Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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1
INTRODUCTION
1
10
[ "B6", "B7", "B8", "B9", "B10", "B11 B12 B13", "B14", "B15" ]
19,465,379
pmid-11731503|pmid-16601728|pmid-15687504|pmid-16899655|pmid-16449501|pmid-10200254|pmid-11525815|pmid-14759257|pmid-14557537|pmid-14993205
Other approaches for studying the evolution of protein pathways or complexes have been mostly based on sequence similarity only (10).
[ "6", "7", "8", "9", "10", "11–13", "14", "15" ]
133
40,918
1
false
Other approaches for studying the evolution of protein pathways or complexes have been mostly based on sequence similarity only.
[ "10" ]
Other approaches for studying the evolution of protein pathways or complexes have been mostly based on sequence similarity only.
true
true
true
true
true
7,050
1
INTRODUCTION
1
11–13
[ "B6", "B7", "B8", "B9", "B10", "B11 B12 B13", "B14", "B15" ]
19,465,379
pmid-11731503|pmid-16601728|pmid-15687504|pmid-16899655|pmid-16449501|pmid-10200254|pmid-11525815|pmid-14759257|pmid-14557537|pmid-14993205
Functionally linked proteins were shown to have a tendency to evolve together (11–13); conversely, proteins with similar phylogenetic profiles were shown to have higher chances of participating in the same biochemical pathways (14).
[ "6", "7", "8", "9", "10", "11–13", "14", "15" ]
232
40,919
1
false
Functionally linked proteins were shown to have a tendency to evolve together ; conversely, proteins with similar phylogenetic profiles were shown to have higher chances of participating in the same biochemical pathways.
[ "11–13", "14" ]
Functionally linked proteins were shown to have a tendency to evolve together ; conversely, proteins with similar phylogenetic profiles were shown to have higher chances of participating in the same biochemical pathways.
true
true
true
true
true
7,050
1
INTRODUCTION
1
15
[ "B6", "B7", "B8", "B9", "B10", "B11 B12 B13", "B14", "B15" ]
19,465,379
pmid-11731503|pmid-16601728|pmid-15687504|pmid-16899655|pmid-16449501|pmid-10200254|pmid-11525815|pmid-14759257|pmid-14557537|pmid-14993205
Another study (15) showed that phylogenetic profiles of proteins in the same functional module tend to be significantly coherent, with variations in the level of coherence between different types of modules.
[ "6", "7", "8", "9", "10", "11–13", "14", "15" ]
207
40,920
1
false
Another study showed that phylogenetic profiles of proteins in the same functional module tend to be significantly coherent, with variations in the level of coherence between different types of modules.
[ "15" ]
Another study showed that phylogenetic profiles of proteins in the same functional module tend to be significantly coherent, with variations in the level of coherence between different types of modules.
true
true
true
true
true
7,050
2
INTRODUCTION
1
16
[ "B16", "B17", "B10" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
The evolution of modularity in PPI networks was studied by Pereira-Leal and coworkers (16,17), who proposed that the duplication of self-interacting proteins plays a key role in the formation of a modular network structure.
[ "16", "17", "10" ]
223
40,921
0
false
The evolution of modularity in PPI networks was studied by Pereira-Leal and coworkers, who proposed that the duplication of self-interacting proteins plays a key role in the formation of a modular network structure.
[ "16,17" ]
The evolution of modularity in PPI networks was studied by Pereira-Leal and coworkers, who proposed that the duplication of self-interacting proteins plays a key role in the formation of a modular network structure.
true
true
true
true
true
7,051
2
INTRODUCTION
1
16
[ "B16", "B17", "B10" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
Furthermore, they suggested that duplication of whole complexes is also a contributing factor for modularity, observing that a significant fraction of the complexes in Saccharomyces cerevisiae bare strong similarity to each other.
[ "16", "17", "10" ]
230
40,922
0
false
Furthermore, they suggested that duplication of whole complexes is also a contributing factor for modularity, observing that a significant fraction of the complexes in Saccharomyces cerevisiae bare strong similarity to each other.
[]
Furthermore, they suggested that duplication of whole complexes is also a contributing factor for modularity, observing that a significant fraction of the complexes in Saccharomyces cerevisiae bare strong similarity to each other.
true
true
true
true
true
7,051
2
INTRODUCTION
1
10
[ "B16", "B17", "B10" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
An additional recent work (10) studied evolutionary cohesive modules in PPI networks, i.e.
[ "16", "17", "10" ]
90
40,923
1
false
An additional recent work studied evolutionary cohesive modules in PPI networks, i.e.
[ "10" ]
An additional recent work studied evolutionary cohesive modules in PPI networks, i.e.
true
true
true
true
true
7,051
2
INTRODUCTION
1
16
[ "B16", "B17", "B10" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
modules whose components have a uniform pattern of loss and gain throughout evolution.
[ "16", "17", "10" ]
86
40,924
0
false
modules whose components have a uniform pattern of loss and gain throughout evolution.
[]
modules whose components have a uniform pattern of loss and gain throughout evolution.
false
true
true
true
false
7,051
2
INTRODUCTION
1
16
[ "B16", "B17", "B10" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
It was shown that younger cohesive modules play different roles than older ones and are more likely to be horizontally transferred.
[ "16", "17", "10" ]
131
40,925
0
false
It was shown that younger cohesive modules play different roles than older ones and are more likely to be horizontally transferred.
[]
It was shown that younger cohesive modules play different roles than older ones and are more likely to be horizontally transferred.
true
true
true
true
true
7,051
2
INTRODUCTION
1
16
[ "B16", "B17", "B10" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
In addition, the cohesiveness of a module was shown to correlate with its size and inter-connectivity, and inversely correlate with the rate of duplication among the member proteins.
[ "16", "17", "10" ]
182
40,926
0
false
In addition, the cohesiveness of a module was shown to correlate with its size and inter-connectivity, and inversely correlate with the rate of duplication among the member proteins.
[]
In addition, the cohesiveness of a module was shown to correlate with its size and inter-connectivity, and inversely correlate with the rate of duplication among the member proteins.
true
true
true
true
true
7,051
3
INTRODUCTION
1
18
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
In this study, we present a novel computational framework for reconstructing the evolutionary history of protein complexes from a network perspective.
[ "18", "19", "15–17", "10", "15", "8" ]
150
40,927
0
false
In this study, we present a novel computational framework for reconstructing the evolutionary history of protein complexes from a network perspective.
[]
In this study, we present a novel computational framework for reconstructing the evolutionary history of protein complexes from a network perspective.
true
true
true
true
true
7,052
3
INTRODUCTION
1
18
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
Our method is based on generalizing established evolutionary measures for single proteins (18,19) to the level of protein subnetworks.
[ "18", "19", "15–17", "10", "15", "8" ]
134
40,928
0
false
Our method is based on generalizing established evolutionary measures for single proteins to the level of protein subnetworks.
[ "18,19" ]
Our method is based on generalizing established evolutionary measures for single proteins to the level of protein subnetworks.
true
true
true
true
true
7,052
3
INTRODUCTION
1
18
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
Specifically, we define statistical measures for the level of homology between pairs of complexes, and use these measures to search for sets of orthologous complexes across species.
