Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
1
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6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
rDNA transcription accounts for ∼60% of the transcription in a rapidly growing yeast cell.
[ "60", "61", "52", "62", "64" ]
90
7,200
0
false
rDNA transcription accounts for ∼60% of the transcription in a rapidly growing yeast cell.
[]
rDNA transcription accounts for ∼60% of the transcription in a rapidly growing yeast cell.
false
true
true
true
false
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
However, only about half of the ∼150 copies of the rDNA are active at any given time, whereas the remaining copies are maintained in a silenced state.
[ "60", "61", "52", "62", "64" ]
150
7,201
0
false
However, only about half of the ∼150 copies of the rDNA are active at any given time, whereas the remaining copies are maintained in a silenced state.
[]
However, only about half of the ∼150 copies of the rDNA are active at any given time, whereas the remaining copies are maintained in a silenced state.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
This ratio of active to inactive genes is stably propagated throughout the cell cycle and is independent of the transcriptional activity of the cell.
[ "60", "61", "52", "62", "64" ]
149
7,202
0
false
This ratio of active to inactive genes is stably propagated throughout the cell cycle and is independent of the transcriptional activity of the cell.
[]
This ratio of active to inactive genes is stably propagated throughout the cell cycle and is independent of the transcriptional activity of the cell.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
The regulatory mechanism that controls the ratio of active to inactive rDNA genes is poorly understood, but rDNA silencing is one of the factors that establish and maintain the transcriptionally inactive rDNA genes.
[ "60", "61", "52", "62", "64" ]
215
7,203
0
false
The regulatory mechanism that controls the ratio of active to inactive rDNA genes is poorly understood, but rDNA silencing is one of the factors that establish and maintain the transcriptionally inactive rDNA genes.
[]
The regulatory mechanism that controls the ratio of active to inactive rDNA genes is poorly understood, but rDNA silencing is one of the factors that establish and maintain the transcriptionally inactive rDNA genes.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
We showed that Pwp1p associates with the rDNA chromatin, and its association is dependent on the H4-tail.
[ "60", "61", "52", "62", "64" ]
105
7,204
0
false
We showed that Pwp1p associates with the rDNA chromatin, and its association is dependent on the H4-tail.
[]
We showed that Pwp1p associates with the rDNA chromatin, and its association is dependent on the H4-tail.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
The importance of the H4-tail for rDNA regulation was also suggested by studies of a mammalian nucleolar remodeling complex (NoRC) and a yeast regulator of nucleolar silencing and telophase exit (RENT) complex, which both regulate rDNA silencing.
[ "60", "61", "52", "62", "64" ]
246
7,205
0
false
The importance of the H4-tail for rDNA regulation was also suggested by studies of a mammalian nucleolar remodeling complex (NoRC) and a yeast regulator of nucleolar silencing and telophase exit (RENT) complex, which both regulate rDNA silencing.
[]
The importance of the H4-tail for rDNA regulation was also suggested by studies of a mammalian nucleolar remodeling complex (NoRC) and a yeast regulator of nucleolar silencing and telophase exit (RENT) complex, which both regulate rDNA silencing.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
The NoRC induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion, and the NoRC-directed rDNA repression requires the histone H4-tail (60,61).
[ "60", "61", "52", "62", "64" ]
161
7,206
0
false
The NoRC induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion, and the NoRC-directed rDNA repression requires the histone H4-tail.
[ "60,61" ]
The NoRC induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion, and the NoRC-directed rDNA repression requires the histone H4-tail.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
The RENT complex mediates the rDNA silencing and deacetylates the acetylated K16 of the H4-tail by Sir2p (52,62–64).
[ "60", "61", "52", "62", "64" ]
116
7,207
0
false
The RENT complex mediates the rDNA silencing and deacetylates the acetylated K16 of the H4-tail by Sir2p.
[ "52,62–64" ]
The RENT complex mediates the rDNA silencing and deacetylates the acetylated K16 of the H4-tail by Sir2p.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
These studies raised the possibility that the H4-tail binding protein that associates with the rDNA chromatin performs a role similar to that of Sir3p in the silencing at telomeric and HM loci.
[ "60", "61", "52", "62", "64" ]
193
7,208
0
false
These studies raised the possibility that the H4-tail binding protein that associates with the rDNA chromatin performs a role similar to that of Sir3p in the silencing at telomeric and HM loci.
[]
These studies raised the possibility that the H4-tail binding protein that associates with the rDNA chromatin performs a role similar to that of Sir3p in the silencing at telomeric and HM loci.
true
true
true
true
true
1,167
6
DISCUSSION
1
60
[ "b60", "b61", "b52", "b62", "b64" ]
16,855,292
pmid-11532953|pmid-16085498|pmid-12923057|pmid-10219245|pmid-15282295
Pwp1p may be the factor that links the RENT complex to the rDNA chromatin through the H4-tail.
[ "60", "61", "52", "62", "64" ]
94
7,209
0
false
Pwp1p may be the factor that links the RENT complex to the rDNA chromatin through the H4-tail.
[]
Pwp1p may be the factor that links the RENT complex to the rDNA chromatin through the H4-tail.
true
true
true
true
true
1,167
7
DISCUSSION
1
27
[ "b27", "b37", "b63", "b65", "b66" ]
16,855,292
pmid-11805826|pmid-14981505|pmid-10219244|pmid-12093911|pmid-10966455
The yTAP-C288 complex consists of eight subunits: Act1p, Eno2p, Fpr4p, Nan1p, Pol5p, Pwp1p, Smc1p and YPL207Wp (27).
[ "27", "37", "63", "65", "66" ]
116
7,210
1
false
The yTAP-C288 complex consists of eight subunits: Act1p, Eno2p, Fpr4p, Nan1p, Pol5p, Pwp1p, Smc1p and YPL207Wp.
