences from ∼100 bp segments of the PR and RT-coding regions for seven samples of viral populations.
true
true
true
true
true
893
5
INTRODUCTION
1
14
[ "B14", "B15", "B16" ]
17,576,693
pmid-16056220|pmid-17299583|pmid-8944025
These data identified a variety of minor drug resistance alleles in patient samples of potential clinical significance, and demonstrate the feasibility of using pyrosequencing for efficient HIV genotyping.
[ "14", "15", "16" ]
205
5,352
0
false
These data identified a variety of minor drug resistance alleles in patient samples of potential clinical significance, and demonstrate the feasibility of using pyrosequencing for efficient HIV genotyping.
[]
These data identified a variety of minor drug resistance alleles in patient samples of potential clinical significance, and demonstrate the feasibility of using pyrosequencing for efficient HIV genotyping.
true
true
true
true
true
893
5
INTRODUCTION
1
14
[ "B14", "B15", "B16" ]
17,576,693
pmid-16056220|pmid-17299583|pmid-8944025
Multiplex analysis of many bar coded samples in a single sequencing experiment offers the potential to drive down the cost of each genotype determination.
[ "14", "15", "16" ]
154
5,353
0
false
Multiplex analysis of many bar coded samples in a single sequencing experiment offers the potential to drive down the cost of each genotype determination.
[]
Multiplex analysis of many bar coded samples in a single sequencing experiment offers the potential to drive down the cost of each genotype determination.
true
true
true
true
true
893
5
INTRODUCTION
1
14
[ "B14", "B15", "B16" ]
17,576,693
pmid-16056220|pmid-17299583|pmid-8944025
Table 1.Viral populations characterized in this studySampleAmplification templateDescriptionBar codeNumber of sequence reads1Viral RNAHIV LAI RNA from particlesd(ACTG)174342Plasmid DNAHIV LAI cloned DNAd(AGTC)138563Viral RNAHIV NL4-3 mixed with drug resistant NL4-3d(CTGA)73984Viral RNAMixture of HIV particles from subt...
[ "14", "15", "16" ]
485
5,354
0
false
Table 1.Viral populations characterized in this studySampleAmplification templateDescriptionBar codeNumber of sequence reads1Viral RNAHIV LAI RNA from particlesd(ACTG)174342Plasmid DNAHIV LAI cloned DNAd(AGTC)138563Viral RNAHIV NL4-3 mixed with drug resistant NL4-3d(CTGA)73984Viral RNAMixture of HIV particles from subt...
[]
Table 1.Viral populations characterized in this studySampleAmplification templateDescriptionBar codeNumber of sequence reads1Viral RNAHIV LAI RNA from particlesd(ACTG)174342Plasmid DNAHIV LAI cloned DNAd(AGTC)138563Viral RNAHIV NL4-3 mixed with drug resistant NL4-3d(CTGA)73984Viral RNAMixture of HIV particles from subt...
true
true
false
true
false
893
5
INTRODUCTION
1
14
[ "B14", "B15", "B16" ]
17,576,693
pmid-16056220|pmid-17299583|pmid-8944025
2d(TGAC)20845
[ "14", "15", "16" ]
13
5,355
0
false
2d(TGAC)20845
[]
2d(TGAC)20845
false
false
false
true
false
893
6
INTRODUCTION
0
null
null
17,576,693
null
Viral populations characterized in this study
null
45
5,356
0
false
null
null
Viral populations characterized in this study
true
true
false
true
false
894
0
DISCUSSION
0
null
null
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
Here we describe the use of DNA bar coding and pyrosequencing in detecting minor drug resistance mutations in HIV populations.
null
126
5,357
0
false
null
null
Here we describe the use of DNA bar coding and pyrosequencing in detecting minor drug resistance mutations in HIV populations.
true
true
true
true
true
895
0
DISCUSSION
0
null
null
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
We used pyrosequencing to generate 118 093 sequence reads from the pol region of seven samples of viral populations or controls.
null
128
5,358
0
false
null
null
We used pyrosequencing to generate 118 093 sequence reads from the pol region of seven samples of viral populations or controls.
true
true
true
true
true
895
0
DISCUSSION
0
null
null
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
The seven samples were analyzed in a single sequencing experiment, made possible by use of DNA bar coding to distinguish the different samples.