[ "18", "19", "15–17", "10", "15", "8" ]
181
40,929
0
false
Specifically, we define statistical measures for the level of homology between pairs of complexes, and use these measures to search for sets of orthologous complexes across species.
[]
Specifically, we define statistical measures for the level of homology between pairs of complexes, and use these measures to search for sets of orthologous complexes across species.
true
true
true
true
true
7,052
3
INTRODUCTION
1
18
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
The settings of our analysis differ from previous studies in three key points: (i)
[ "18", "19", "15–17", "10", "15", "8" ]
82
40,930
0
false
The settings of our analysis differ from previous studies in three key points: (i)
[]
The settings of our analysis differ from previous studies in three key points: (i)
true
true
false
true
false
7,052
3
INTRODUCTION
1
15–17
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
In contrast to previous studies (15–17) that restricted their analysis to known complexes and metabolic pathways, we consider a comprehensive set of computationally derived putative protein complexes in all of the studied species.
[ "18", "19", "15–17", "10", "15", "8" ]
230
40,931
1
false
In contrast to previous studies that restricted their analysis to known complexes and metabolic pathways, we consider a comprehensive set of computationally derived putative protein complexes in all of the studied species.
[ "15–17" ]
In contrast to previous studies that restricted their analysis to known complexes and metabolic pathways, we consider a comprehensive set of computationally derived putative protein complexes in all of the studied species.
true
true
true
true
true
7,052
3
INTRODUCTION
1
18
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
(ii) We identify conserved protein complexes by taking into account both sequence and interaction patterns rather than testing conservation based on sequence only
[ "18", "19", "15–17", "10", "15", "8" ]
162
40,932
0
false
(ii) We identify conserved protein complexes by taking into account both sequence and interaction patterns rather than testing conservation based on sequence only
[]
(ii) We identify conserved protein complexes by taking into account both sequence and interaction patterns rather than testing conservation based on sequence only
false
false
false
true
false
7,052
3
INTRODUCTION
1
18
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
[as in (10)] or interaction only [as in (15)].
[ "18", "19", "15–17", "10", "15", "8" ]
46
40,933
0
false
or interaction only.
[ "as in (10)", "as in (15)" ]
or interaction only.
false
true
true
true
false
7,052
3
INTRODUCTION
1
18
[ "B18", "B19", "B15 B16 B17", "B10", "B15", "B8" ]
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
(iii) We consider all patterns of conservation rather than restricting the analysis to complexes that are conserved in all species [as in (8)].
[ "18", "19", "15–17", "10", "15", "8" ]
143
40,934
0
false
(iii) We consider all patterns of conservation rather than restricting the analysis to complexes that are conserved in all species.
[ "as in (8)" ]
(iii) We consider all patterns of conservation rather than restricting the analysis to complexes that are conserved in all species.
false
false
true
true
false
7,052
4
INTRODUCTION
0
null
null
19,465,379
null
We use the sets of orthologous complexes to infer evolutionary rate and age estimates for the member complexes.
null
111
40,935
0
false
null
null
We use the sets of orthologous complexes to infer evolutionary rate and age estimates for the member complexes.
true
true
true
true
true
7,053
4
INTRODUCTION
0
null
null
19,465,379
null
These estimates are validated in several ways and employed to investigate mechanistic aspects of protein complex evolution.
null
123
40,936
0
false
null
null
These estimates are validated in several ways and employed to investigate mechanistic aspects of protein complex evolution.
true
true
true
true
true
7,053
4
INTRODUCTION
0
null
null
19,465,379
null
We find a high level of agreement between the evolutionary rates of proteins and those of the complexes they form, supporting the view that protein complexes tend to undergo evolution as coherent units.
null
202
40,937
0
false
null
null
We find a high level of agreement between the evolutionary rates of proteins and those of the complexes they form, supporting the view that protein complexes tend to undergo evolution as coherent units.
true
true
true
true
true
7,053
4
INTRODUCTION
0
null
null
19,465,379
null
Secondly, we study the role of duplication of self-interacting proteins in the evolution of protein complexes, showing that about one quarter of the sets of orthologous complexes are likely to have originated from conserved cores of homodimers that underwent duplication and divergence.
null
286
40,938
0
false
null
null
Secondly, we study the role of duplication of self-interacting proteins in the evolution of protein complexes, showing that about one quarter of the sets of orthologous complexes are likely to have originated from conserved cores of homodimers that underwent duplication and divergence.
true
true
true
true
true
7,053
0
DISCUSSION
0
null
null
19,465,379
pmid-16262681|pmid-12634793|pmid-11752321|pmid-16381927|pmid-17145710
We presented a framework for evolutionary analysis of protein complexes.
null
72
40,939
0
false
null
null
We presented a framework for evolutionary analysis of protein complexes.
true
true
true
true
true
7,054
0
DISCUSSION
0
null
null
19,465,379
pmid-16262681|pmid-12634793|pmid-11752321|pmid-16381927|pmid-17145710
By generalizing concepts from the level of single proteins, we constructed orthologous sets containing clusters from seven different species.
null
141
40,940
0
false
null
null
By generalizing concepts from the level of single proteins, we constructed orthologous sets containing clusters from seven different species.
true
true
true
true
true
7,054
0
DISCUSSION
0
null
null
19,465,379
pmid-16262681|pmid-12634793|pmid-11752321|pmid-16381927|pmid-17145710
These sets allow us to infer patterns of presence and absence across the evolutionary tree, and consequently to estimate the propensity for loss in evolution and evolutionary age.
null
179
40,941
0
false
null
null
These sets allow us to infer patterns of presence and absence across the evolutionary tree, and consequently to estimate the propensity for loss in evolution and evolutionary age.
true
true
true
true
true
7,054
0
DISCUSSION
0
null
null
19,465,379
pmid-16262681|pmid-12634793|pmid-11752321|pmid-16381927|pmid-17145710
We verified the orthologous sets in several ways including reconstructing the participating species' phylogeny and manually investigating a small set of hand-curated complexes.
null
176
40,942
0
false
null
null
We verified the orthologous sets in several ways including reconstructing the participating species' phylogeny and manually investigating a small set of hand-curated complexes.
true
true
true
true
true
7,054
1
DISCUSSION
0
null
null
19,465,379
pmid-11731503|pmid-16601728|pmid-15687504|pmid-16899655|pmid-16449501|pmid-10200254|pmid-11525815|pmid-14759257|pmid-14557537|pmid-14993205
We used the inferred SOCs to investigate mechanistic aspects of protein complex evolution.
null
90
40,943
0
false
null
null
We used the inferred SOCs to investigate mechanistic aspects of protein complex evolution.
true
true
true
true
true
7,055
1
DISCUSSION
0
null
null
19,465,379
pmid-11731503|pmid-16601728|pmid-15687504|pmid-16899655|pmid-16449501|pmid-10200254|pmid-11525815|pmid-14759257|pmid-14557537|pmid-14993205
First, we probed the relationship between the evolutionary characteristics of a cluster as a whole and that of its constituents, observing a significant correlation between the two.
null
181
40,944
0
false
null
null
First, we probed the relationship between the evolutionary characteristics of a cluster as a whole and that of its constituents, observing a significant correlation between the two.
true
true
true
true
true
7,055
1
DISCUSSION
0
null
null
19,465,379
pmid-11731503|pmid-16601728|pmid-15687504|pmid-16899655|pmid-16449501|pmid-10200254|pmid-11525815|pmid-14759257|pmid-14557537|pmid-14993205
Second, we have shown the importance of gene duplication as a mechanism for the evolution of protein complexes.
null
111
40,945
0
false
null
null
Second, we have shown the importance of gene duplication as a mechanism for the evolution of protein complexes.
true
true
true
true
true
7,055
2
DISCUSSION
1
18
[ "B18", "B19" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
The resulting new evolutionary measures can be employed to study other aspects of protein complex evolution beyond the mechanistic aspects studied here.