[ "27" ]
The yTAP-C288 complex consists of eight subunits: Act1p, Eno2p, Fpr4p, Nan1p, Pol5p, Pwp1p, Smc1p and YPL207Wp.
true
true
true
true
true
1,168
7
DISCUSSION
1
27
[ "b27", "b37", "b63", "b65", "b66" ]
16,855,292
pmid-11805826|pmid-14981505|pmid-10219244|pmid-12093911|pmid-10966455
Other subunits besides Pwp1p may also function in the rDNA regulation.
[ "27", "37", "63", "65", "66" ]
70
7,211
0
false
Other subunits besides Pwp1p may also function in the rDNA regulation.
[]
Other subunits besides Pwp1p may also function in the rDNA regulation.
true
true
true
true
true
1,168
7
DISCUSSION
1
37
[ "b27", "b37", "b63", "b65", "b66" ]
16,855,292
pmid-11805826|pmid-14981505|pmid-10219244|pmid-12093911|pmid-10966455
For instance, Fpr4p binds to rDNA chromatin and regulates rDNA silencing (37); Nan1p associates with the RENT complex (63) and Pol5p is required for the synthesis of rRNA (65).
[ "27", "37", "63", "65", "66" ]
176
7,212
1
false
For instance, Fpr4p binds to rDNA chromatin and regulates rDNA silencing ; Nan1p associates with the RENT complex and Pol5p is required for the synthesis of rRNA.
[ "37", "63", "65" ]
For instance, Fpr4p binds to rDNA chromatin and regulates rDNA silencing ; Nan1p associates with the RENT complex and Pol5p is required for the synthesis of rRNA.
true
true
true
true
true
1,168
7
DISCUSSION
1
66
[ "b27", "b37", "b63", "b65", "b66" ]
16,855,292
pmid-11805826|pmid-14981505|pmid-10219244|pmid-12093911|pmid-10966455
In addition, Smc1p is a member of a ubiquitous family of chromosome-associated ATPases and plays a role in chromosome dynamics (66).
[ "27", "37", "63", "65", "66" ]
132
7,213
1
false
In addition, Smc1p is a member of a ubiquitous family of chromosome-associated ATPases and plays a role in chromosome dynamics.
[ "66" ]
In addition, Smc1p is a member of a ubiquitous family of chromosome-associated ATPases and plays a role in chromosome dynamics.
true
true
true
true
true
1,168
7
DISCUSSION
1
27
[ "b27", "b37", "b63", "b65", "b66" ]
16,855,292
pmid-11805826|pmid-14981505|pmid-10219244|pmid-12093911|pmid-10966455
Taken together, we propose that the yTAP-C228 complex associates with rDNA chromatin by the histone H4-tail and regulates rDNA transcription by modulating the chromatin structure.
[ "27", "37", "63", "65", "66" ]
179
7,214
0
false
Taken together, we propose that the yTAP-C228 complex associates with rDNA chromatin by the histone H4-tail and regulates rDNA transcription by modulating the chromatin structure.
[]
Taken together, we propose that the yTAP-C228 complex associates with rDNA chromatin by the histone H4-tail and regulates rDNA transcription by modulating the chromatin structure.
true
true
true
true
true
1,168
8
DISCUSSION
0
null
null
16,855,292
null
We compared the Mg2+-dependent oligomerized chromatins isolated from H4 tail deletion cells and wild type cells by the protein differential display approach in 2DGE, and effectively identified histone-tail binding proteins.
null
223
7,215
0
false
null
null
We compared the Mg2+-dependent oligomerized chromatins isolated from H4 tail deletion cells and wild type cells by the protein differential display approach in 2DGE, and effectively identified histone-tail binding proteins.
true
true
true
true
true
1,169
8
DISCUSSION
0
null
null
16,855,292
null
Other tail-deleted and point mutant cells are possible sources for the identification of tail-binding proteins for other core histones and specifically modified histones, respectively.
null
184
7,216
0
false
null
null
Other tail-deleted and point mutant cells are possible sources for the identification of tail-binding proteins for other core histones and specifically modified histones, respectively.
true
true
true
true
true
1,169
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,537,814
pmid-5789433|pmid-10812473
Eukaryotic gene expression is achieved by multiple layers of regulation, including transcription regulation, which requires transcription factors (TFs) to bind to their respective DNA binding sites (TFBSs) in a correct spatial and temporal manner (1).
[ "1", "2" ]
251
7,217
1
false
Eukaryotic gene expression is achieved by multiple layers of regulation, including transcription regulation, which requires transcription factors (TFs) to bind to their respective DNA binding sites (TFBSs) in a correct spatial and temporal manner.
[ "1" ]
Eukaryotic gene expression is achieved by multiple layers of regulation, including transcription regulation, which requires transcription factors (TFs) to bind to their respective DNA binding sites (TFBSs) in a correct spatial and temporal manner.
true
true
true
true
true
1,170
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,537,814
pmid-5789433|pmid-10812473
Identifying and characterizing the binding sites of TFs can permit a more comprehensive and quantitative mapping of the regulatory mechanisms within cells.
[ "1", "2" ]
155
7,218
0
false
Identifying and characterizing the binding sites of TFs can permit a more comprehensive and quantitative mapping of the regulatory mechanisms within cells.
[]
Identifying and characterizing the binding sites of TFs can permit a more comprehensive and quantitative mapping of the regulatory mechanisms within cells.
true
true
true
true
true
1,170
0
INTRODUCTION
1
2
[ "B1", "B2" ]
17,537,814
pmid-5789433|pmid-10812473
Unfortunately, TFBSs are usually short (∼5–15 bp) and degenerate (2), making it difficult to define TFBSs experimentally or computationally.
[ "1", "2" ]
140
7,219
1
false
Unfortunately, TFBSs are usually short and degenerate, making it difficult to define TFBSs experimentally or computationally.
