Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
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pmid
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cited_id
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sentences
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all_sent_cites
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sentence_batch_index
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qc_fail
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cited_sentence
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cites_in_sentence
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cln_sentence
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cit_qc
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lgtm
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__index_level_0__
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4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
(1-1/128)1000].
[ "17", "14" ]
15
7,000
0
false
(1-1/128)1000].
[]
1000].
false
false
true
true
false
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
This sharply contrasts with the observation that over half of the 4-base-recognizing RE genes do not have their own sites in their coding sequences (Table 2).
[ "17", "14" ]
158
7,001
0
false
This sharply contrasts with the observation that over half of the 4-base-recognizing RE genes do not have their own sites in their coding sequences (Table 2).
[]
This sharply contrasts with the observation that over half of the 4-base-recognizing RE genes do not have their own sites in their coding sequences (Table 2).
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
Table 2.Statistics of restriction endonuclease genes having their own recognition sites within their coding sequences*Number of genes w/sites (percentage)Recognition site lengthTotal number0 site1 site2 sitesMore than 2 sites4
[ "17", "14" ]
226
7,002
0
false
Table 2.Statistics of restriction endonuclease genes having their own recognition sites within their coding sequences*Number of genes w/sites (percentage)Recognition site lengthTotal number0 site1 site2 sitesMore than 2 sites4
[]
Table 2.Statistics of restriction endonuclease genes having their own recognition sites within their coding sequences*Number of genes w/sites (percentage)Recognition site lengthTotal number0 site1 site2 sitesMore than 2 sites4
true
true
false
true
false
1,140
4
DISCUSSION
1
14
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
base11764(55%)32 (27%)14(12%)7(6%)5 base8052(65%)19(23%)6(8%)3(4%)6 base157138(88%)14(9%)4(3%)1(1%)7 base1511(73%)4(23%)008 base1010(100%)000*All sequence data were retrieved from REBASE (14) as of February 2007.
[ "17", "14" ]
212
7,003
1
false
base11764(55%)32 (27%)14(12%)7(6%)5 base8052(65%)19(23%)6(8%)3(4%)6 base157138(88%)14(9%)4(3%)1(1%)7 base1511(73%)4(23%)008 base1010(100%)000*All sequence data were retrieved from REBASE as of February 2007.
[ "14" ]
base11764(55%)32 (27%)147(6%)5 base8052(65%)19(23%)6(8%)36 base157138(88%)14(9%)4(3%)17 base1511(73%)4(23%)008 base1010000*All sequence data were retrieved from REBASE as of February 2007.
false
true
true
true
false
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
Only experimentally verified RE genes are included in the analysis.
[ "17", "14" ]
67
7,004
0
false
Only experimentally verified RE genes are included in the analysis.
[]
Only experimentally verified RE genes are included in the analysis.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
Degenerate bases, ‘RYMKSW’ (e.g.
[ "17", "14" ]
32
7,005
0
false
Degenerate bases, ‘RYMKSW’ (e.g.
[]
Degenerate bases, ‘RYMKSW’ (e.g.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
R = A or G) are counted as 0.5 base; while ‘BDHV’ (e.g.
[ "17", "14" ]
55
7,006
0
false
R = A or G) are counted as 0.5 base; while ‘BDHV’ (e.g.
[]
R = A or G) are counted as 0.5 base; while ‘BDHV’ (e.g.
true
true
true
true
true
1,140
4
DISCUSSION
1
17
[ "B17", "B14" ]
17,567,609
pmid-15247348|pmid-17202163
B = C or G or T) are counted as 0.25 base.
[ "17", "14" ]
42
7,007
0
false
B = C or G or T) are counted as 0.25 base.
[]
B = C or G or T) are counted as 0.25 base.
true
true
true
true
true
1,140
5
DISCUSSION
0
null
null
17,567,609
null
Statistics of restriction endonuclease genes having their own recognition sites within their coding sequences*
null
110
7,008
0
false
null
null
Statistics of restriction endonuclease genes having their own recognition sites within their coding sequences*
true
true
false
true
false
1,141
6
DISCUSSION
1
14
[ "B14" ]
17,567,609
pmid-17202163
*All sequence data were retrieved from REBASE (14) as of February 2007.
[ "14" ]
71
7,009
1
false
*All sequence data were retrieved from REBASE as of February 2007.
[ "14" ]
*All sequence data were retrieved from REBASE as of February 2007.
false
false
true
true
false
1,142
6
DISCUSSION
1
14
[ "B14" ]
17,567,609
pmid-17202163
Only experimentally verified RE genes are included in the analysis.
[ "14" ]
67
7,010
0
false
Only experimentally verified RE genes are included in the analysis.
[]
Only experimentally verified RE genes are included in the analysis.
true
true
true
true
true
1,142
6
DISCUSSION
1
14
[ "B14" ]
17,567,609
pmid-17202163
Degenerate bases, ‘RYMKSW’ (e.g.
[ "14" ]
32
7,011
0
false
Degenerate bases, ‘RYMKSW’ (e.g.
[]
Degenerate bases, ‘RYMKSW’ (e.g.
true
true
true
true
true
1,142
6
DISCUSSION
1
14
[ "B14" ]
17,567,609
pmid-17202163
R = A or G) are counted as 0.5 base; while ‘BDHV’ (e.g.
[ "14" ]
55
7,012
0
false
R = A or G) are counted as 0.5 base; while ‘BDHV’ (e.g.
[]
R = A or G) are counted as 0.5 base; while ‘BDHV’ (e.g.
true
true
true
true
true
1,142
6
DISCUSSION
1
14
[ "B14" ]
17,567,609
pmid-17202163
B = C or G or T) are counted as 0.25 base.
[ "14" ]
42
7,013
0
false
B = C or G or T) are counted as 0.25 base.