[ "18", "19" ]
152
40,946
0
false
The resulting new evolutionary measures can be employed to study other aspects of protein complex evolution beyond the mechanistic aspects studied here.
[]
The resulting new evolutionary measures can be employed to study other aspects of protein complex evolution beyond the mechanistic aspects studied here.
true
true
true
true
true
7,056
2
DISCUSSION
1
18
[ "B18", "B19" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
A fundamental question in this regard is how different functional attributes impact the evolution of a complex.
[ "18", "19" ]
111
40,947
0
false
A fundamental question in this regard is how different functional attributes impact the evolution of a complex.
[]
A fundamental question in this regard is how different functional attributes impact the evolution of a complex.
true
true
true
true
true
7,056
2
DISCUSSION
1
18
[ "B18", "B19" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
In the Supplementary Data we show that the evolutionary rate of a complex significantly correlates with its level of connectivity in the network, the specificity of its function and its essentiality.
[ "18", "19" ]
199
40,948
0
false
In the Supplementary Data we show that the evolutionary rate of a complex significantly correlates with its level of connectivity in the network, the specificity of its function and its essentiality.
[]
In the Supplementary Data we show that the evolutionary rate of a complex significantly correlates with its level of connectivity in the network, the specificity of its function and its essentiality.
true
true
true
true
true
7,056
2
DISCUSSION
1
18
[ "B18", "B19" ]
19,465,379
pmid-17411433|pmid-15805495|pmid-16449501|pmid-9381173|pmid-14525925
These findings are consistent with those previously reported for single proteins (18,19) and agree with our previous findings on the coherent evolution of the protein members of a complex.
[ "18", "19" ]
188
40,949
0
false
These findings are consistent with those previously reported for single proteins and agree with our previous findings on the coherent evolution of the protein members of a complex.
[ "18,19" ]
These findings are consistent with those previously reported for single proteins and agree with our previous findings on the coherent evolution of the protein members of a complex.
true
true
true
true
true
7,056
3
DISCUSSION
0
null
null
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
It is pleasing to see that current PPI networks are already rich enough to enable the careful study of intricate processes like protein complex evolution, after carefully controlling for the yet considerable rates of false positive and false negative interactions.
null
264
40,950
0
false
null
null
It is pleasing to see that current PPI networks are already rich enough to enable the careful study of intricate processes like protein complex evolution, after carefully controlling for the yet considerable rates of false positive and false negative interactions.
true
true
true
true
true
7,057
3
DISCUSSION
0
null
null
19,465,379
pmid-9381173|pmid-14525925|pmid-14993205|pmid-17411433|pmid-15805495|pmid-16449501|pmid-14993205|pmid-15687504
But not less important, the integrated computational approach laid out here is likely to lead to many further new insights concerning protein complex evolution as molecular interaction databases continue to expand in their size, accuracy and species coverage.
null
259
40,951
0
false
null
null
But not less important, the integrated computational approach laid out here is likely to lead to many further new insights concerning protein complex evolution as molecular interaction databases continue to expand in their size, accuracy and species coverage.
true
true
true
true
true
7,057
0
INTRODUCTION
1
1
[ "B1" ]
19,858,101
pmid-8384700
DNA transposons are not as numerous as the retrotransposons, which constitute a major fraction of the genome in mammals.
[ "1" ]
120
40,952
0
false
DNA transposons are not as numerous as the retrotransposons, which constitute a major fraction of the genome in mammals.
[]
DNA transposons are not as numerous as the retrotransposons, which constitute a major fraction of the genome in mammals.
true
true
true
true
true
7,058
0
INTRODUCTION
1
1
[ "B1" ]
19,858,101
pmid-8384700
Nevertheless, DNA transposons are almost ubiquitous and have colonized all branches of the tree of life.
[ "1" ]
104
40,953
0
false
Nevertheless, DNA transposons are almost ubiquitous and have colonized all branches of the tree of life.
[]
Nevertheless, DNA transposons are almost ubiquitous and have colonized all branches of the tree of life.
true
true
true
true
true
7,058
0
INTRODUCTION
1
1
[ "B1" ]
19,858,101
pmid-8384700
If judged by the breadth of its phylogenetic distribution, the mariner family is one of the most successful groups of DNA transposons, having been found in almost all animal genomes in which they have been sought (1).
[ "1" ]
217
40,954
1
false
If judged by the breadth of its phylogenetic distribution, the mariner family is one of the most successful groups of DNA transposons, having been found in almost all animal genomes in which they have been sought.
[ "1" ]
If judged by the breadth of its phylogenetic distribution, the mariner family is one of the most successful groups of DNA transposons, having been found in almost all animal genomes in which they have been sought.
true
true
true
true
true
7,058
1
INTRODUCTION
1
2
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
DNA transposons, such as mariner, have an unusual life cycle thought to depend on frequent horizontal transfer into new hosts (2,3).
[ "2", "3", "4" ]
132
40,955
0
false
DNA transposons, such as mariner, have an unusual life cycle thought to depend on frequent horizontal transfer into new hosts.
[ "2,3" ]
DNA transposons, such as mariner, have an unusual life cycle thought to depend on frequent horizontal transfer into new hosts.
true
true
true
true
true
7,059
1
INTRODUCTION
1
2
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
Horizontal transfer is followed by a burst of transposition in the newly invaded genome, followed by a gradual decline in activity, brought about by several different factors.
[ "2", "3", "4" ]
175
40,956
0
false
Horizontal transfer is followed by a burst of transposition in the newly invaded genome, followed by a gradual decline in activity, brought about by several different factors.
[]
Horizontal transfer is followed by a burst of transposition in the newly invaded genome, followed by a gradual decline in activity, brought about by several different factors.
true
true
true
true
true
7,059
1
INTRODUCTION
1
2
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
First of all, there is probably an intrinsic limit on the maximum rate of transposition that can be achieved as the number of copies of the element increases: it appears that the increase in transposase concentration, caused by amplification of the transposon, may cause a net decrease in transposition.
[ "2", "3", "4" ]
303
40,957
0
false
First of all, there is probably an intrinsic limit on the maximum rate of transposition that can be achieved as the number of copies of the element increases: it appears that the increase in transposase concentration, caused by amplification of the transposon, may cause a net decrease in transposition.