[ "∼5–15 bp", "2" ]
Unfortunately, TFBSs are usually short and degenerate, making it difficult to define TFBSs experimentally or computationally.
true
true
true
true
true
1,170
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7" ]
17,537,814
pmid-10487868|pmid-12399584|pmid-15343339|pmid-12748633|pmid-12775844
In Saccharomyces cerevisiae, there are only a limited number of functional TFBSs that have been experimentally verified (3).
[ "3", "4", "5", "6", "7" ]
124
7,220
1
false
In Saccharomyces cerevisiae, there are only a limited number of functional TFBSs that have been experimentally verified.
[ "3" ]
In Saccharomyces cerevisiae, there are only a limited number of functional TFBSs that have been experimentally verified.
true
true
true
true
true
1,171
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7" ]
17,537,814
pmid-10487868|pmid-12399584|pmid-15343339|pmid-12748633|pmid-12775844
Inference of TFBSs has thus been relying heavily on computational approaches.
[ "3", "4", "5", "6", "7" ]
77
7,221
0
false
Inference of TFBSs has thus been relying heavily on computational approaches.
[]
Inference of TFBSs has thus been relying heavily on computational approaches.
true
true
true
true
true
1,171
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7" ]
17,537,814
pmid-10487868|pmid-12399584|pmid-15343339|pmid-12748633|pmid-12775844
A number of plausible motif consensus sequences have been deduced by different bioinformatics methods that exploit sequence information.
[ "3", "4", "5", "6", "7" ]
136
7,222
0
false
A number of plausible motif consensus sequences have been deduced by different bioinformatics methods that exploit sequence information.
[]
A number of plausible motif consensus sequences have been deduced by different bioinformatics methods that exploit sequence information.
true
true
true
true
true
1,171
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7" ]
17,537,814
pmid-10487868|pmid-12399584|pmid-15343339|pmid-12748633|pmid-12775844
However, there have been reservations on using those consensuses to annotate the genome due to excessive false positives.
[ "3", "4", "5", "6", "7" ]
121
7,223
0
false
However, there have been reservations on using those consensuses to annotate the genome due to excessive false positives.
[]
However, there have been reservations on using those consensuses to annotate the genome due to excessive false positives.
true
true
true
true
true
1,171
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7" ]
17,537,814
pmid-10487868|pmid-12399584|pmid-15343339|pmid-12748633|pmid-12775844
Fortunately, the chromatin-immunoprecipitation DNA chip (ChIP-chip) technique (4,5) provides a powerful way to verify the DNA-binding affinity of TFs.
[ "3", "4", "5", "6", "7" ]
150
7,224
0
false
Fortunately, the chromatin-immunoprecipitation DNA chip (ChIP-chip) technique provides a powerful way to verify the DNA-binding affinity of TFs.
[ "4,5" ]
Fortunately, the chromatin-immunoprecipitation DNA chip (ChIP-chip) technique provides a powerful way to verify the DNA-binding affinity of TFs.
true
true
true
true
true
1,171
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7" ]
17,537,814
pmid-10487868|pmid-12399584|pmid-15343339|pmid-12748633|pmid-12775844
In addition, phylogenetic footprinting methods that assume conservation of functional elements during evolution have been utilized to reveal TFBSs that are conserved across species (6,7).
[ "3", "4", "5", "6", "7" ]
187
7,225
0
false
In addition, phylogenetic footprinting methods that assume conservation of functional elements during evolution have been utilized to reveal TFBSs that are conserved across species.
[ "6,7" ]
In addition, phylogenetic footprinting methods that assume conservation of functional elements during evolution have been utilized to reveal TFBSs that are conserved across species.
true
true
true
true
true
1,171
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
A fair amount of confident TFBS information has been accumulated in various databases during the last few years.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
112
7,226
0
false
A fair amount of confident TFBS information has been accumulated in various databases during the last few years.
[]
A fair amount of confident TFBS information has been accumulated in various databases during the last few years.
true
true
true
true
true
1,172
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
For example, SCPD (3), SGD (8), TRANSFAC (9), YPD (10) and YEASTRACT (11) contain an array of TF motif consensus sequences derived from the literature and experimental data.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
173
7,227
1
false
For example, SCPD, SGD, TRANSFAC, YPD and YEASTRACT contain an array of TF motif consensus sequences derived from the literature and experimental data.
[ "3", "8", "9", "10", "11" ]
For example, SCPD, SGD, TRANSFAC, YPD and YEASTRACT contain an array of TF motif consensus sequences derived from the literature and experimental data.
true
true
true
true
true
1,172
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
Some of them use simple sequence matching schemes to annotate the genome, which is noisy.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
89
7,228
0
false
Some of them use simple sequence matching schemes to annotate the genome, which is noisy.
[]
Some of them use simple sequence matching schemes to annotate the genome, which is noisy.
true
true
true
true
true
1,172
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
SGD in particular remaps the TFBSs inferred by Harbison et al.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
62
7,229
0
false
SGD in particular remaps the TFBSs inferred by Harbison et al.
[]
SGD in particular remaps the TFBSs inferred by Harbison et al.
true
true
true
true
true
1,172
2
INTRODUCTION
1
5
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
(5), which took advantage of ChIP-chip data and phylogenetic information.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
73
7,230
1
false
, which took advantage of ChIP-chip data and phylogenetic information.
[ "5" ]
, which took advantage of ChIP-chip data and phylogenetic information.
false
false
true
true
false
1,172
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
However, SGD has a priori assumptions about the degree of conservation across species and binding affinities of TFs.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
116
7,231
0
false
However, SGD has a priori assumptions about the degree of conservation across species and binding affinities of TFs.