[]
B = C or G or T) are counted as 0.25 base.
true
true
true
true
true
1,142
7
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-15247328
The in vitro method described here has the potential to be extended to other applications, with the most relevant being the directed evolution of genes encoding enzymes (4).
[ "4" ]
173
7,014
1
false
The in vitro method described here has the potential to be extended to other applications, with the most relevant being the directed evolution of genes encoding enzymes.
[ "4" ]
The in vitro method described here has the potential to be extended to other applications, with the most relevant being the directed evolution of genes encoding enzymes.
true
true
true
true
true
1,143
7
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-15247328
This requires both extreme specificity and sensitivity in the selection method to allow an efficient search in the vast sequence space.
[ "4" ]
135
7,015
0
false
This requires both extreme specificity and sensitivity in the selection method to allow an efficient search in the vast sequence space.
[]
This requires both extreme specificity and sensitivity in the selection method to allow an efficient search in the vast sequence space.
true
true
true
true
true
1,143
7
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-15247328
In fact, even with the ability to select from a 1010 library, one can only possibly vary 6–7 codons with saturation.
[ "4" ]
116
7,016
0
false
In fact, even with the ability to select from a 1010 library, one can only possibly vary 6–7 codons with saturation.
[]
In fact, even with the ability to select from a 1010 library, one can only possibly vary 6–7 codons with saturation.
true
true
true
true
true
1,143
7
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-15247328
Nonetheless, numerous directed evolution experiments suggest that sometimes only a few amino acid substitutions could bring considerable changes in biochemical properties.
[ "4" ]
171
7,017
0
false
Nonetheless, numerous directed evolution experiments suggest that sometimes only a few amino acid substitutions could bring considerable changes in biochemical properties.
[]
Nonetheless, numerous directed evolution experiments suggest that sometimes only a few amino acid substitutions could bring considerable changes in biochemical properties.
true
true
true
true
true
1,143
7
DISCUSSION
1
4
[ "B4" ]
17,567,609
pmid-15247328
For highly diverse libraries, theoretical derivations under simplified assumptions in this article support a reasonable strategy of using relatively large amounts of template in the early rounds of selections, with sacrificed specificity but presumably a high sensitivity, and decreasing amounts of the library in later ...
[ "4" ]
353
7,018
0
false
For highly diverse libraries, theoretical derivations under simplified assumptions in this article support a reasonable strategy of using relatively large amounts of template in the early rounds of selections, with sacrificed specificity but presumably a high sensitivity, and decreasing amounts of the library in later ...
[]
For highly diverse libraries, theoretical derivations under simplified assumptions in this article support a reasonable strategy of using relatively large amounts of template in the early rounds of selections, with sacrificed specificity but presumably a high sensitivity, and decreasing amounts of the library in later ...
true
true
true
true
true
1,143
8
DISCUSSION
1
18
[ "B18", "B8" ]
17,567,609
pmid-16356846|pmid-16843558
The method we describe in this article depends on our ability to select the desired genotype based on a specific alteration caused by its translated phenotype.
[ "18", "8" ]
159
7,019
0
false
The method we describe in this article depends on our ability to select the desired genotype based on a specific alteration caused by its translated phenotype.
[]
The method we describe in this article depends on our ability to select the desired genotype based on a specific alteration caused by its translated phenotype.
true
true
true
true
true
1,144
8
DISCUSSION
1
18
[ "B18", "B8" ]
17,567,609
pmid-16356846|pmid-16843558
The reconstituted in vitro transcription/translation system plays a crucial role: it is free of many unwanted constraints that are often lethal when using living hosts, and it offers considerable modularity for potential engineering.
[ "18", "8" ]
233
7,020
0
false
The reconstituted in vitro transcription/translation system plays a crucial role: it is free of many unwanted constraints that are often lethal when using living hosts, and it offers considerable modularity for potential engineering.
[]
The reconstituted in vitro transcription/translation system plays a crucial role: it is free of many unwanted constraints that are often lethal when using living hosts, and it offers considerable modularity for potential engineering.
true
true
true
true
true
1,144
8
DISCUSSION
1
18
[ "B18", "B8" ]
17,567,609
pmid-16356846|pmid-16843558
A similar approach should allow the isolation of mutants with specifically desired properties, such as altered cleavage positions that might result in novel sticky ends, improved thermal stability by selecting at a desired temperature as well as numerous other properties that might increase the practical utility of the...
[ "18", "8" ]
331
7,021
0
false
A similar approach should allow the isolation of mutants with specifically desired properties, such as altered cleavage positions that might result in novel sticky ends, improved thermal stability by selecting at a desired temperature as well as numerous other properties that might increase the practical utility of the...
[]
A similar approach should allow the isolation of mutants with specifically desired properties, such as altered cleavage positions that might result in novel sticky ends, improved thermal stability by selecting at a desired temperature as well as numerous other properties that might increase the practical utility of the...
true
true
true
true
true
1,144
8
DISCUSSION
1
18
[ "B18", "B8" ]
17,567,609
pmid-16356846|pmid-16843558
In all of these cases, the selections can be done on bulk preparations thanks to the DNA-modifying nature of these enzymes.
[ "18", "8" ]
123
7,022
0
false
In all of these cases, the selections can be done on bulk preparations thanks to the DNA-modifying nature of these enzymes.
[]
In all of these cases, the selections can be done on bulk preparations thanks to the DNA-modifying nature of these enzymes.
true
true
true
true
true
1,144
8
DISCUSSION
1
18
[ "B18", "B8" ]
17,567,609
pmid-16356846|pmid-16843558
For a wide variety of other useful enzymes, it is desirable to be able to interrogate individual droplets by using some novel emulsion formulations (18) or by flow cytometry or microfluidics (8) in a high-throughput way, both of which have shown promise.