[]
First of all, there is probably an intrinsic limit on the maximum rate of transposition that can be achieved as the number of copies of the element increases: it appears that the increase in transposase concentration, caused by amplification of the transposon, may cause a net decrease in transposition.
true
true
true
true
true
7,059
1
INTRODUCTION
1
2
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
This phenomenon is called overproduction inhibition (OPI).
[ "2", "3", "4" ]
58
40,958
0
false
This phenomenon is called overproduction inhibition (OPI).
[]
This phenomenon is called overproduction inhibition (OPI).
true
true
true
true
true
7,059
1
INTRODUCTION
1
2
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
Furthermore, as different copies of the element acquire inactivating mutations over time, mutant transposases will impair the activity of the wild-type transposase by dominant-negative complementation.
[ "2", "3", "4" ]
201
40,959
0
false
Furthermore, as different copies of the element acquire inactivating mutations over time, mutant transposases will impair the activity of the wild-type transposase by dominant-negative complementation.
[]
Furthermore, as different copies of the element acquire inactivating mutations over time, mutant transposases will impair the activity of the wild-type transposase by dominant-negative complementation.
true
true
true
true
true
7,059
1
INTRODUCTION
1
4
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
Finally, active transposase protein will be titrated by the inverted terminal repeats (ITRs) of defective copies that retain the transposase binding activity (4).
[ "2", "3", "4" ]
162
40,960
1
false
Finally, active transposase protein will be titrated by the inverted terminal repeats (ITRs) of defective copies that retain the transposase binding activity.
[ "4" ]
Finally, active transposase protein will be titrated by the inverted terminal repeats (ITRs) of defective copies that retain the transposase binding activity.
true
true
true
true
true
7,059
1
INTRODUCTION
1
2
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
All the three mechanisms are proposed to cause a decrease in transposition, eventually causing the vertical inactivation of the elements.
[ "2", "3", "4" ]
137
40,961
0
false
All the three mechanisms are proposed to cause a decrease in transposition, eventually causing the vertical inactivation of the elements.
[]
All the three mechanisms are proposed to cause a decrease in transposition, eventually causing the vertical inactivation of the elements.
true
true
true
true
true
7,059
1
INTRODUCTION
1
2
[ "B2", "B3", "B4" ]
19,858,101
pmid-7476131|pmid-7877497|pmid-9154003
In consequence, DNA transposons have a narrow window of activity following genome invasion, and most organisms therefore contain only inactive copies of DNA transposons.
[ "2", "3", "4" ]
169
40,962
0
false
In consequence, DNA transposons have a narrow window of activity following genome invasion, and most organisms therefore contain only inactive copies of DNA transposons.
[]
In consequence, DNA transposons have a narrow window of activity following genome invasion, and most organisms therefore contain only inactive copies of DNA transposons.
true
true
true
true
true
7,059
2
INTRODUCTION
1
5–7
[ "B5 B6 B7", "B5", "B6", "B8", "B5", "B6", "B9", "B10" ]
19,858,101
pmid-9461395|pmid-16672366|pmid-17339369|pmid-9461395|pmid-16672366|pmid-17130240|pmid-9461395|pmid-16672366|pmid-18790802|pmid-19390626
The Hsmar1 transposon is one of the youngest DNA transposons in the human genome (5–7).
[ "5–7", "5", "6", "8", "5", "6", "9", "10" ]
87
40,963
1
false
The Hsmar1 transposon is one of the youngest DNA transposons in the human genome.
[ "5–7" ]
The Hsmar1 transposon is one of the youngest DNA transposons in the human genome.
true
true
true
true
true
7,060
2
INTRODUCTION
1
5–7
[ "B5 B6 B7", "B5", "B6", "B8", "B5", "B6", "B9", "B10" ]
19,858,101
pmid-9461395|pmid-16672366|pmid-17339369|pmid-9461395|pmid-16672366|pmid-17130240|pmid-9461395|pmid-16672366|pmid-18790802|pmid-19390626
It appeared in the primate lineage ∼58 million years ago and was probably active until ∼37 million years ago.
[ "5–7", "5", "6", "8", "5", "6", "9", "10" ]
109
40,964
0
false
It appeared in the primate lineage ∼58 million years ago and was probably active until ∼37 million years ago.
[]
It appeared in the primate lineage ∼58 million years ago and was probably active until ∼37 million years ago.
true
true
true
true
true
7,060
2
INTRODUCTION
1
5–7
[ "B5 B6 B7", "B5", "B6", "B8", "B5", "B6", "B9", "B10" ]
19,858,101
pmid-9461395|pmid-16672366|pmid-17339369|pmid-9461395|pmid-16672366|pmid-17130240|pmid-9461395|pmid-16672366|pmid-18790802|pmid-19390626
During this time, about 200 copies of the full-length element were produced, along with several thousand copies of an 80-bp MITE that we refer to as MiHsmar1 (mini-Hsmar1) (5,6,8).
[ "5–7", "5", "6", "8", "5", "6", "9", "10" ]
180
40,965
0
false
During this time, about 200 copies of the full-length element were produced, along with several thousand copies of an 80-bp MITE that we refer to as MiHsmar1 (mini-Hsmar1).
[ "5,6,8" ]
During this time, about 200 copies of the full-length element were produced, along with several thousand copies of an 80-bp MITE that we refer to as MiHsmar1 (mini-Hsmar1).
true
true
true
true
true
7,060
2
INTRODUCTION
1
5
[ "B5 B6 B7", "B5", "B6", "B8", "B5", "B6", "B9", "B10" ]
19,858,101
pmid-9461395|pmid-16672366|pmid-17339369|pmid-9461395|pmid-16672366|pmid-17130240|pmid-9461395|pmid-16672366|pmid-18790802|pmid-19390626
One copy of the Hsmar1 transposase was domesticated when it was fused to a histone H3 methylase gene (5).
[ "5–7", "5", "6", "8", "5", "6", "9", "10" ]
105
40,966
1
false
One copy of the Hsmar1 transposase was domesticated when it was fused to a histone H3 methylase gene.
[ "5" ]
One copy of the Hsmar1 transposase was domesticated when it was fused to a histone H3 methylase gene.
true
true
true
true
true
7,060
2
INTRODUCTION
1
6
[ "B5 B6 B7", "B5", "B6", "B8", "B5", "B6", "B9", "B10" ]
19,858,101
pmid-9461395|pmid-16672366|pmid-17339369|pmid-9461395|pmid-16672366|pmid-17130240|pmid-9461395|pmid-16672366|pmid-18790802|pmid-19390626
This gene, called SETMAR, is under purifying selection and appears to be a bona fide component of the human genome (6).
[ "5–7", "5", "6", "8", "5", "6", "9", "10" ]
119
40,967
1
false
This gene, called SETMAR, is under purifying selection and appears to be a bona fide component of the human genome.