[]
However, SGD has a priori assumptions about the degree of conservation across species and binding affinities of TFs.
true
true
true
true
true
1,172
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
SwissRegulon (12,13) is another database where the site annotations were produced using several algorithms to perform on related genomes in combination with known sites from the literature, in addition to using ChIP-chip binding data.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
234
7,232
0
false
SwissRegulon is another database where the site annotations were produced using several algorithms to perform on related genomes in combination with known sites from the literature, in addition to using ChIP-chip binding data.
[ "12,13" ]
SwissRegulon is another database where the site annotations were produced using several algorithms to perform on related genomes in combination with known sites from the literature, in addition to using ChIP-chip binding data.
true
true
true
true
true
1,172
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
SwissRegulon contains a variety of experimentally verified or computationally predicted TFBSs for the entire genomes of 18 organisms.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
133
7,233
0
false
SwissRegulon contains a variety of experimentally verified or computationally predicted TFBSs for the entire genomes of 18 organisms.
[]
SwissRegulon contains a variety of experimentally verified or computationally predicted TFBSs for the entire genomes of 18 organisms.
true
true
true
true
true
1,172
2
INTRODUCTION
1
3
[ "B3", "B8", "B9", "B10", "B11", "B5", "B12", "B13" ]
17,537,814
pmid-10487868|pmid-9399804|pmid-11125113|pmid-9847145|pmid-16381908|pmid-15343339|pmid-17130146|pmid-16477324
However, SwissRegulon currently lacks information about the degree of conservation across species and related condition-specific ChIP-chip experiments for TFBSs.
[ "3", "8", "9", "10", "11", "5", "12", "13" ]
161
7,234
0
false
However, SwissRegulon currently lacks information about the degree of conservation across species and related condition-specific ChIP-chip experiments for TFBSs.
[]
However, SwissRegulon currently lacks information about the degree of conservation across species and related condition-specific ChIP-chip experiments for TFBSs.
true
true
true
true
true
1,172
3
INTRODUCTION
0
null
null
17,537,814
null
Since the degree of conservation across species and binding affinities of TFs vary among TFs, we construct a comprehensive web server, mining yeast binding sites (MYBS), which integrates several types of data related to transcriptional regulation in S. cerevisiae.
null
264
7,235
0
false
null
null
Since the degree of conservation across species and binding affinities of TFs vary among TFs, we construct a comprehensive web server, mining yeast binding sites (MYBS), which integrates several types of data related to transcriptional regulation in S. cerevisiae.
true
true
true
true
true
1,173
3
INTRODUCTION
0
null
null
17,537,814
null
Via simple motif or gene queries, MYBS allows users to apply ChIP-chip data and phylogenetic footprinting filters on genomic data to perform dynamic binding site mapping.
null
170
7,236
0
false
null
null
Via simple motif or gene queries, MYBS allows users to apply ChIP-chip data and phylogenetic footprinting filters on genomic data to perform dynamic binding site mapping.
true
true
true
true
true
1,173
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
MYBS is an interactive web-based service that integrates an array of predicted and known TFBS PWMs, DNA-binding affinity data from ChIP-chip and phylogenetic footprinting data of TFBSs in eight related yeast species.
null
216
7,237
0
false
null
null
MYBS is an interactive web-based service that integrates an array of predicted and known TFBS PWMs, DNA-binding affinity data from ChIP-chip and phylogenetic footprinting data of TFBSs in eight related yeast species.
true
true
true
true
true
1,174
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
An important feature of MYBS is its versatility and flexibility in binding site annotation.
null
91
7,238
0
false
null
null
An important feature of MYBS is its versatility and flexibility in binding site annotation.
true
true
true
true
true
1,174
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
In the process of binding site annotation, two filters can be customized according to the user's prior knowledge and confidence in the DNA-binding affinity data and phylogenic information, and MYBS reports the binding sites accordingly.
null
236
7,239
0
false
null
null
In the process of binding site annotation, two filters can be customized according to the user's prior knowledge and confidence in the DNA-binding affinity data and phylogenic information, and MYBS reports the binding sites accordingly.
true
true
true
true
true
1,174
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
Since the binding affinities and degree of conservation vary from TF to TF, the service provides an opportunity for scientists to incorporate one's knowledge and preference in the process of data retrieval.
null
206
7,240
0
false
null
null
Since the binding affinities and degree of conservation vary from TF to TF, the service provides an opportunity for scientists to incorporate one's knowledge and preference in the process of data retrieval.
true
true
true
true
true
1,174
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
The motif information is also compiled and organized in a way that is easy to query from any directions—by partial motifs, by TF or by gene.
null
140
7,241
0
false
null
null
The motif information is also compiled and organized in a way that is easy to query from any directions—by partial motifs, by TF or by gene.
true
true
true
true
true
1,174
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
As exemplified by the case study mentioned above, the regulatory associations feature could initiate and facilitate investigations by providing an intuitive look at the relationships between genes and TFs.
null
205
7,242
0
false
null
null
As exemplified by the case study mentioned above, the regulatory associations feature could initiate and facilitate investigations by providing an intuitive look at the relationships between genes and TFs.
true
true
true
true
true
1,174
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
Similarly, the identification of target genes for TF pairs could serve as a starting point for analysis of combinatorial regulation of TFs.
null
139
7,243
0
false
null
null
Similarly, the identification of target genes for TF pairs could serve as a starting point for analysis of combinatorial regulation of TFs.
true
true
true
true
true
1,174
0
DISCUSSION
0
null
null
17,537,814
pmid-5789433|pmid-10812473
Through the user-friendly interface, MYBS allows for dynamic binding site mapping, in addition to visualization and elucidation of potential regulatory relationships.
null
166
7,244
0
false
null
null
Through the user-friendly interface, MYBS allows for dynamic binding site mapping, in addition to visualization and elucidation of potential regulatory relationships.
true
true
true
true
true
1,174
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
Several studies have suggested that there are marked differences in the complement of DNA-binding domains (DBDs) in eukaryotic transcription factors (TFs) vis-à-vis their prokaryotic counterparts (1–5).