null
143
5,359
0
false
null
null
The seven samples were analyzed in a single sequencing experiment, made possible by use of DNA bar coding to distinguish the different samples.
true
true
true
true
true
895
0
DISCUSSION
0
null
null
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
As controls we analyzed a DNA plasmid encoding HIV LAI and HIV LAI RNA from viral particles, allowing an empirical estimation of error at each codon at risk for mutation to drug resistance.
null
189
5,360
0
false
null
null
As controls we analyzed a DNA plasmid encoding HIV LAI and HIV LAI RNA from viral particles, allowing an empirical estimation of error at each codon at risk for mutation to drug resistance.
true
true
true
true
true
895
0
DISCUSSION
0
null
null
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
To test the assay sensitivity, we analyzed a mixture containing HIV NL4-3 wild-type virions mixed with 5% of mutant virions containing five drug resistance mutations.
null
166
5,361
0
false
null
null
To test the assay sensitivity, we analyzed a mixture containing HIV NL4-3 wild-type virions mixed with 5% of mutant virions containing five drug resistance mutations.
true
true
true
true
true
895
0
DISCUSSION
0
null
null
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
All five mutations were called as present in the mixture without false positives, demonstrating the accuracy of the method.
null
123
5,362
0
false
null
null
All five mutations were called as present in the mixture without false positives, demonstrating the accuracy of the method.
true
true
true
true
true
895
0
DISCUSSION
0
null
null
17,576,693
pmid-14999114|pmid-15199315|pmid-12167680|pmid-17205459|pmid-16299012
Analysis of viral populations from three patients harboring drug-resistant HIV revealed all the mutations called by the conventional genotyping method (Viroseq), plus four additional less abundant drug resistance mutations comprising from 11.6% to 0.65% of the population.
null
272
5,363
0
false
null
null
Analysis of viral populations from three patients harboring drug-resistant HIV revealed all the mutations called by the conventional genotyping method (Viroseq), plus four additional less abundant drug resistance mutations comprising from 11.6% to 0.65% of the population.
true
true
true
true
true
895
1
DISCUSSION
1
10
[ "B10", "B11" ]
17,576,693
pmid-16825395|pmid-17206150
Previously several methods have been reported for sensitive detection of rare drug-resistant mutations, some with impressive sensitivity (10,11).
[ "10", "11" ]
145
5,364
0
false
Previously several methods have been reported for sensitive detection of rare drug-resistant mutations, some with impressive sensitivity.
[ "10,11" ]
Previously several methods have been reported for sensitive detection of rare drug-resistant mutations, some with impressive sensitivity.
true
true
true
true
true
896
1
DISCUSSION
1
10
[ "B10", "B11" ]
17,576,693
pmid-16825395|pmid-17206150
However, only the combination of DNA bar coding and pyrosequencing offers the opportunity to determine the full sequence of genomic regions with drug-resistant mutations from many samples in a single sequencing experiment.
[ "10", "11" ]
222
5,365
0
false
However, only the combination of DNA bar coding and pyrosequencing offers the opportunity to determine the full sequence of genomic regions with drug-resistant mutations from many samples in a single sequencing experiment.
[]
However, only the combination of DNA bar coding and pyrosequencing offers the opportunity to determine the full sequence of genomic regions with drug-resistant mutations from many samples in a single sequencing experiment.
true
true
true
true
true
896
1
DISCUSSION
1
10
[ "B10", "B11" ]
17,576,693
pmid-16825395|pmid-17206150
Using this method, sequence polymorphisms that were not specifically targeted for analysis can be identified and analyzed for possible correlations with drug resistance, which is not possible with most of the alternative methods.
[ "10", "11" ]
229
5,366
0
false
Using this method, sequence polymorphisms that were not specifically targeted for analysis can be identified and analyzed for possible correlations with drug resistance, which is not possible with most of the alternative methods.
[]
Using this method, sequence polymorphisms that were not specifically targeted for analysis can be identified and analyzed for possible correlations with drug resistance, which is not possible with most of the alternative methods.
true
true
true
true
true
896
1
DISCUSSION
1
10
[ "B10", "B11" ]
17,576,693
pmid-16825395|pmid-17206150
Here we analyzed seven viral populations in a single picoliter sequencing plate, but there is no reason that the number could not be much larger.