[ "6" ]
This gene, called SETMAR, is under purifying selection and appears to be a bona fide component of the human genome.
true
true
true
true
true
7,060
2
INTRODUCTION
1
5–7
[ "B5 B6 B7", "B5", "B6", "B8", "B5", "B6", "B9", "B10" ]
19,858,101
pmid-9461395|pmid-16672366|pmid-17339369|pmid-9461395|pmid-16672366|pmid-17130240|pmid-9461395|pmid-16672366|pmid-18790802|pmid-19390626
The SETMAR protein (sometimes also called METNASE) is expressed in many tissues, and although several activities have been demonstrated, its precise function remains unclear (9,10).
[ "5–7", "5", "6", "8", "5", "6", "9", "10" ]
181
40,968
0
false
The SETMAR protein (sometimes also called METNASE) is expressed in many tissues, and although several activities have been demonstrated, its precise function remains unclear.
[ "9,10" ]
The SETMAR protein (sometimes also called METNASE) is expressed in many tissues, and although several activities have been demonstrated, its precise function remains unclear.
true
true
true
true
true
7,060
3
INTRODUCTION
1
8
[ "B8", "B11" ]
19,858,101
pmid-17130240|pmid-17403897
All of the Hsmar1 elements in the human genome have mutations that inactivate the transposase.
[ "8", "11" ]
94
40,969
0
false
All of the Hsmar1 elements in the human genome have mutations that inactivate the transposase.
[]
All of the Hsmar1 elements in the human genome have mutations that inactivate the transposase.
true
true
true
true
true
7,061
3
INTRODUCTION
1
8
[ "B8", "B11" ]
19,858,101
pmid-17130240|pmid-17403897
The first attempt to resurrect the activity of Hsmar1 was to express the transposase domain of the SETMAR protein (8).
[ "8", "11" ]
118
40,970
1
false
The first attempt to resurrect the activity of Hsmar1 was to express the transposase domain of the SETMAR protein.
[ "8" ]
The first attempt to resurrect the activity of Hsmar1 was to express the transposase domain of the SETMAR protein.
true
true
true
true
true
7,061
3
INTRODUCTION
1
8
[ "B8", "B11" ]
19,858,101
pmid-17130240|pmid-17403897
Transposition events were detected using a very sensitive genetic assay, but the protein was barely active.
[ "8", "11" ]
107
40,971
0
false
Transposition events were detected using a very sensitive genetic assay, but the protein was barely active.
[]
Transposition events were detected using a very sensitive genetic assay, but the protein was barely active.
true
true
true
true
true
7,061
3
INTRODUCTION
1
11
[ "B8", "B11" ]
19,858,101
pmid-17130240|pmid-17403897
A further successful attempt was made when the sequence of an ancestral transposase gene was reconstructed using phylogenetic analysis of various Hsmar1 copies (11).
[ "8", "11" ]
165
40,972
1
false
A further successful attempt was made when the sequence of an ancestral transposase gene was reconstructed using phylogenetic analysis of various Hsmar1 copies.
[ "11" ]
A further successful attempt was made when the sequence of an ancestral transposase gene was reconstructed using phylogenetic analysis of various Hsmar1 copies.
true
true
true
true
true
7,061
3
INTRODUCTION
1
8
[ "B8", "B11" ]
19,858,101
pmid-17130240|pmid-17403897
When expressed, this sequence provided an active transposase that we will henceforth refer to simply as Hsmar1 transposase.
[ "8", "11" ]
123
40,973
0
false
When expressed, this sequence provided an active transposase that we will henceforth refer to simply as Hsmar1 transposase.
[]
When expressed, this sequence provided an active transposase that we will henceforth refer to simply as Hsmar1 transposase.
true
true
true
true
true
7,061
4
INTRODUCTION
1
12
[ "B12", "B13", "B14 B15 B16 B17 B18", "B19", "B20" ]
19,858,101
NA|pmid-12535535|pmid-17412704|pmid-19593448|pmid-19720743|pmid-18354502|pmid-15616554|pmid-10911996|pmid-16511570
We are interested in mariner transposition because it appears to use a different biochemical mechanism from most other families of cut-and-paste transposons (12,13).
[ "12", "13", "14–18", "19", "20" ]
165
40,974
0
false
We are interested in mariner transposition because it appears to use a different biochemical mechanism from most other families of cut-and-paste transposons.
[ "12,13" ]
We are interested in mariner transposition because it appears to use a different biochemical mechanism from most other families of cut-and-paste transposons.
true
true
true
true
true
7,062
4
INTRODUCTION
1
12
[ "B12", "B13", "B14 B15 B16 B17 B18", "B19", "B20" ]
19,858,101
NA|pmid-12535535|pmid-17412704|pmid-19593448|pmid-19720743|pmid-18354502|pmid-15616554|pmid-10911996|pmid-16511570
Most DDE (aspartate-aspartate-glutamate) family cut-and-paste transposases use a single-active site to cleave both strands of DNA at the transposon end via a DNA–hairpin intermediate [(14–18) and references therein].
[ "12", "13", "14–18", "19", "20" ]
216
40,975
0
false
Most DDE (aspartate-aspartate-glutamate) family cut-and-paste transposases use a single-active site to cleave both strands of DNA at the transposon end via a DNA–hairpin intermediate.
[ "(14–18) and references therein" ]
Most DDE (aspartate-aspartate-glutamate) family cut-and-paste transposases use a single-active site to cleave both strands of DNA at the transposon end via a DNA–hairpin intermediate.
true
true
true
true
true
7,062
4
INTRODUCTION
1
12
[ "B12", "B13", "B14 B15 B16 B17 B18", "B19", "B20" ]
19,858,101
NA|pmid-12535535|pmid-17412704|pmid-19593448|pmid-19720743|pmid-18354502|pmid-15616554|pmid-10911996|pmid-16511570
There are exceptions to this paradigm, such as the heteromeric Tn7 transposase.
[ "12", "13", "14–18", "19", "20" ]
79
40,976
0
false
There are exceptions to this paradigm, such as the heteromeric Tn7 transposase.
[]
There are exceptions to this paradigm, such as the heteromeric Tn7 transposase.
true
true
true
true
true
7,062
4
INTRODUCTION
1
19
[ "B12", "B13", "B14 B15 B16 B17 B18", "B19", "B20" ]
19,858,101
NA|pmid-12535535|pmid-17412704|pmid-19593448|pmid-19720743|pmid-18354502|pmid-15616554|pmid-10911996|pmid-16511570
In this case, the transposase subunit cuts the first strand at the transposon end and joins it to the target site, while the second strand is cut by a protomer related to the type II restriction endonucleases (19).
[ "12", "13", "14–18", "19", "20" ]
214
40,977
1
false
In this case, the transposase subunit cuts the first strand at the transposon end and joins it to the target site, while the second strand is cut by a protomer related to the type II restriction endonucleases.
[ "19" ]
In this case, the transposase subunit cuts the first strand at the transposon end and joins it to the target site, while the second strand is cut by a protomer related to the type II restriction endonucleases.
true
true
true
true
true
7,062
4
INTRODUCTION
1
12
[ "B12", "B13", "B14 B15 B16 B17 B18", "B19", "B20" ]
19,858,101
NA|pmid-12535535|pmid-17412704|pmid-19593448|pmid-19720743|pmid-18354502|pmid-15616554|pmid-10911996|pmid-16511570
The mariner family was expected to conform to the DNA–hairpin paradigm because it encodes a homomeric transposase.