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
202
7,245
0
false
Several studies have suggested that there are marked differences in the complement of DNA-binding domains (DBDs) in eukaryotic transcription factors (TFs) vis-à-vis their prokaryotic counterparts.
[ "1–5" ]
Several studies have suggested that there are marked differences in the complement of DNA-binding domains (DBDs) in eukaryotic transcription factors (TFs) vis-à-vis their prokaryotic counterparts.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
In practically all prokaryotes studied to date, belonging to both the bacterial and archaeal super-kingdoms, the helix–turn–helix domain (HTH) is the most prevalent DBD of TFs.
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
176
7,246
0
false
In practically all prokaryotes studied to date, belonging to both the bacterial and archaeal super-kingdoms, the helix–turn–helix domain (HTH) is the most prevalent DBD of TFs.
[]
In practically all prokaryotes studied to date, belonging to both the bacterial and archaeal super-kingdoms, the helix–turn–helix domain (HTH) is the most prevalent DBD of TFs.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
TFs with HTH domains constitute >90% of TFs found in any given prokaryotic genome and show a power-law scaling in their numerical distribution with respect to proteome size (3,6,7).
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
181
7,247
0
false
TFs with HTH domains constitute >90% of TFs found in any given prokaryotic genome and show a power-law scaling in their numerical distribution with respect to proteome size.
[ "3,6,7" ]
TFs with HTH domains constitute >90% of TFs found in any given prokaryotic genome and show a power-law scaling in their numerical distribution with respect to proteome size.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
In contrast, it has been noted that most eukaryotes show lineage-specific expansions of TFs with DBDs belonging to a wide variety of structural scaffolds.
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
154
7,248
0
false
In contrast, it has been noted that most eukaryotes show lineage-specific expansions of TFs with DBDs belonging to a wide variety of structural scaffolds.
[]
In contrast, it has been noted that most eukaryotes show lineage-specific expansions of TFs with DBDs belonging to a wide variety of structural scaffolds.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
Although specific versions of the HTH domain, such as the homeodomain, are highly prevalent in crown group eukaryotes such as animals, fungi, slime moulds and plants, they are entirely absent or exceedingly rare in other eukaryotic lineages such as the diplomonads (Giardia), kinetoplastids, apicomplexans and ciliates (...
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
341
7,249
0
false
Although specific versions of the HTH domain, such as the homeodomain, are highly prevalent in crown group eukaryotes such as animals, fungi, slime moulds and plants, they are entirely absent or exceedingly rare in other eukaryotic lineages such as the diplomonads (Giardia), kinetoplastids, apicomplexans and ciliates (...
[ "3,8,9" ]
Although specific versions of the HTH domain, such as the homeodomain, are highly prevalent in crown group eukaryotes such as animals, fungi, slime moulds and plants, they are entirely absent or exceedingly rare in other eukaryotic lineages such as the diplomonads (Giardia), kinetoplastids, apicomplexans and ciliates (...
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
Similarly, TFs with DBDs of the VP1 superfamily are currently only known from plants, whereas those of the POU-type of HTH domains are found only in animals (5,10).
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
164
7,250
0
false
Similarly, TFs with DBDs of the VP1 superfamily are currently only known from plants, whereas those of the POU-type of HTH domains are found only in animals.
[ "5,10" ]
Similarly, TFs with DBDs of the VP1 superfamily are currently only known from plants, whereas those of the POU-type of HTH domains are found only in animals.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
In addition to this lineage-specific diversity, TFs of earlier branching eukaryotic groups are poorly known due to lack of experimental studies on their transcription apparatus.
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
177
7,251
0
false
In addition to this lineage-specific diversity, TFs of earlier branching eukaryotic groups are poorly known due to lack of experimental studies on their transcription apparatus.
[]
In addition to this lineage-specific diversity, TFs of earlier branching eukaryotic groups are poorly known due to lack of experimental studies on their transcription apparatus.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
These observations pose a general question regarding the origins of various eukaryotic TFs.
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
91
7,252
0
false
These observations pose a general question regarding the origins of various eukaryotic TFs.
[]
These observations pose a general question regarding the origins of various eukaryotic TFs.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
Given their structural diversity, it is clear that their evolutionary history needs to be approached on a case-by-case basis.
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
125
7,253
0
false
Given their structural diversity, it is clear that their evolutionary history needs to be approached on a case-by-case basis.
[]
Given their structural diversity, it is clear that their evolutionary history needs to be approached on a case-by-case basis.
true
true
true
true
true
1,175
0
INTRODUCTION
1
1
[ "b1", "b5", "b3", "b6", "b7", "b3", "b8", "b9", "b5", "b10" ]
17,130,173
pmid-12097341|pmid-10556324|pmid-15808743|pmid-15095866|pmid-16530225|pmid-15808743|pmid-16020728|pmid-15342554|pmid-10556324|pmid-11183772
At the same time, it is worthwhile to investigate general trends in their evolutionary trajectories, which might throw light on the causes for the apparent diversity of DBDs recruited as TFs.
[ "1", "5", "3", "6", "7", "3", "8", "9", "5", "10" ]
191
7,254
0
false
At the same time, it is worthwhile to investigate general trends in their evolutionary trajectories, which might throw light on the causes for the apparent diversity of DBDs recruited as TFs.
[]
At the same time, it is worthwhile to investigate general trends in their evolutionary trajectories, which might throw light on the causes for the apparent diversity of DBDs recruited as TFs.
true
true
true
true
true
1,175
1
INTRODUCTION
1
1
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
In structural terms, one prevalent structural category of DBDs, which appears to have been extensively used, primarily in eukaryotes, is the metal-chelating class.