[ "18", "8" ]
254
7,023
1
false
For a wide variety of other useful enzymes, it is desirable to be able to interrogate individual droplets by using some novel emulsion formulations or by flow cytometry or microfluidics in a high-throughput way, both of which have shown promise.
[ "18", "8" ]
For a wide variety of other useful enzymes, it is desirable to be able to interrogate individual droplets by using some novel emulsion formulations or by flow cytometry or microfluidics in a high-throughput way, both of which have shown promise.
true
true
true
true
true
1,144
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
An army of more than 250 transcription factors controls gene expression in Escherichia coli.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
92
7,024
0
false
An army of more than 250 transcription factors controls gene expression in Escherichia coli.
[]
An army of more than 250 transcription factors controls gene expression in Escherichia coli.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
Some of these factors are operon-specific while others, known as global regulators, coordinate the expression of scores of promoters in response to specific environmental cues [reviewed in (1–3)].
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
196
7,025
0
false
Some of these factors are operon-specific while others, known as global regulators, coordinate the expression of scores of promoters in response to specific environmental cues.
[ "reviewed in (1–3)" ]
Some of these factors are operon-specific while others, known as global regulators, coordinate the expression of scores of promoters in response to specific environmental cues.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
The advent of whole-genome DNA sequencing, and associated advances in DNA microarray technology, has enabled investigation of the battery of genes regulated by each of these global factors.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
189
7,026
0
false
The advent of whole-genome DNA sequencing, and associated advances in DNA microarray technology, has enabled investigation of the battery of genes regulated by each of these global factors.
[]
The advent of whole-genome DNA sequencing, and associated advances in DNA microarray technology, has enabled investigation of the battery of genes regulated by each of these global factors.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
The E.coli FNR protein (regulator of fumarate and nitrate reduction) is the global transcription factor that manages the distribution of RNA polymerase in response to oxygen starvation.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
185
7,027
0
false
The E.coli FNR protein (regulator of fumarate and nitrate reduction) is the global transcription factor that manages the distribution of RNA polymerase in response to oxygen starvation.
[]
The E.coli FNR protein (regulator of fumarate and nitrate reduction) is the global transcription factor that manages the distribution of RNA polymerase in response to oxygen starvation.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
FNR senses oxygen via an N-terminal iron–sulfur cluster.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
56
7,028
0
false
FNR senses oxygen via an N-terminal iron–sulfur cluster.
[]
FNR senses oxygen via an N-terminal iron–sulfur cluster.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
Hence, in anaerobic conditions, FNR is able to bind to specific DNA targets at promoters and modulate transcription.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
116
7,029
0
false
Hence, in anaerobic conditions, FNR is able to bind to specific DNA targets at promoters and modulate transcription.
[]
Hence, in anaerobic conditions, FNR is able to bind to specific DNA targets at promoters and modulate transcription.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
In aerobic conditions, FNR is converted to a form, unable to bind these targets [reviewed in (4,5)].
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
100
7,030
0
false
In aerobic conditions, FNR is converted to a form, unable to bind these targets.
[ "reviewed in (4,5)" ]
In aerobic conditions, FNR is converted to a form, unable to bind these targets.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
Bioinformatic analysis has been used to search the E.coli genome for DNA sequences that resemble known FNR binding sites (6,7) and DNA microarrays have been used to study differences in the transcriptome that arise when the fnr gene is deleted from the genome (8–10).
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
267
7,031
0
false
Bioinformatic analysis has been used to search the E.coli genome for DNA sequences that resemble known FNR binding sites and DNA microarrays have been used to study differences in the transcriptome that arise when the fnr gene is deleted from the genome.
[ "6,7", "8–10" ]
Bioinformatic analysis has been used to search the E.coli genome for DNA sequences that resemble known FNR binding sites and DNA microarrays have been used to study differences in the transcriptome that arise when the fnr gene is deleted from the genome.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
These studies illustrate the complexity of the FNR regulon and predict that, while FNR directly regulates ∼100 transcription units, it indirectly affects up to 1000 genes.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
171
7,032
0
false
These studies illustrate the complexity of the FNR regulon and predict that, while FNR directly regulates ∼100 transcription units, it indirectly affects up to 1000 genes.
[]
These studies illustrate the complexity of the FNR regulon and predict that, while FNR directly regulates ∼100 transcription units, it indirectly affects up to 1000 genes.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
In this study, we used chromatin immunoprecipitation (ChIP), in conjunction with high-density microarrays (ChIP-chip), to measure the binding of FNR across the E.coli chromosome directly, and in vivo, for the first time.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
220
7,033
0
false
In this study, we used chromatin immunoprecipitation (ChIP), in conjunction with high-density microarrays (ChIP-chip), to measure the binding of FNR across the E.coli chromosome directly, and in vivo, for the first time.
[]
In this study, we used chromatin immunoprecipitation (ChIP), in conjunction with high-density microarrays (ChIP-chip), to measure the binding of FNR across the E.coli chromosome directly, and in vivo, for the first time.
true
true
true
true
true
1,145
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b6", "b7", "b8", "b10" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
This allowed us to identify 63 DNA targets for FNR, some of which are adjacent to poorly expressed genes where FNR has minor regulatory effects.
[ "1", "3", "4", "5", "6", "7", "8", "10" ]
144
7,034
0
false
This allowed us to identify 63 DNA targets for FNR, some of which are adjacent to poorly expressed genes where FNR has minor regulatory effects.
[]
This allowed us to identify 63 DNA targets for FNR, some of which are adjacent to poorly expressed genes where FNR has minor regulatory effects.
true
true
true
true
true
1,145
1
INTRODUCTION
1
11
[ "b11", "b12" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
In the second part of the study, we studied the distribution of FNR as growing E.coli cells enter stationary phase, and found that it is largely unchanged.
[ "11", "12" ]
155
7,035
0
false
In the second part of the study, we studied the distribution of FNR as growing E.coli cells enter stationary phase, and found that it is largely unchanged.