[ "12", "13", "14–18", "19", "20" ]
114
40,978
0
false
The mariner family was expected to conform to the DNA–hairpin paradigm because it encodes a homomeric transposase.
[]
The mariner family was expected to conform to the DNA–hairpin paradigm because it encodes a homomeric transposase.
true
true
true
true
true
7,062
4
INTRODUCTION
1
20
[ "B12", "B13", "B14 B15 B16 B17 B18", "B19", "B20" ]
19,858,101
NA|pmid-12535535|pmid-17412704|pmid-19593448|pmid-19720743|pmid-18354502|pmid-15616554|pmid-10911996|pmid-16511570
However, the hairpin intermediate has been excluded for mariner transposition and the mechanism of cleavage remains unknown (20).
[ "12", "13", "14–18", "19", "20" ]
129
40,979
1
false
However, the hairpin intermediate has been excluded for mariner transposition and the mechanism of cleavage remains unknown.
[ "20" ]
However, the hairpin intermediate has been excluded for mariner transposition and the mechanism of cleavage remains unknown.
true
true
true
true
true
7,062
5
INTRODUCTION
1
21
[ "B21" ]
19,858,101
pmid-15989951
In the hairpin mechanism the first strand is cleaved by hydrolysis.
[ "21" ]
67
40,980
0
false
In the hairpin mechanism the first strand is cleaved by hydrolysis.
[]
In the hairpin mechanism the first strand is cleaved by hydrolysis.
true
true
true
true
true
7,063
5
INTRODUCTION
1
21
[ "B21" ]
19,858,101
pmid-15989951
The 3′-OH then takes the place of the water in the active site and the second strand is cleaved by a direct transesterification reaction.
[ "21" ]
137
40,981
0
false
The 3′-OH then takes the place of the water in the active site and the second strand is cleaved by a direct transesterification reaction.
[]
The 3′-OH then takes the place of the water in the active site and the second strand is cleaved by a direct transesterification reaction.
true
true
true
true
true
7,063
5
INTRODUCTION
1
21
[ "B21" ]
19,858,101
pmid-15989951
In the absence of crystal structures of the intermediates it is unclear exactly how this is achieved.
[ "21" ]
101
40,982
0
false
In the absence of crystal structures of the intermediates it is unclear exactly how this is achieved.
[]
In the absence of crystal structures of the intermediates it is unclear exactly how this is achieved.
true
true
true
true
true
7,063
5
INTRODUCTION
1
21
[ "B21" ]
19,858,101
pmid-15989951
However, the hairpin mechanism does provide a partial explanation of how DNA strands of opposite polarity are cleaved while minimizing the conformational changes required in the active site (21).
[ "21" ]
195
40,983
1
false
However, the hairpin mechanism does provide a partial explanation of how DNA strands of opposite polarity are cleaved while minimizing the conformational changes required in the active site.
[ "21" ]
However, the hairpin mechanism does provide a partial explanation of how DNA strands of opposite polarity are cleaved while minimizing the conformational changes required in the active site.
true
true
true
true
true
7,063
6
INTRODUCTION
1
22
[ "B22", "B12", "B21" ]
19,858,101
pmid-12750473|NA|pmid-15989951
In the absence of a hairpin intermediate, mariner transposase must cleave the two strands of the DNA at each transposon end by sequential hydrolysis reactions.
[ "22", "12", "21" ]
159
40,984
0
false
In the absence of a hairpin intermediate, mariner transposase must cleave the two strands of the DNA at each transposon end by sequential hydrolysis reactions.
[]
In the absence of a hairpin intermediate, mariner transposase must cleave the two strands of the DNA at each transposon end by sequential hydrolysis reactions.
true
true
true
true
true
7,064
6
INTRODUCTION
1
22
[ "B22", "B12", "B21" ]
19,858,101
pmid-12750473|NA|pmid-15989951
Cleavage of the first and second strands at each transposon end may be performed either by the repeated action of a single active site (the one subunit mechanism), or by the sequential action of two active sites belonging to different transposase monomers (the two subunit mechanism).
[ "22", "12", "21" ]
284
40,985
0
false
Cleavage of the first and second strands at each transposon end may be performed either by the repeated action of a single active site (the one subunit mechanism), or by the sequential action of two active sites belonging to different transposase monomers (the two subunit mechanism).
[]
Cleavage of the first and second strands at each transposon end may be performed either by the repeated action of a single active site (the one subunit mechanism), or by the sequential action of two active sites belonging to different transposase monomers (the two subunit mechanism).
true
true
true
true
true
7,064
6
INTRODUCTION
1
22
[ "B22", "B12", "B21" ]
19,858,101
pmid-12750473|NA|pmid-15989951
These models describe only the number of active sites required to cleave the two strands of DNA at each transposon end: they are not meant to imply the overall stoichiometry of the active complex, which may contain subunits engaged in a purely structural role.
[ "22", "12", "21" ]
260
40,986
0
false
These models describe only the number of active sites required to cleave the two strands of DNA at each transposon end: they are not meant to imply the overall stoichiometry of the active complex, which may contain subunits engaged in a purely structural role.
[]
These models describe only the number of active sites required to cleave the two strands of DNA at each transposon end: they are not meant to imply the overall stoichiometry of the active complex, which may contain subunits engaged in a purely structural role.
true
true
true
true
true
7,064
6
INTRODUCTION
1
22
[ "B22", "B12", "B21" ]
19,858,101
pmid-12750473|NA|pmid-15989951
In the single subunit mechanism, the active site would have to nick DNA strands of opposite polarity.
[ "22", "12", "21" ]
101
40,987
0
false
In the single subunit mechanism, the active site would have to nick DNA strands of opposite polarity.
[]
In the single subunit mechanism, the active site would have to nick DNA strands of opposite polarity.
true
true
true
true
true
7,064
6
INTRODUCTION
1
22
[ "B22", "B12", "B21" ]
19,858,101
pmid-12750473|NA|pmid-15989951
To our knowledge, this would be unprecedented except for the unrelated BfiI restriction endonuclease, in which the active site is formed at the dimer interface (22).
[ "22", "12", "21" ]
165
40,988
1
false
To our knowledge, this would be unprecedented except for the unrelated BfiI restriction endonuclease, in which the active site is formed at the dimer interface.
[ "22" ]
To our knowledge, this would be unprecedented except for the unrelated BfiI restriction endonuclease, in which the active site is formed at the dimer interface.
true
true
true
true
true
7,064
6
INTRODUCTION
1
22
[ "B22", "B12", "B21" ]
19,858,101
pmid-12750473|NA|pmid-15989951
In the two subunit mechanism, the first subunit would have to move away from the cleavage site to allow access to the second subunit.
[ "22", "12", "21" ]
133
40,989
0
false
In the two subunit mechanism, the first subunit would have to move away from the cleavage site to allow access to the second subunit.