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
163
7,255
0
false
In structural terms, one prevalent structural category of DBDs, which appears to have been extensively used, primarily in eukaryotes, is the metal-chelating class.
[]
In structural terms, one prevalent structural category of DBDs, which appears to have been extensively used, primarily in eukaryotes, is the metal-chelating class.
true
true
true
true
true
1,176
1
INTRODUCTION
1
1
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
Examples include the classical C2H2 Zn-finger, versions of the treble clef fold, such as the GATA type Zn-finger and the nuclear hormone receptor Zn-finger, the double-sex domain, the fungal-type bi-nuclear (C6) Zn-finger and the plant-specific SBT domain (1,11–15).
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
266
7,256
0
false
Examples include the classical C2H2 Zn-finger, versions of the treble clef fold, such as the GATA type Zn-finger and the nuclear hormone receptor Zn-finger, the double-sex domain, the fungal-type bi-nuclear (C6) Zn-finger and the plant-specific SBT domain.
[ "1,11–15" ]
Examples include the classical C2H2 Zn-finger, versions of the treble clef fold, such as the GATA type Zn-finger and the nuclear hormone receptor Zn-finger, the double-sex domain, the fungal-type bi-nuclear (C6) Zn-finger and the plant-specific SBT domain.
true
true
true
true
true
1,176
1
INTRODUCTION
1
1
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
Some of these scaffolds, e.g.
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
29
7,257
0
false
Some of these scaffolds, e.g.
[]
Some of these scaffolds, e.g.
true
true
true
true
true
1,176
1
INTRODUCTION
1
16
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
the C2H2 Zn-finger (found in low copy numbers in archaeal proteomes) (16) and the treble clef domain (found in the endonuclease VII/HNH fold DNAses), appear to be ancient and have representatives in prokaryotes (11,12,17).
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
222
7,258
1
false
the C2H2 Zn-finger (found in low copy numbers in archaeal proteomes) and the treble clef domain (found in the endonuclease VII/HNH fold DNAses), appear to be ancient and have representatives in prokaryotes.
[ "16", "11,12,17" ]
the C2H2 Zn-finger (found in low copy numbers in archaeal proteomes) and the treble clef domain (found in the endonuclease VII/HNH fold DNAses), appear to be ancient and have representatives in prokaryotes.
false
true
true
true
false
1,176
1
INTRODUCTION
1
1
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
However, the above domains, as well as eukaryote-specific Zn-chelating DBDs underwent proliferation as TFs only much later in eukaryotic evolution (11,13).
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
155
7,259
0
false
However, the above domains, as well as eukaryote-specific Zn-chelating DBDs underwent proliferation as TFs only much later in eukaryotic evolution.
[ "11,13" ]
However, the above domains, as well as eukaryote-specific Zn-chelating DBDs underwent proliferation as TFs only much later in eukaryotic evolution.
true
true
true
true
true
1,176
1
INTRODUCTION
1
1
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
Another generic trend observed in eukaryotes is the relationship between DBDs of their TFs and those found in diverse transposases, integrases and other mobile selfish elements.
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
177
7,260
0
false
Another generic trend observed in eukaryotes is the relationship between DBDs of their TFs and those found in diverse transposases, integrases and other mobile selfish elements.
[]
Another generic trend observed in eukaryotes is the relationship between DBDs of their TFs and those found in diverse transposases, integrases and other mobile selfish elements.
true
true
true
true
true
1,176
1
INTRODUCTION
1
18
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
For example, the AP2 DBD, which is highly prevalent in the TFs of plants, apicomplexans and diatom algae, is also found in the transposases of different elements and the integrase of lysogenic lambdoid phages (18).
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
214
7,261
1
false
For example, the AP2 DBD, which is highly prevalent in the TFs of plants, apicomplexans and diatom algae, is also found in the transposases of different elements and the integrase of lysogenic lambdoid phages.
[ "18" ]
For example, the AP2 DBD, which is highly prevalent in the TFs of plants, apicomplexans and diatom algae, is also found in the transposases of different elements and the integrase of lysogenic lambdoid phages.
true
true
true
true
true
1,176
1
INTRODUCTION
1
19
[ "b1", "b11", "b15", "b16", "b11", "b12", "b17", "b11", "b13", "b18", "b19", "b20", "b21", "b22" ]
17,130,173
pmid-12097341|pmid-16679012|pmid-11118137|pmid-11772643|pmid-16679012|pmid-12527760|pmid-10982859|pmid-16679012|pmid-9851918|pmid-16040597|pmid-10973053|pmid-12575992|pmid-11151303|pmid-15548737
Similarly, other DBDs such as the BED finger (19), the THAP finger (20), the Paired domain (21) and the VP1 domain are also shared by several lineage-specific eukaryotic TFs and proteins of selfish elements such as transposases, integrases and restriction endonucleases (22).
[ "1", "11", "15", "16", "11", "12", "17", "11", "13", "18", "19", "20", "21", "22" ]
275
7,262
1
false
Similarly, other DBDs such as the BED finger, the THAP finger, the Paired domain and the VP1 domain are also shared by several lineage-specific eukaryotic TFs and proteins of selfish elements such as transposases, integrases and restriction endonucleases.
[ "19", "20", "21", "22" ]
Similarly, other DBDs such as the BED finger, the THAP finger, the Paired domain and the VP1 domain are also shared by several lineage-specific eukaryotic TFs and proteins of selfish elements such as transposases, integrases and restriction endonucleases.
true
true
true
true
true
1,176
2
INTRODUCTION
1
1
[ "b1", "b15", "b23", "b24", "b23", "b25", "b26", "b26", "b27", "b28", "b31" ]
17,130,173
pmid-12097341|pmid-11118137|pmid-16106749|pmid-15629062|pmid-16106749|pmid-15875012|pmid-15705956|pmid-15705956|pmid-12682016|pmid-15806101|pmid-16449570
The WRKY domain is a Zn-chelating DBD that is lineage-specifically expanded along with MADS, AP2, VP1 and Myb domains in plant TFs (1,15,23,24).