[]
In the second part of the study, we studied the distribution of FNR as growing E.coli cells enter stationary phase, and found that it is largely unchanged.
true
true
true
true
true
1,146
1
INTRODUCTION
1
11
[ "b11", "b12" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
Recall that transcription patterns change dramatically when cells cease to grow (11,12) but little is known about the distribution and binding of transcription factors in stationary phase cells.
[ "11", "12" ]
194
7,036
0
false
Recall that transcription patterns change dramatically when cells cease to grow but little is known about the distribution and binding of transcription factors in stationary phase cells.
[ "11,12" ]
Recall that transcription patterns change dramatically when cells cease to grow but little is known about the distribution and binding of transcription factors in stationary phase cells.
true
true
true
true
true
1,146
1
INTRODUCTION
1
11
[ "b11", "b12" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
In control experiments, we showed that the binding pattern of IHF, a nucleoid-associated protein, is also unchanged, whereas the distribution of RNA polymerase is radically altered.
[ "11", "12" ]
181
7,037
0
false
In control experiments, we showed that the binding pattern of IHF, a nucleoid-associated protein, is also unchanged, whereas the distribution of RNA polymerase is radically altered.
[]
In control experiments, we showed that the binding pattern of IHF, a nucleoid-associated protein, is also unchanged, whereas the distribution of RNA polymerase is radically altered.
true
true
true
true
true
1,146
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
In this work, we have applied ChIP-chip technology to produce the first chromosome-wide direct analysis of DNA binding in vivo by the global E.coli transcription regulator, FNR.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
177
7,038
0
false
In this work, we have applied ChIP-chip technology to produce the first chromosome-wide direct analysis of DNA binding in vivo by the global E.coli transcription regulator, FNR.
[]
In this work, we have applied ChIP-chip technology to produce the first chromosome-wide direct analysis of DNA binding in vivo by the global E.coli transcription regulator, FNR.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
The advantage of this approach to studying the FNR regulon is that it avoids complications due to genes that are indirectly controlled by FNR or genes that are regulated by multiple transcription factors.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
204
7,039
0
false
The advantage of this approach to studying the FNR regulon is that it avoids complications due to genes that are indirectly controlled by FNR or genes that are regulated by multiple transcription factors.
[]
The advantage of this approach to studying the FNR regulon is that it avoids complications due to genes that are indirectly controlled by FNR or genes that are regulated by multiple transcription factors.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
Moreover, FNR binding at sites adjacent to poorly transcribed genes, or genes where FNR has little impact on transcription, can be detected and the effects of environmental conditions can be studied.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
199
7,040
0
false
Moreover, FNR binding at sites adjacent to poorly transcribed genes, or genes where FNR has little impact on transcription, can be detected and the effects of environmental conditions can be studied.
[]
Moreover, FNR binding at sites adjacent to poorly transcribed genes, or genes where FNR has little impact on transcription, can be detected and the effects of environmental conditions can be studied.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
We identified 63 locations at which FNR binds to the E.coli chromosome, including a group of five targets adjacent to genes encoding proteins that manipulate DNA and RNA.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
170
7,041
0
false
We identified 63 locations at which FNR binds to the E.coli chromosome, including a group of five targets adjacent to genes encoding proteins that manipulate DNA and RNA.
[]
We identified 63 locations at which FNR binds to the E.coli chromosome, including a group of five targets adjacent to genes encoding proteins that manipulate DNA and RNA.
true
true
true
true
true
1,147
0
DISCUSSION
1
16
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
None of these five targets were identified as FNR regulated by previous transcriptome analyses (8,9,10), none are listed as FNR targets by the Ecocyc database (16), and, to our knowledge, FNR-dependent regulation of such proteins has not been documented.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
254
7,042
1
false
None of these five targets were identified as FNR regulated by previous transcriptome analyses, none are listed as FNR targets by the Ecocyc database, and, to our knowledge, FNR-dependent regulation of such proteins has not been documented.
[ "8,9,10", "16" ]
None of these five targets were identified as FNR regulated by previous transcriptome analyses, none are listed as FNR targets by the Ecocyc database, and, to our knowledge, FNR-dependent regulation of such proteins has not been documented.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
At 10 of the 63 targets of FNR binding, we were unable to identify a match to the canonical FNR binding sequence.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
113
7,043
0
false
At 10 of the 63 targets of FNR binding, we were unable to identify a match to the canonical FNR binding sequence.
[]
At 10 of the 63 targets of FNR binding, we were unable to identify a match to the canonical FNR binding sequence.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
These may be locations at which FNR binds cooperatively with another factor.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
76
7,044
0
false
These may be locations at which FNR binds cooperatively with another factor.
[]
These may be locations at which FNR binds cooperatively with another factor.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
We note that the profile of FNR binding presented here consists of discrete peaks (Figure 1A).
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
94
7,045
0
false
We note that the profile of FNR binding presented here consists of discrete peaks (Figure 1A).
[]
We note that the profile of FNR binding presented here consists of discrete peaks (Figure 1A).
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
In contrast, the published binding profile for the related transcription activator, CRP, is far more complex, due to the existence of ∼10 000 low affinity binding sites for CRP scattered throughout the genome (6,13).
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
216
7,046
0
false
In contrast, the published binding profile for the related transcription activator, CRP, is far more complex, due to the existence of ∼10 000 low affinity binding sites for CRP scattered throughout the genome.
[ "6,13" ]
In contrast, the published binding profile for the related transcription activator, CRP, is far more complex, due to the existence of ∼10 000 low affinity binding sites for CRP scattered throughout the genome.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
Consistent with this, Robison et al.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
36
7,047
0
false
Consistent with this, Robison et al.