[]
In the two subunit mechanism, the first subunit would have to move away from the cleavage site to allow access to the second subunit.
true
true
true
true
true
7,064
6
INTRODUCTION
1
22
[ "B22", "B12", "B21" ]
19,858,101
pmid-12750473|NA|pmid-15989951
In either case, a significant conformational change is probably required between first- and second-strand cleavage (12,21).
[ "22", "12", "21" ]
123
40,990
0
false
In either case, a significant conformational change is probably required between first- and second-strand cleavage.
[ "12,21" ]
In either case, a significant conformational change is probably required between first- and second-strand cleavage.
true
true
true
true
true
7,064
7
INTRODUCTION
1
13
[ "B13", "B23", "B24", "B24", "B25" ]
19,858,101
pmid-12535535|pmid-8895590|pmid-18675277|pmid-18675277|pmid-15340089
Before Hsmar1, three mariner family transposons had been studied in vitro: Himar1, Mos1 and Mboumar1 (13,23,24).
[ "13", "23", "24", "24", "25" ]
112
40,991
0
false
Before Hsmar1, three mariner family transposons had been studied in vitro: Himar1, Mos1 and Mboumar1.
[ "13,23,24" ]
Before Hsmar1, three mariner family transposons had been studied in vitro: Himar1, Mos1 and Mboumar1.
true
true
true
true
true
7,065
7
INTRODUCTION
1
13
[ "B13", "B23", "B24", "B24", "B25" ]
19,858,101
pmid-12535535|pmid-8895590|pmid-18675277|pmid-18675277|pmid-15340089
Although experiments with these elements provided significant insight into the molecular mechanism of the reaction, technical difficulties have precluded detailed biochemical analysis.
[ "13", "23", "24", "24", "25" ]
184
40,992
0
false
Although experiments with these elements provided significant insight into the molecular mechanism of the reaction, technical difficulties have precluded detailed biochemical analysis.
[]
Although experiments with these elements provided significant insight into the molecular mechanism of the reaction, technical difficulties have precluded detailed biochemical analysis.
true
true
true
true
true
7,065
7
INTRODUCTION
1
13
[ "B13", "B23", "B24", "B24", "B25" ]
19,858,101
pmid-12535535|pmid-8895590|pmid-18675277|pmid-18675277|pmid-15340089
We have worked with all three elements and found that transposition activity is low at physiological pH (24,25) (Takac,M.
[ "13", "23", "24", "24", "25" ]
121
40,993
0
false
We have worked with all three elements and found that transposition activity is low at physiological pH (Takac,M.
[ "24,25" ]
We have worked with all three elements and found that transposition activity is low at physiological pH (Takac,M.
true
true
true
true
true
7,065
7
INTRODUCTION
1
13
[ "B13", "B23", "B24", "B24", "B25" ]
19,858,101
pmid-12535535|pmid-8895590|pmid-18675277|pmid-18675277|pmid-15340089
and R.C., unpublished data).
[ "13", "23", "24", "24", "25" ]
28
40,994
0
false
and R.C., unpublished data).
[]
and R.C., unpublished data).
false
true
true
true
false
7,065
7
INTRODUCTION
1
13
[ "B13", "B23", "B24", "B24", "B25" ]
19,858,101
pmid-12535535|pmid-8895590|pmid-18675277|pmid-18675277|pmid-15340089
At higher pH, transposon excision increases, but this is accompanied by a decrease in integration and, in some cases, the appearance of an activity that causes non-specific DNA degradation (Takac,M.
[ "13", "23", "24", "24", "25" ]
198
40,995
0
false
At higher pH, transposon excision increases, but this is accompanied by a decrease in integration and, in some cases, the appearance of an activity that causes non-specific DNA degradation (Takac,M.
[]
At higher pH, transposon excision increases, but this is accompanied by a decrease in integration and, in some cases, the appearance of an activity that causes non-specific DNA degradation (Takac,M.
true
true
true
true
true
7,065
8
INTRODUCTION
0
null
null
19,858,101
null
We have now completed an exploratory analysis of the Hsmar1 reaction in vitro.
null
78
40,997
0
false
null
null
We have now completed an exploratory analysis of the Hsmar1 reaction in vitro.
true
true
true
true
true
7,066
8
INTRODUCTION
0
null
null
19,858,101
null
We find that up to 100% of the substrate can be converted into product under ideal conditions, and that the DNA degrading activity that affects other related transposases is absent.
null
181
40,998
0
false
null
null
We find that up to 100% of the substrate can be converted into product under ideal conditions, and that the DNA degrading activity that affects other related transposases is absent.
true
true
true
true
true
7,066
8
INTRODUCTION
0
null
null
19,858,101
null
This provides a mariner transposition system that clearly reproduces the full range of products and intermediates previously observed in other cut-and-paste elements such as Tn10 and Tn5.
null
187
40,999
0
false
null
null
This provides a mariner transposition system that clearly reproduces the full range of products and intermediates previously observed in other cut-and-paste elements such as Tn10 and Tn5.
true
true
true
true
true
7,066
8
INTRODUCTION
0
null
null
19,858,101
null
The clarity of the Hsmar1 in vitro reaction reveals some simple mechanistic insights, and provides important directions for future work.
null
136
41,000
0
false
null
null
The clarity of the Hsmar1 in vitro reaction reveals some simple mechanistic insights, and provides important directions for future work.
true
true
true
true
true
7,066
9
INTRODUCTION
0
null
null
19,858,101
null
We find that when the flanking TA dinucleotides, typical of mariner insertions, are mutated to TG the reaction stalls after the first nick.
null
139
41,001
0
false
null
null
We find that when the flanking TA dinucleotides, typical of mariner insertions, are mutated to TG the reaction stalls after the first nick.
true
true
true
true
true
7,067
9
INTRODUCTION
0
null
null
19,858,101
null
This corresponds to the conformational change postulated to be required between first- and second-strand cleavage.
null
114
41,002
0
false
null
null
This corresponds to the conformational change postulated to be required between first- and second-strand cleavage.
true
true
true
true
true
7,067
9
INTRODUCTION
0
null
null
19,858,101
null
We also show that physiological pH is sub-optimal for transposition, and that the nicked and single-end break (SEB) intermediates accumulate at this pH.
null
152
41,003
0
false
null
null
We also show that physiological pH is sub-optimal for transposition, and that the nicked and single-end break (SEB) intermediates accumulate at this pH.
true
true
true
true
true
7,067
9
INTRODUCTION
0
null
null
19,858,101
null
The nicked intermediate corresponds to the transition between first- and second-strand cleavage just mentioned above.
null
117
41,004
0
false
null
null
The nicked intermediate corresponds to the transition between first- and second-strand cleavage just mentioned above.
true
true
true
true
true
7,067
9
INTRODUCTION
0
null
null
19,858,101
null
Since the effects of changing pH are usually mediated by the ionization of amino acid side chains, it may therefore be possible, in the future, to isolate transposase mutations that provide improved activity at physiological pH.
null
228
41,005
0
false
null
null
Since the effects of changing pH are usually mediated by the ionization of amino acid side chains, it may therefore be possible, in the future, to isolate transposase mutations that provide improved activity at physiological pH.
true
true
true
true
true
7,067
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
Ovarian sex cord stromal tumors are classified, inter alia, as granulosa stromal cell tumors, Sertoli's stromal tumors, and steroid cell tumors.