[ "1", "15", "23", "24", "23", "25", "26", "26", "27", "28", "31" ]
144
7,263
0
false
The WRKY domain is a Zn-chelating DBD that is lineage-specifically expanded along with MADS, AP2, VP1 and Myb domains in plant TFs.
[ "1,15,23,24" ]
The WRKY domain is a Zn-chelating DBD that is lineage-specifically expanded along with MADS, AP2, VP1 and Myb domains in plant TFs.
true
true
true
true
true
1,177
2
INTRODUCTION
1
26
[ "b1", "b15", "b23", "b24", "b23", "b25", "b26", "b26", "b27", "b28", "b31" ]
17,130,173
pmid-12097341|pmid-11118137|pmid-16106749|pmid-15629062|pmid-16106749|pmid-15875012|pmid-15705956|pmid-15705956|pmid-12682016|pmid-15806101|pmid-16449570
It has also been detected in a few other eukaryotes such as Dictyostelium and Giardia (23–25), and recent structural studies have shown it to contain an unusual DBD that is believed to be distinct from most other well-characterized Zn-chelating domains (26).
[ "1", "15", "23", "24", "23", "25", "26", "26", "27", "28", "31" ]
258
7,264
1
false
It has also been detected in a few other eukaryotes such as Dictyostelium and Giardia, and recent structural studies have shown it to contain an unusual DBD that is believed to be distinct from most other well-characterized Zn-chelating domains.
[ "23–25", "26" ]
It has also been detected in a few other eukaryotes such as Dictyostelium and Giardia, and recent structural studies have shown it to contain an unusual DBD that is believed to be distinct from most other well-characterized Zn-chelating domains.
true
true
true
true
true
1,177
2
INTRODUCTION
1
1
[ "b1", "b15", "b23", "b24", "b23", "b25", "b26", "b26", "b27", "b28", "b31" ]
17,130,173
pmid-12097341|pmid-11118137|pmid-16106749|pmid-15629062|pmid-16106749|pmid-15875012|pmid-15705956|pmid-15705956|pmid-12682016|pmid-15806101|pmid-16449570
The only other Zn-chelating domain with a similar fold is the DBD of the Glial Cell Missing (GCM1) TFs of coelomate animals (26,27).
[ "1", "15", "23", "24", "23", "25", "26", "26", "27", "28", "31" ]
132
7,265
0
false
The only other Zn-chelating domain with a similar fold is the DBD of the Glial Cell Missing TFs of coelomate animals.
[ "GCM1", "26,27" ]
The only other Zn-chelating domain with a similar fold is the DBD of the Glial Cell Missing TFs of coelomate animals.
true
true
true
true
true
1,177
2
INTRODUCTION
1
1
[ "b1", "b15", "b23", "b24", "b23", "b25", "b26", "b26", "b27", "b28", "b31" ]
17,130,173
pmid-12097341|pmid-11118137|pmid-16106749|pmid-15629062|pmid-16106749|pmid-15875012|pmid-15705956|pmid-15705956|pmid-12682016|pmid-15806101|pmid-16449570
Furthermore, anecdotal observations have pointed to possible relationship between the WRKY domain and a domain conserved in transposases with the MudR-type transposase domain.
[ "1", "15", "23", "24", "23", "25", "26", "26", "27", "28", "31" ]
175
7,266
0
false
Furthermore, anecdotal observations have pointed to possible relationship between the WRKY domain and a domain conserved in transposases with the MudR-type transposase domain.
[]
Furthermore, anecdotal observations have pointed to possible relationship between the WRKY domain and a domain conserved in transposases with the MudR-type transposase domain.
true
true
true
true
true
1,177
2
INTRODUCTION
1
1
[ "b1", "b15", "b23", "b24", "b23", "b25", "b26", "b26", "b27", "b28", "b31" ]
17,130,173
pmid-12097341|pmid-11118137|pmid-16106749|pmid-15629062|pmid-16106749|pmid-15875012|pmid-15705956|pmid-15705956|pmid-12682016|pmid-15806101|pmid-16449570
The unusual phyletic patterns, unique structure, availability of different high-throughput expression and ChIP-chip data (28–31) and possible links to transposases prompted us to systematically investigate the natural history of the WRKY TFs.
[ "1", "15", "23", "24", "23", "25", "26", "26", "27", "28", "31" ]
242
7,267
0
false
The unusual phyletic patterns, unique structure, availability of different high-throughput expression and ChIP-chip data and possible links to transposases prompted us to systematically investigate the natural history of the WRKY TFs.
[ "28–31" ]
The unusual phyletic patterns, unique structure, availability of different high-throughput expression and ChIP-chip data and possible links to transposases prompted us to systematically investigate the natural history of the WRKY TFs.
true
true
true
true
true
1,177
2
INTRODUCTION
1
1
[ "b1", "b15", "b23", "b24", "b23", "b25", "b26", "b26", "b27", "b28", "b31" ]
17,130,173
pmid-12097341|pmid-11118137|pmid-16106749|pmid-15629062|pmid-16106749|pmid-15875012|pmid-15705956|pmid-15705956|pmid-12682016|pmid-15806101|pmid-16449570
We hoped that they might provide a general model for understanding evolution of lineage-specific DBDs and their expansions, as well as the rise of lineage-specific global regulatory hubs in transcriptional networks of eukaryotes.
[ "1", "15", "23", "24", "23", "25", "26", "26", "27", "28", "31" ]
229
7,268
0
false
We hoped that they might provide a general model for understanding evolution of lineage-specific DBDs and their expansions, as well as the rise of lineage-specific global regulatory hubs in transcriptional networks of eukaryotes.