[ "10", "11" ]
145
5,367
0
false
Here we analyzed seven viral populations in a single picoliter sequencing plate, but there is no reason that the number could not be much larger.
[]
Here we analyzed seven viral populations in a single picoliter sequencing plate, but there is no reason that the number could not be much larger.
true
true
true
true
true
896
1
DISCUSSION
1
10
[ "B10", "B11" ]
17,576,693
pmid-16825395|pmid-17206150
In another study, we have successfully sequenced 42 different DNA bar codes in a single plate (unpublished data), indicating the potential.
[ "10", "11" ]
139
5,368
0
false
In another study, we have successfully sequenced 42 different DNA bar codes in a single plate (unpublished data), indicating the potential.
[]
In another study, we have successfully sequenced 42 different DNA bar codes in a single plate (unpublished data), indicating the potential.
true
true
true
true
true
896
2
DISCUSSION
0
null
null
17,576,693
pmid-14999114
Several of the low abundance drug resistance mutations detected here are of potential clinical significance, since they may confer reduced sensitivity to drugs that otherwise might seem attractive for therapy.
null
209
5,369
0
false
null
null
Several of the low abundance drug resistance mutations detected here are of potential clinical significance, since they may confer reduced sensitivity to drugs that otherwise might seem attractive for therapy.
true
true
true
true
true
897
2
DISCUSSION
0
null
null
17,576,693
pmid-14999114
For example, patient 3 was found to harbor low level resistance alleles in RT at K70 and M184, which would be likely to impair therapy with several of the NRTIs, though not with all NRTIs.
null
188
5,370
0
false
null
null
For example, patient 3 was found to harbor low level resistance alleles in RT at K70 and M184, which would be likely to impair therapy with several of the NRTIs, though not with all NRTIs.
true
true
true
true
true
897
2
DISCUSSION
0
null
null
17,576,693
pmid-14999114
Patient 3 had been treated with NRTIs known to elicit these mutations, probably explaining their presence.
null
106
5,371
0
false
null
null
Patient 3 had been treated with NRTIs known to elicit these mutations, probably explaining their presence.
true
true
true
true
true
897
2
DISCUSSION
0
null
null
17,576,693
pmid-14999114
Because alternative NRTIs are available for which all of the patient 3 viruses would remain sensitive, knowledge of the minor alleles could have improved the ability to choose effective therapy in this case.
null
207
5,372
0
false
null
null
Because alternative NRTIs are available for which all of the patient 3 viruses would remain sensitive, knowledge of the minor alleles could have improved the ability to choose effective therapy in this case.
true
true
true
true
true
897
2
DISCUSSION
0
null
null
17,576,693
pmid-14999114
Looking forward, it will be important to test more fully the importance of minor HIV drug-resistant populations on antiretroviral responses and the impact of such information on treatment outcomes.
null
197
5,373
0
false
null
null
Looking forward, it will be important to test more fully the importance of minor HIV drug-resistant populations on antiretroviral responses and the impact of such information on treatment outcomes.
true
true
true
true
true
897
3
DISCUSSION
0
null
null
17,576,693
NA|pmid-15635002|pmid-15247339|pmid-17215531
Lastly, the methods described here may be useful in implementing drug resistance genotyping in resource-limited settings.
null
121
5,374
0
false
null
null
Lastly, the methods described here may be useful in implementing drug resistance genotyping in resource-limited settings.
true
true
true
true
true
898
3
DISCUSSION
0
null
null
17,576,693
NA|pmid-15635002|pmid-15247339|pmid-17215531
Using the DNA bar coding strategy, it should be possible to multiplex large numbers of patient samples in single sequencing runs, thereby driving down costs.
null
157
5,375
0
false
null
null
Using the DNA bar coding strategy, it should be possible to multiplex large numbers of patient samples in single sequencing runs, thereby driving down costs.
true
true
true
true
true
898
3
DISCUSSION
0
null
null
17,576,693
NA|pmid-15635002|pmid-15247339|pmid-17215531
Though many logistical obstacles would need to be overcome, the combination of DNA bar coding and pyrosequencing offers a prototype technology for affordable HIV genotyping.
null
173
5,376
0
false
null
null
Though many logistical obstacles would need to be overcome, the combination of DNA bar coding and pyrosequencing offers a prototype technology for affordable HIV genotyping.
true
true
true
true
true
898
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b7", "b8", "b9" ]
16,916,791
pmid-11834782|pmid-15372043|pmid-10617568|pmid-10778853|pmid-11498593|pmid-11373684|NA|pmid-12546893|pmid-11373684
A number of different approaches have been advanced to validate the function of genes, including the function of a number of genes involved in cancer cell migration and invasion.