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
144
41,006
0
false
Ovarian sex cord stromal tumors are classified, inter alia, as granulosa stromal cell tumors, Sertoli's stromal tumors, and steroid cell tumors.
[]
Ovarian sex cord stromal tumors are classified, inter alia, as granulosa stromal cell tumors, Sertoli's stromal tumors, and steroid cell tumors.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
SSTs, along with granulosa cell tumors, thecomas and fibromas, are granulosa stromal cell tumors (6), and were first described as a distinct entity among ovarian sex cord stromal tumors by Chalvardjian and Scully in 1973 (7).
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
225
41,007
1
false
SSTs, along with granulosa cell tumors, thecomas and fibromas, are granulosa stromal cell tumors, and were first described as a distinct entity among ovarian sex cord stromal tumors by Chalvardjian and Scully in 1973.
[ "6", "7" ]
SSTs, along with granulosa cell tumors, thecomas and fibromas, are granulosa stromal cell tumors, and were first described as a distinct entity among ovarian sex cord stromal tumors by Chalvardjian and Scully in 1973.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
They are known to have the following characteristic clinical features: first, they usually occur in a younger age group, among those aged 27 or 28 years (1, 4, 5); whereas other types of stromal tumors are most common in the fifth and sixth decades, about 80% of SSTs are encountered during the second and third decades ...
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
332
41,008
0
false
They are known to have the following characteristic clinical features: first, they usually occur in a younger age group, among those aged 27 or 28 years ; whereas other types of stromal tumors are most common in the fifth and sixth decades, about 80% of SSTs are encountered during the second and third decades.
[ "1, 4, 5", "1-3, 5, 8" ]
They are known to have the following characteristic clinical features: first, they usually occur in a younger age group, among those aged 27 or 28 years ; whereas other types of stromal tumors are most common in the fifth and sixth decades, about 80% of SSTs are encountered during the second and third decades.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
In our study, two of three patients were aged less than 30, and the other was 39.
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
81
41,009
0
false
In our study, two of three patients were aged less than 30, and the other was 39.
[]
In our study, two of three patients were aged less than 30, and the other was 39.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
Second, the most common presenting symptom is menstrual irregularity (3-5), and this occurred in all our three patients.
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
120
41,010
0
false
Second, the most common presenting symptom is menstrual irregularity, and this occurred in all our three patients.
[ "3-5" ]
Second, the most common presenting symptom is menstrual irregularity, and this occurred in all our three patients.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
Third, ascites occurs, but is rare (2, 4, 7, 9).
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
48
41,011
0
false
Third, ascites occurs, but is rare.
[ "2, 4, 7, 9" ]
Third, ascites occurs, but is rare.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
In all our three cases, however, there was some ascites around the mass or in the cul-de-sac, and in several previous case reports the presence of ascites was also noted (1-2).
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
176
41,012
0
false
In all our three cases, however, there was some ascites around the mass or in the cul-de-sac, and in several previous case reports the presence of ascites was also noted.
[ "1-2" ]
In all our three cases, however, there was some ascites around the mass or in the cul-de-sac, and in several previous case reports the presence of ascites was also noted.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
To date, malignant SST has not been reported (1, 4).
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
52
41,013
0
false
To date, malignant SST has not been reported.
[ "1, 4" ]
To date, malignant SST has not been reported.
true
true
true
true
true
7,068
0
DISCUSSION
1
6
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
In our study, all three SSTs originated from the left ovary, and in several previously published reports, occurrence on this same side was also described (1-3, 5).
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
163
41,014
0
false
In our study, all three SSTs originated from the left ovary, and in several previously published reports, occurrence on this same side was also described.
[ "1-3, 5" ]
In our study, all three SSTs originated from the left ovary, and in several previously published reports, occurrence on this same side was also described.
true
true
true
true
true
7,068
0
DISCUSSION
1
4
[ "B6", "B7", "B1", "B4", "B5", "B1", "B3", "B5", "B8", "B3", "B5", "B2", "B4", "B7", "B9", "B1", "B2", "B1", "B4", "B1", "B3", "B5", "B4" ]
14,530,650
pmid-9821198|pmid-4348335|pmid-10433285|pmid-11316320|pmid-11242213|pmid-10433285|pmid-9422320|pmid-11242213|pmid-12432104|pmid-9422320|pmid-11242213|pmid-10460370|pmid-11316320|pmid-4348335|pmid-1143729|pmid-10433285|pmid-10460370|pmid-10433285|pmid-11316320|pmid-10433285|pmid-9422320|pmid-11242213|pmid-11316320
In another study, however, this was not the case (4).
[ "6", "7", "1", "4", "5", "1", "3", "5", "8", "3", "5", "2", "4", "7", "9", "1", "2", "1", "4", "1", "3", "5", "4" ]
53
41,015
1
false
In another study, however, this was not the case.
[ "4" ]
In another study, however, this was not the case.
true
true
true
true
true
7,068
1
DISCUSSION
1
1
[ "B1", "B9", "B10" ]
14,530,650
pmid-10433285|pmid-1143729|pmid-7155488
Hormonal activity has been reported in a few documented cases (1, 9-10), and though none of our patients underwent hormonal assay, they demonstrated no symptoms suggesting hormonal activity.
[ "1", "9", "10" ]
190
41,016
0
false
Hormonal activity has been reported in a few documented cases, and though none of our patients underwent hormonal assay, they demonstrated no symptoms suggesting hormonal activity.
[ "1, 9-10" ]
Hormonal activity has been reported in a few documented cases, and though none of our patients underwent hormonal assay, they demonstrated no symptoms suggesting hormonal activity.
true
true
true
true
true
7,069
2
DISCUSSION
1
4
[ "B4" ]
14,530,650
pmid-11316320
In a previous report by Lee et al.
[ "4" ]
34
41,017
0
false
In a previous report by Lee et al.
[]
In a previous report by Lee et al.
true
true
true
true
true
7,070
2
DISCUSSION
1
4
[ "B4" ]
14,530,650
pmid-11316320
(4), SSTs were shown at ultrasonography to be solid and cystic adnexal masses with centrally located, multiple, round or cleft-like cysts, and two patients in our study, in one of whom the cyst was entirely solid and homogeneously echogenic, showed similar features.
[ "4" ]
266
41,018
1
false
, SSTs were shown at ultrasonography to be solid and cystic adnexal masses with centrally located, multiple, round or cleft-like cysts, and two patients in our study, in one of whom the cyst was entirely solid and homogeneously echogenic, showed similar features.
[ "4" ]
, SSTs were shown at ultrasonography to be solid and cystic adnexal masses with centrally located, multiple, round or cleft-like cysts, and two patients in our study, in one of whom the cyst was entirely solid and homogeneously echogenic, showed similar features.
false
false
true
true
false
7,070