[]
Consistent with this, Robison et al.
true
true
true
true
true
1,147
0
DISCUSSION
1
6
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
(6) predicted only ∼500 low affinity targets for FNR in the E.coli chromosome.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
78
7,048
1
false
predicted only ∼500 low affinity targets for FNR in the E.coli chromosome.
[ "6" ]
predicted only ∼500 low affinity targets for FNR in the E.coli chromosome.
false
true
true
true
false
1,147
0
DISCUSSION
1
16
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
Although our experiments identified 63 discrete targets for FNR binding, these targets include only 20 out of the 65 validated targets listed in the Ecocyc database (16).
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
170
7,049
1
false
Although our experiments identified 63 discrete targets for FNR binding, these targets include only 20 out of the 65 validated targets listed in the Ecocyc database.
[ "16" ]
Although our experiments identified 63 discrete targets for FNR binding, these targets include only 20 out of the 65 validated targets listed in the Ecocyc database.
true
true
true
true
true
1,147
0
DISCUSSION
1
8
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
This highlights an important limitation of the ChIP-chip methodology.
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
69
7,050
0
false
This highlights an important limitation of the ChIP-chip methodology.
[]
This highlights an important limitation of the ChIP-chip methodology.
true
true
true
true
true
1,147
0
DISCUSSION
1
18
[ "b8", "b9", "b10", "b16", "b6", "b13", "b6", "b16", "b18" ]
17,164,287
pmid-15035009|pmid-12582243|NA|pmid-15550941|pmid-9813115|pmid-11282972|pmid-12754220|pmid-16377617|pmid-12754220|pmid-15659690|pmid-16377617|NA|pmid-9813115|pmid-16301522|pmid-9813115|NA|pmid-14986705
Its inability to detect all FNR-DNA interactions is likely to be due to inefficient crosslinking at some locations, or epitope masking (18).
[ "8", "9", "10", "16", "6", "13", "6", "16", "18" ]
140
7,051
1
false
Its inability to detect all FNR-DNA interactions is likely to be due to inefficient crosslinking at some locations, or epitope masking.
[ "18" ]
Its inability to detect all FNR-DNA interactions is likely to be due to inefficient crosslinking at some locations, or epitope masking.
true
true
true
true
true
1,147
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
Although major changes in gene expression and nucleoid structure occur when E.coli cells enter stationary phase (11,12,19), it is not known if changes in the distribution of global DNA binding proteins occur.
[ "11", "12", "19", "13", "20", "21" ]
208
7,052
0
false
Although major changes in gene expression and nucleoid structure occur when E.coli cells enter stationary phase, it is not known if changes in the distribution of global DNA binding proteins occur.
[ "11,12,19" ]
Although major changes in gene expression and nucleoid structure occur when E.coli cells enter stationary phase, it is not known if changes in the distribution of global DNA binding proteins occur.
true
true
true
true
true
1,148
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
Our observation that the DNA binding profile for FNR is largely unaltered in stationary phase cells shows that the compaction of the stationary phase chromosome does not occlude FNR binding sites.
[ "11", "12", "19", "13", "20", "21" ]
196
7,053
0
false
Our observation that the DNA binding profile for FNR is largely unaltered in stationary phase cells shows that the compaction of the stationary phase chromosome does not occlude FNR binding sites.
[]
Our observation that the DNA binding profile for FNR is largely unaltered in stationary phase cells shows that the compaction of the stationary phase chromosome does not occlude FNR binding sites.
true
true
true
true
true
1,148
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
This surprising result prompted us to examine the nucleoid-associated protein IHF and we came to the same conclusion; the distribution of the protein is similar in growing and stationary phase cells.
[ "11", "12", "19", "13", "20", "21" ]
199
7,054
0
false
This surprising result prompted us to examine the nucleoid-associated protein IHF and we came to the same conclusion; the distribution of the protein is similar in growing and stationary phase cells.
[]
This surprising result prompted us to examine the nucleoid-associated protein IHF and we came to the same conclusion; the distribution of the protein is similar in growing and stationary phase cells.
true
true
true
true
true
1,148
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
In sharp contrast, as expected, the binding profile of RNA polymerase was completely altered.
[ "11", "12", "19", "13", "20", "21" ]
93
7,055
0
false
In sharp contrast, as expected, the binding profile of RNA polymerase was completely altered.
[]
In sharp contrast, as expected, the binding profile of RNA polymerase was completely altered.
true
true
true
true
true
1,148
1
DISCUSSION
1
13
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
In growing cells, most RNA polymerase is associated with ∼90 transcription units encoding factors required for protein synthesis, motility and ATP production (13).
[ "11", "12", "19", "13", "20", "21" ]
163
7,056
1
false
In growing cells, most RNA polymerase is associated with ∼90 transcription units encoding factors required for protein synthesis, motility and ATP production.
[ "13" ]
In growing cells, most RNA polymerase is associated with ∼90 transcription units encoding factors required for protein synthesis, motility and ATP production.
true
true
true
true
true
1,148
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
In stationary phase, this RNA polymerase is liberated and is distributed more equitably between the different genes (Figure 5A).
[ "11", "12", "19", "13", "20", "21" ]
128
7,057
0
false
In stationary phase, this RNA polymerase is liberated and is distributed more equitably between the different genes (Figure 5A).
[]
In stationary phase, this RNA polymerase is liberated and is distributed more equitably between the different genes (Figure 5A).
true
true
true
true
true
1,148
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
Interestingly, for most transcription units, RNA polymerase binding is skewed toward the 5′ end (e.g.
[ "11", "12", "19", "13", "20", "21" ]
101
7,058
0
false
Interestingly, for most transcription units, RNA polymerase binding is skewed toward the 5′ end (e.g.
[]
Interestingly, for most transcription units, RNA polymerase binding is skewed toward the 5′ end (e.g.
true
true
true
true
true
1,148
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
are shown in Figure 5B) and thus, in stationary phase, the proportion of RNA polymerase bound to non-coding parts of the genome is increased (Figure 5C).