[ "1", "2", "3", "5", "6", "7", "8", "9" ]
178
5,377
0
false
A number of different approaches have been advanced to validate the function of genes, including the function of a number of genes involved in cancer cell migration and invasion.
[]
A number of different approaches have been advanced to validate the function of genes, including the function of a number of genes involved in cancer cell migration and invasion.
true
true
true
true
true
899
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b7", "b8", "b9" ]
16,916,791
pmid-11834782|pmid-15372043|pmid-10617568|pmid-10778853|pmid-11498593|pmid-11373684|NA|pmid-12546893|pmid-11373684
The use of RNAi is generally regarded to be one of the most promising approaches since, at least in non-mammalian systems, it acts systemically (1), thus providing the potential to carry out both in vitro and in vivo target validation.
[ "1", "2", "3", "5", "6", "7", "8", "9" ]
235
5,378
1
false
The use of RNAi is generally regarded to be one of the most promising approaches since, at least in non-mammalian systems, it acts systemically, thus providing the potential to carry out both in vitro and in vivo target validation.
[ "1" ]
The use of RNAi is generally regarded to be one of the most promising approaches since, at least in non-mammalian systems, it acts systemically, thus providing the potential to carry out both in vitro and in vivo target validation.
true
true
true
true
true
899
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b5", "b6", "b7", "b8", "b9" ]
16,916,791
pmid-11834782|pmid-15372043|pmid-10617568|pmid-10778853|pmid-11498593|pmid-11373684|NA|pmid-12546893|pmid-11373684
RNAi was initially described in plants, where it was believed to play a key role in protection against viral pathogens (2).
[ "1", "2", "3", "5", "6", "7", "8", "9" ]
123
5,379
1
false
RNAi was initially described in plants, where it was believed to play a key role in protection against viral pathogens.
[ "2" ]
RNAi was initially described in plants, where it was believed to play a key role in protection against viral pathogens.
true
true
true
true
true
899
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b7", "b8", "b9" ]
16,916,791
pmid-11834782|pmid-15372043|pmid-10617568|pmid-10778853|pmid-11498593|pmid-11373684|NA|pmid-12546893|pmid-11373684
The pathway involves a dsRNA of >21 bp triggering an RNaseIII-like enzyme now called Dicer (3–5).
[ "1", "2", "3", "5", "6", "7", "8", "9" ]
97
5,380
0
false
The pathway involves a dsRNA of >21 bp triggering an RNaseIII-like enzyme now called Dicer.
[ "3–5" ]
The pathway involves a dsRNA of >21 bp triggering an RNaseIII-like enzyme now called Dicer.
true
true
true
true
true
899
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b7", "b8", "b9" ]
16,916,791
pmid-11834782|pmid-15372043|pmid-10617568|pmid-10778853|pmid-11498593|pmid-11373684|NA|pmid-12546893|pmid-11373684
Dicer cleaves long dsRNAs, into small interfering RNAs (siRNAs) of 21–25 bp.
[ "1", "2", "3", "5", "6", "7", "8", "9" ]
76
5,381
0
false
Dicer cleaves long dsRNAs, into small interfering RNAs (siRNAs) of 21–25 bp.
[]
Dicer cleaves long dsRNAs, into small interfering RNAs (siRNAs) of 21–25 bp.
true
true
true
true
true
899
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b7", "b8", "b9" ]
16,916,791
pmid-11834782|pmid-15372043|pmid-10617568|pmid-10778853|pmid-11498593|pmid-11373684|NA|pmid-12546893|pmid-11373684
These siRNAs are then incorporated into a multi-subunit RNA-induced silencing complex (RISC), which acts catalytically to target degradation of cellular mRNA in a sequence dependent manner (6,7).
[ "1", "2", "3", "5", "6", "7", "8", "9" ]
195
5,382
0
false
These siRNAs are then incorporated into a multi-subunit RNA-induced silencing complex (RISC), which acts catalytically to target degradation of cellular mRNA in a sequence dependent manner.