[ "11", "12", "19", "13", "20", "21" ]
153
7,059
0
false
are shown in Figure 5B) and thus, in stationary phase, the proportion of RNA polymerase bound to non-coding parts of the genome is increased (Figure 5C).
[]
are shown in Figure 5B) and thus, in stationary phase, the proportion of RNA polymerase bound to non-coding parts of the genome is increased (Figure 5C).
false
true
true
true
false
1,148
1
DISCUSSION
1
20
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
Consistent with this, Lee and Gralla (20) showed that some σS-dependent promoters have the ability to trap RNA polymerase.
[ "11", "12", "19", "13", "20", "21" ]
122
7,060
1
false
Consistent with this, Lee and Gralla showed that some σS-dependent promoters have the ability to trap RNA polymerase.
[ "20" ]
Consistent with this, Lee and Gralla showed that some σS-dependent promoters have the ability to trap RNA polymerase.
true
true
true
true
true
1,148
1
DISCUSSION
1
21
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
We note that, in their study of RNA polymerase distribution in stationary phase S.cerevisiae, Radonjic and colleagues identified a similar phenomenon (21).
[ "11", "12", "19", "13", "20", "21" ]
155
7,061
1
false
We note that, in their study of RNA polymerase distribution in stationary phase S.cerevisiae, Radonjic and colleagues identified a similar phenomenon.
[ "21" ]
We note that, in their study of RNA polymerase distribution in stationary phase S.cerevisiae, Radonjic and colleagues identified a similar phenomenon.
true
true
true
true
true
1,148
1
DISCUSSION
1
11
[ "b11", "b12", "b19", "b13", "b20", "b21" ]
17,164,287
pmid-11101804|pmid-15716429|pmid-11101804|pmid-15716429|pmid-15060178|pmid-16301522|pmid-15099515|pmid-15837421
This suggests that trapping of RNA polymerase at promoters may be an evolutionarily conserved mechanism to regulate transcription in response to growth rate.
[ "11", "12", "19", "13", "20", "21" ]
157
7,062
0
false
This suggests that trapping of RNA polymerase at promoters may be an evolutionarily conserved mechanism to regulate transcription in response to growth rate.
[]
This suggests that trapping of RNA polymerase at promoters may be an evolutionarily conserved mechanism to regulate transcription in response to growth rate.
true
true
true
true
true
1,148
2
DISCUSSION
0
null
null
17,164,287
null
Increased association of RNA polymerase with non-coding DNA during stationary phase.
null
84
7,063
0
false
null
null
Increased association of RNA polymerase with non-coding DNA during stationary phase.
true
true
true
true
true
1,149
2
DISCUSSION
0
null
null
17,164,287
null
The figure shows an overview of results from ChIP-chip experiments that measure the profile of RNA polymerase binding across the E.coli chromosome during stationary phase.
null
171
7,064
0
false
null
null
The figure shows an overview of results from ChIP-chip experiments that measure the profile of RNA polymerase binding across the E.coli chromosome during stationary phase.
true
true
true
true
true
1,149
2
DISCUSSION
0
null
null
17,164,287
null
Binding signals (y-axis) are plotted against their location on the 4.64 Mb E.coli chromosome (x-axis).
null
102
7,065
0
false
null
null
Binding signals (y-axis) are plotted against their location on the 4.64 Mb E.coli chromosome (x-axis).
true
true
true
true
true
1,149
2
DISCUSSION
0
null
null
17,164,287
null
The locations of selected signals are labelled.
null
47
7,066
0
false
null
null
The locations of selected signals are labelled.
true
true
true
true
true
1,149
2
DISCUSSION
0
null
null
17,164,287
null
(B) Skewed distribution of RNA polymerase across transcribed regions during stationary phase.
null
93
7,067
0
false
null
null
(B) Skewed distribution of RNA polymerase across transcribed regions during stationary phase.
false
false
true
true
false
1,149
2
DISCUSSION
0
null
null
17,164,287
null
The figure illustrates of selected regions highlighted in (A).
null
62
7,068
0
false
null
null
The figure illustrates of selected regions highlighted in (A).
true
true
true
true
true
1,149
2
DISCUSSION
0
null
null
17,164,287
null
Data for RNA polymerase binding during stationary phase are shown in black and RNA polymerase binding during mid-log phase is shown in grey.
null
140
7,069
0
false
null
null
Data for RNA polymerase binding during stationary phase are shown in black and RNA polymerase binding during mid-log phase is shown in grey.
true
true
true
true
true
1,149
2
DISCUSSION
0
null
null
17,164,287
null
(C) Increased association of RNA polymerase with non-coding DNA during stationary phase.
null
88
7,070
0
false
null
null
(C) Increased association of RNA polymerase with non-coding DNA during stationary phase.
false
false
true
true
false
1,149
2
DISCUSSION
0
null
null
17,164,287
null
The ChIP-chip datasets for RNA polymerase binding during rapid growth (grey) and stationary phase (black) were aligned and a range of Cy5/Cy3 cut-offs were applied to select the upper 50, 100, 200, 400, 800, 1600, 3200 and 6400 probes for each dataset.
null
252
7,071
0
false
null
null
The ChIP-chip datasets for RNA polymerase binding during rapid growth (grey) and stationary phase (black) were aligned and a range of Cy5/Cy3 cut-offs were applied to select the upper 50, 100, 200, 400, 800, 1600, 3200 and 6400 probes for each dataset.
true
true
true
true
true
1,149
2
DISCUSSION
0
null
null
17,164,287
null
We then determined the distribution of probes passing the cut-offs between coding and non-coding DNA.
null
101
7,072
0
false
null
null
We then determined the distribution of probes passing the cut-offs between coding and non-coding DNA.
true
true
true
true
true
1,149
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
Computational docking has proven to be a valuable tool in the study of biomolecular complexes (1,2).
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
100
7,073
0
false
Computational docking has proven to be a valuable tool in the study of biomolecular complexes.
[ "1,2" ]
Computational docking has proven to be a valuable tool in the study of biomolecular complexes.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
In particular, the field of ‘ab initio’ protein−protein docking has made considerable progress as illustrated by recent results from the community-wide CAPRI experiment [critical assessment of predicted interactions (3,4)].
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
223
7,074
0
false
In particular, the field of ‘ab initio’ protein−protein docking has made considerable progress as illustrated by recent results from the community-wide CAPRI experiment.
[ "critical assessment of predicted interactions (3,4)" ]
In particular, the field of ‘ab initio’ protein−protein docking has made considerable progress as illustrated by recent results from the community-wide CAPRI experiment.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
However, where this field has in many ways matured, the development of docking methods to model protein−DNA interactions has lagged behind.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
139
7,075
0
false
However, where this field has in many ways matured, the development of docking methods to model protein−DNA interactions has lagged behind.
[]
However, where this field has in many ways matured, the development of docking methods to model protein−DNA interactions has lagged behind.
true
true
true
true
true
1,150
0
INTRODUCTION
1
5
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
These play an important role in recognition and gene expression (5).
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
68
7,076
1
false
These play an important role in recognition and gene expression.
[ "5" ]
These play an important role in recognition and gene expression.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
Powerful protein−DNA docking methods would thus be of great benefit for their study.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
84
7,077
0
false
Powerful protein−DNA docking methods would thus be of great benefit for their study.
[]
Powerful protein−DNA docking methods would thus be of great benefit for their study.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
However, two particular problems have hampered the development of efficient docking methods: the sparsity of the information to define the DNA-binding interface and the inherent flexibility of DNA.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
197
7,078
0
false
However, two particular problems have hampered the development of efficient docking methods: the sparsity of the information to define the DNA-binding interface and the inherent flexibility of DNA.
[]
However, two particular problems have hampered the development of efficient docking methods: the sparsity of the information to define the DNA-binding interface and the inherent flexibility of DNA.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
For protein−protein docking there is often enough information available (e.g.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
77
7,079
0
false
For protein−protein docking there is often enough information available (e.g.
[]
For protein−protein docking there is often enough information available (e.g.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
from sequence, conservation or biological knowledge) to identify the interaction surfaces of the docking partners.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
114
7,080
0
false
from sequence, conservation or biological knowledge) to identify the interaction surfaces of the docking partners.
[]
from sequence, conservation or biological knowledge) to identify the interaction surfaces of the docking partners.
false
true
true
true
false
1,150
0
INTRODUCTION
1
6
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
This information can be used to drive the docking (6) and limit the conformational space to be searched.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
104
7,081
1
false
This information can be used to drive the docking and limit the conformational space to be searched.
[ "6" ]
This information can be used to drive the docking and limit the conformational space to be searched.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
Identification of the interaction surface on DNA is less straightforward than on proteins.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
90
7,082
0
false
Identification of the interaction surface on DNA is less straightforward than on proteins.
[]
Identification of the interaction surface on DNA is less straightforward than on proteins.
true
true
true
true
true
1,150
0
INTRODUCTION
1
7
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
There is still no general recognition code and the global conformation of the DNA can play an important role in modulating the eventual interaction surface (7).
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
160
7,083
1
false
There is still no general recognition code and the global conformation of the DNA can play an important role in modulating the eventual interaction surface.
[ "7" ]
There is still no general recognition code and the global conformation of the DNA can play an important role in modulating the eventual interaction surface.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
DNA indeed often exhibits large conformational changes upon binding to a protein, which can greatly alter the shape of the interaction surface.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
143
7,084
0
false
DNA indeed often exhibits large conformational changes upon binding to a protein, which can greatly alter the shape of the interaction surface.
[]
DNA indeed often exhibits large conformational changes upon binding to a protein, which can greatly alter the shape of the interaction surface.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
Owing to this, the total conformational space that needs to be searched in order to find favourable conformations becomes even larger.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
134
7,085
0
false
Owing to this, the total conformational space that needs to be searched in order to find favourable conformations becomes even larger.
[]
Owing to this, the total conformational space that needs to be searched in order to find favourable conformations becomes even larger.
true
true
true
true
true
1,150
0
INTRODUCTION
1
8
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
Flexibility in DNA can be separated into global and local components (8).
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
73
7,086
1
false
Flexibility in DNA can be separated into global and local components.
[ "8" ]
Flexibility in DNA can be separated into global and local components.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
Global flexibility is constrained to two primary motions: bending and twisting.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
79
7,087
0
false
Global flexibility is constrained to two primary motions: bending and twisting.
[]
Global flexibility is constrained to two primary motions: bending and twisting.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
It results from a combination of conformational changes in the flexible base pairs and sugar-phosphate backbone.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
112
7,088
0
false
It results from a combination of conformational changes in the flexible base pairs and sugar-phosphate backbone.
[]
It results from a combination of conformational changes in the flexible base pairs and sugar-phosphate backbone.
true
true
true
true
true
1,150
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8" ]
16,820,531
pmid-12001221|pmid-14754428|pmid-12784359|pmid-12784368|pmid-8735272|NA|pmid-10966773|NA
Allowing for global and local flexibility in DNA during docking while maintaining the relevant conformation is a major challenge in protein−DNA docking.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
152
7,089
0
false
Allowing for global and local flexibility in DNA during docking while maintaining the relevant conformation is a major challenge in protein−DNA docking.
[]
Allowing for global and local flexibility in DNA during docking while maintaining the relevant conformation is a major challenge in protein−DNA docking.
true
true
true
true
true
1,150
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
In the last few years several methods have been developed to solve one or both of these problems, each with varying degrees of success.