[ "6,7" ]
These siRNAs are then incorporated into a multi-subunit RNA-induced silencing complex (RISC), which acts catalytically to target degradation of cellular mRNA in a sequence dependent manner.
true
true
true
true
true
899
0
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Given the systemic and catalytic nature of RNAi, this class of molecules has been proposed for use both in target identification/validation and the development of therapeutics (8,9).
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Given the systemic and catalytic nature of RNAi, this class of molecules has been proposed for use both in target identification/validation and the development of therapeutics.
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Given the systemic and catalytic nature of RNAi, this class of molecules has been proposed for use both in target identification/validation and the development of therapeutics.
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While the great majority of the target validation studies using RNAi have been focused on a specific target, the efficiency of RNAi has led to the recognition that this technology may represent an exceptionally strong approach to functional genomics through the creation of RNAi libraries.
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While the great majority of the target validation studies using RNAi have been focused on a specific target, the efficiency of RNAi has led to the recognition that this technology may represent an exceptionally strong approach to functional genomics through the creation of RNAi libraries.
[]
While the great majority of the target validation studies using RNAi have been focused on a specific target, the efficiency of RNAi has led to the recognition that this technology may represent an exceptionally strong approach to functional genomics through the creation of RNAi libraries.
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INTRODUCTION
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Libraries of siRNA molecules targeting a specific gene can be produced synthetically, although new enzymatic approaches (10) have reduced the time and costs associated with producing libraries, and allow for the selection of the siRNA with the highest level of activity against the target of interest.
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Libraries of siRNA molecules targeting a specific gene can be produced synthetically, although new enzymatic approaches have reduced the time and costs associated with producing libraries, and allow for the selection of the siRNA with the highest level of activity against the target of interest.
[ "10" ]
Libraries of siRNA molecules targeting a specific gene can be produced synthetically, although new enzymatic approaches have reduced the time and costs associated with producing libraries, and allow for the selection of the siRNA with the highest level of activity against the target of interest.
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Functional RNAi libraries have been designed and synthesized to study cytoskeleton organization in Drosophila (11) and are being used extensively to study gene function in Caenorhabditis elegans, including the functional analysis of entire chromosomes and the full genome (12,13), but have only recently been described f...
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Functional RNAi libraries have been designed and synthesized to study cytoskeleton organization in Drosophila and are being used extensively to study gene function in Caenorhabditis elegans, including the functional analysis of entire chromosomes and the full genome, but have only recently been described for use in mam...
[ "11", "12,13", "14" ]
Functional RNAi libraries have been designed and synthesized to study cytoskeleton organization in Drosophila and are being used extensively to study gene function in Caenorhabditis elegans, including the functional analysis of entire chromosomes and the full genome, but have only recently been described for use in mam...
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While the above laboratories reported the ability to generate functional libraries of siRNAs against specific targets and the ability to generate a complex, 415 000 member siRNA library from an existing cDNA library, they did not report that this latter library was functional.
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While the above laboratories reported the ability to generate functional libraries of siRNAs against specific targets and the ability to generate a complex, 415 000 member siRNA library from an existing cDNA library, they did not report that this latter library was functional.
[]
While the above laboratories reported the ability to generate functional libraries of siRNAs against specific targets and the ability to generate a complex, 415 000 member siRNA library from an existing cDNA library, they did not report that this latter library was functional.
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INTRODUCTION
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The authors go on to report that they generate on average 34 unique siRNA clones per kilobase of sequence, a distinct advantage since not all siRNAs are active.
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The authors go on to report that they generate on average 34 unique siRNA clones per kilobase of sequence, a distinct advantage since not all siRNAs are active.
[]
The authors go on to report that they generate on average 34 unique siRNA clones per kilobase of sequence, a distinct advantage since not all siRNAs are active.
true
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1
INTRODUCTION
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However, this also points out the limitations of generating siRNA libraries.
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However, this also points out the limitations of generating siRNA libraries.
[]
However, this also points out the limitations of generating siRNA libraries.
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INTRODUCTION
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Significantly larger libraries will be required to ensure that active siRNAs are present for each transcript.
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Significantly larger libraries will be required to ensure that active siRNAs are present for each transcript.
[]
Significantly larger libraries will be required to ensure that active siRNAs are present for each transcript.