[ "9", "10", "11", "12", "12", "11" ]
135
7,090
0
false
In the last few years several methods have been developed to solve one or both of these problems, each with varying degrees of success.
[]
In the last few years several methods have been developed to solve one or both of these problems, each with varying degrees of success.
true
true
true
true
true
1,151
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
The program FTDOCK (9) has been used to perform a large search through conformational space by rotating and translating the protein along the DNA while evaluating shape and electrostatic complementarity; an approximation of flexibility was achieved by allowing some degree of overlap between protein and DNA in the scori...
[ "9", "10", "11", "12", "12", "11" ]
323
7,091
1
false
The program FTDOCK has been used to perform a large search through conformational space by rotating and translating the protein along the DNA while evaluating shape and electrostatic complementarity; an approximation of flexibility was achieved by allowing some degree of overlap between protein and DNA in the scoring.
[ "9" ]
The program FTDOCK has been used to perform a large search through conformational space by rotating and translating the protein along the DNA while evaluating shape and electrostatic complementarity; an approximation of flexibility was achieved by allowing some degree of overlap between protein and DNA in the scoring.
true
true
true
true
true
1,151
1
INTRODUCTION
1
10
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
In another approach, a library of pre-bent DNA structures was used to minimize the search through DNA conformational space (10); a selection was made based on structures that could be electrostatically preorientated in the potential of the protein and these were rotated and translated with respect to the protein.
[ "9", "10", "11", "12", "12", "11" ]
314
7,092
1
false
In another approach, a library of pre-bent DNA structures was used to minimize the search through DNA conformational space ; a selection was made based on structures that could be electrostatically preorientated in the potential of the protein and these were rotated and translated with respect to the protein.
[ "10" ]
In another approach, a library of pre-bent DNA structures was used to minimize the search through DNA conformational space ; a selection was made based on structures that could be electrostatically preorientated in the potential of the protein and these were rotated and translated with respect to the protein.
true
true
true
true
true
1,151
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
To account for some degree of local flexibility protein side chains and DNA base pairs were allowed to move in two separate refinement stages.
[ "9", "10", "11", "12", "12", "11" ]
142
7,093
0
false
To account for some degree of local flexibility protein side chains and DNA base pairs were allowed to move in two separate refinement stages.
[]
To account for some degree of local flexibility protein side chains and DNA base pairs were allowed to move in two separate refinement stages.
true
true
true
true
true
1,151
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
Knegtel et al.
[ "9", "10", "11", "12", "12", "11" ]
14
7,094
0
false
Knegtel et al.
[]
Knegtel et al.
true
true
true
true
true
1,151
1
INTRODUCTION
1
11
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
(11) developed MONTY which uses a Monte Carlo search allowing for flexibility in both protein and DNA and experimentally determined contacts to drive the docking.
[ "9", "10", "11", "12", "12", "11" ]
162
7,095
1
false
developed MONTY which uses a Monte Carlo search allowing for flexibility in both protein and DNA and experimentally determined contacts to drive the docking.
[ "11" ]
developed MONTY which uses a Monte Carlo search allowing for flexibility in both protein and DNA and experimentally determined contacts to drive the docking.
false
true
true
true
false
1,151
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
The initial position of the protein in the predicted complex should, however, not deviate too much from that of the actual complex; small deviations in the position of the protein with respect to the interaction interface of the DNA resulted in DNA curling around the protein.
[ "9", "10", "11", "12", "12", "11" ]
276
7,096
0
false
The initial position of the protein in the predicted complex should, however, not deviate too much from that of the actual complex; small deviations in the position of the protein with respect to the interaction interface of the DNA resulted in DNA curling around the protein.
[]
The initial position of the protein in the predicted complex should, however, not deviate too much from that of the actual complex; small deviations in the position of the protein with respect to the interaction interface of the DNA resulted in DNA curling around the protein.
true
true
true
true
true
1,151
1
INTRODUCTION
1
12
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
Tzou and Hwang (12) modelled the CAP-DNA and Rep-DNA systems from the repressors in their bound conformation and canonical B-DNA in a series of molecular mechanics and dynamics simulations using distance restraints derived from a statistical analysis of homologous protein–DNA complexes.
[ "9", "10", "11", "12", "12", "11" ]
287
7,097
1
false
Tzou and Hwang modelled the CAP-DNA and Rep-DNA systems from the repressors in their bound conformation and canonical B-DNA in a series of molecular mechanics and dynamics simulations using distance restraints derived from a statistical analysis of homologous protein–DNA complexes.
[ "12" ]
Tzou and Hwang modelled the CAP-DNA and Rep-DNA systems from the repressors in their bound conformation and canonical B-DNA in a series of molecular mechanics and dynamics simulations using distance restraints derived from a statistical analysis of homologous protein–DNA complexes.
true
true
true
true
true
1,151
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
This method successfully introduced DNA bending and local opening of the major groove.
[ "9", "10", "11", "12", "12", "11" ]
86
7,098
0
false
This method successfully introduced DNA bending and local opening of the major groove.
[]
This method successfully introduced DNA bending and local opening of the major groove.
true
true
true
true
true
1,151
1
INTRODUCTION
1
9
[ "b9", "b10", "b11", "b12", "b12", "b11" ]
16,820,531
pmid-9849937|pmid-8865343|pmid-7937706|pmid-10465734|pmid-10465734|pmid-7937706|pmid-15981252
All of these docking procedures were able to make predictions that were representative of the published complexes in terms of spatial disposition.
[ "9", "10", "11", "12", "12", "11" ]
146
7,099
0
false
All of these docking procedures were able to make predictions that were representative of the published complexes in terms of spatial disposition.
[]
All of these docking procedures were able to make predictions that were representative of the published complexes in terms of spatial disposition.
true
true
true
true
true
1,151