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900
1
INTRODUCTION
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Other approaches have recently been undertaken to develop functional siRNA libraries ranging from ∼500 to 8000 known genes (15,16).
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Other approaches have recently been undertaken to develop functional siRNA libraries ranging from ∼500 to 8000 known genes.
[ "15,16" ]
Other approaches have recently been undertaken to develop functional siRNA libraries ranging from ∼500 to 8000 known genes.
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1
INTRODUCTION
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Plasmids and retroviral vectors have also been used to generate libraries of short hairpin RNAs (shRNAs) of similar size to the larger siRNA library (17,18), with which genetic screens have been carried out to identify tumor suppressor genes (18–20).
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Plasmids and retroviral vectors have also been used to generate libraries of short hairpin RNAs (shRNAs) of similar size to the larger siRNA library, with which genetic screens have been carried out to identify tumor suppressor genes.
[ "17,18", "18–20" ]
Plasmids and retroviral vectors have also been used to generate libraries of short hairpin RNAs (shRNAs) of similar size to the larger siRNA library, with which genetic screens have been carried out to identify tumor suppressor genes.
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INTRODUCTION
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21
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Recently, libraries corresponding to most known human and mouse genes have been developed (21).
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Recently, libraries corresponding to most known human and mouse genes have been developed.
[ "21" ]
Recently, libraries corresponding to most known human and mouse genes have been developed.
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INTRODUCTION
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Many of these si-and shRNA libraries are commercially available and a database, RNAi Codex, has been developed to annotate the data generated in the various studies (22).
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1
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Many of these si-and shRNA libraries are commercially available and a database, RNAi Codex, has been developed to annotate the data generated in the various studies.
[ "22" ]
Many of these si-and shRNA libraries are commercially available and a database, RNAi Codex, has been developed to annotate the data generated in the various studies.
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INTRODUCTION
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While the above strategies have demonstrated promise for functional genomic screening, most are based on developing libraries using known sequences and when a random library was generated, the complexity was significant.
[ "14", "23", "24" ]
220
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While the above strategies have demonstrated promise for functional genomic screening, most are based on developing libraries using known sequences and when a random library was generated, the complexity was significant.
[]
While the above strategies have demonstrated promise for functional genomic screening, most are based on developing libraries using known sequences and when a random library was generated, the complexity was significant.
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INTRODUCTION
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An alternative approach to that taken in generating the random siRNA library (14), would be to restriction digest cDNA to generate a library of long dsRNAs.
[ "14", "23", "24" ]
156
5,396
1
false
An alternative approach to that taken in generating the random siRNA library, would be to restriction digest cDNA to generate a library of long dsRNAs.
[ "14" ]
An alternative approach to that taken in generating the random siRNA library, would be to restriction digest cDNA to generate a library of long dsRNAs.
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901
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INTRODUCTION
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Long dsRNA libraries have been used to analyze gene function in Drosophila (23,24) but potential off-target effects and induction of the stress response are issues for mammalian gene silencing.
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193
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false
Long dsRNA libraries have been used to analyze gene function in Drosophila but potential off-target effects and induction of the stress response are issues for mammalian gene silencing.
[ "23,24" ]
Long dsRNA libraries have been used to analyze gene function in Drosophila but potential off-target effects and induction of the stress response are issues for mammalian gene silencing.
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INTRODUCTION
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Thus, the focus of this study was to analyze the efficiency, selectivity and toxicity of long dsRNAs in mammalian cells and to determine whether long dsRNAs lead to the desired biological response in these cells, as a first step to generate long dsRNA libraries.
[ "14", "23", "24" ]
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Thus, the focus of this study was to analyze the efficiency, selectivity and toxicity of long dsRNAs in mammalian cells and to determine whether long dsRNAs lead to the desired biological response in these cells, as a first step to generate long dsRNA libraries.
[]
Thus, the focus of this study was to analyze the efficiency, selectivity and toxicity of long dsRNAs in mammalian cells and to determine whether long dsRNAs lead to the desired biological response in these cells, as a first step to generate long dsRNA libraries.
true
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true
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DISCUSSION
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There are a number of types of dsRNAs that have been used to silence gene expression.
[ "7" ]
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0
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There are a number of types of dsRNAs that have been used to silence gene expression.
[]
There are a number of types of dsRNAs that have been used to silence gene expression.
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