[]
We hoped that they might provide a general model for understanding evolution of lineage-specific DBDs and their expansions, as well as the rise of lineage-specific global regulatory hubs in transcriptional networks of eukaryotes.
true
true
true
true
true
1,177
2
INTRODUCTION
1
1
[ "b1", "b15", "b23", "b24", "b23", "b25", "b26", "b26", "b27", "b28", "b31" ]
17,130,173
pmid-12097341|pmid-11118137|pmid-16106749|pmid-15629062|pmid-16106749|pmid-15875012|pmid-15705956|pmid-15705956|pmid-12682016|pmid-15806101|pmid-16449570
We also sought to better understand the more general connection between TFs and selfish elements by using the WRKY domain as a model.
[ "1", "15", "23", "24", "23", "25", "26", "26", "27", "28", "31" ]
133
7,269
0
false
We also sought to better understand the more general connection between TFs and selfish elements by using the WRKY domain as a model.
[]
We also sought to better understand the more general connection between TFs and selfish elements by using the WRKY domain as a model.
true
true
true
true
true
1,177
3
INTRODUCTION
0
null
null
17,130,173
null
We present below results of this study, which uncovered several novel points of interest regarding WRKY proteins.
null
113
7,270
0
false
null
null
We present below results of this study, which uncovered several novel points of interest regarding WRKY proteins.
true
true
true
true
true
1,178
3
INTRODUCTION
0
null
null
17,130,173
null
These include structural connections to other Zn-chelating domains, detection of novel versions of the WRKY domain and evidence for repeated rise of global regulatory hubs within this family in different organisms.
null
214
7,271
0
false
null
null
These include structural connections to other Zn-chelating domains, detection of novel versions of the WRKY domain and evidence for repeated rise of global regulatory hubs within this family in different organisms.
true
true
true
true
true
1,178
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b9", "b10" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
The use of RNA aptamers, short synthetic oligonucleotide sequences that bind to proteins, is emerging as a powerful tool for affinity purification, biosensors, drug discovery and medical therapy (1,2).
[ "1", "2", "3", "5", "6", "9", "10" ]
201
7,272
0
false
The use of RNA aptamers, short synthetic oligonucleotide sequences that bind to proteins, is emerging as a powerful tool for affinity purification, biosensors, drug discovery and medical therapy.
[ "1,2" ]
The use of RNA aptamers, short synthetic oligonucleotide sequences that bind to proteins, is emerging as a powerful tool for affinity purification, biosensors, drug discovery and medical therapy.
true
true
true
true
true
1,179
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5", "b6", "b9", "b10" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
Since the initial efforts in 1990 to develop in vitro methods for selecting RNA aptamers from a large combinatorial library (3–5), aptamers have been attracting considerable attention from researchers for their excellent specificity and affinity towards a variety of target molecules including drugs, peptides, proteins ...
[ "1", "2", "3", "5", "6", "9", "10" ]
347
7,273
0
false
Since the initial efforts in 1990 to develop in vitro methods for selecting RNA aptamers from a large combinatorial library, aptamers have been attracting considerable attention from researchers for their excellent specificity and affinity towards a variety of target molecules including drugs, peptides, proteins and ev...
[ "3–5", "6–9" ]
Since the initial efforts in 1990 to develop in vitro methods for selecting RNA aptamers from a large combinatorial library, aptamers have been attracting considerable attention from researchers for their excellent specificity and affinity towards a variety of target molecules including drugs, peptides, proteins and ev...
true
true
true
true
true
1,179
0
INTRODUCTION
1
10
[ "b1", "b2", "b3", "b5", "b6", "b9", "b10" ]
17,130,155
pmid-16845429|pmid-16283295|pmid-1697402|pmid-2200121|NA|pmid-12124337|pmid-16518379|pmid-12871718|NA|pmid-15516107
For example, the US FDA has recently approved for the first time the use of an aptamer in the clinical treatment of neovascular age-related macular degeneration (10).
[ "1", "2", "3", "5", "6", "9", "10" ]
166
7,274
1
false
For example, the US FDA has recently approved for the first time the use of an aptamer in the clinical treatment of neovascular age-related macular degeneration.
[ "10" ]
For example, the US FDA has recently approved for the first time the use of an aptamer in the clinical treatment of neovascular age-related macular degeneration.
true
true
true
true
true
1,179
1
INTRODUCTION
1
11
[ "b11", "b14" ]
17,130,155
pmid-14997484|pmid-15253644
The coupling of nucleic acid microarray technology with RNA aptamers has obvious benefits for the simultaneous analysis of multiple potential aptamer–protein interactions (11–14).
[ "11", "14" ]
179
7,275
0
false
The coupling of nucleic acid microarray technology with RNA aptamers has obvious benefits for the simultaneous analysis of multiple potential aptamer–protein interactions.
[ "11–14" ]
The coupling of nucleic acid microarray technology with RNA aptamers has obvious benefits for the simultaneous analysis of multiple potential aptamer–protein interactions.
true
true
true
true
true
1,180
1
INTRODUCTION
1
11
[ "b11", "b14" ]
17,130,155
pmid-14997484|pmid-15253644
RNA microarrays could be used to screen a pool of potential aptamers for binding affinity to a specific target protein conveniently in a single measurement.
[ "11", "14" ]
156
7,276
0
false
RNA microarrays could be used to screen a pool of potential aptamers for binding affinity to a specific target protein conveniently in a single measurement.
[]
RNA microarrays could be used to screen a pool of potential aptamers for binding affinity to a specific target protein conveniently in a single measurement.
true
true
true
true
true
1,180
1
INTRODUCTION
1
11
[ "b11", "b14" ]
17,130,155
pmid-14997484|pmid-15253644
Additionally, multiple protein or biomarker targets could be simultaneously identified from a biological sample by a unique adsorption pattern onto an RNA aptamer microarray.
[ "11", "14" ]
174
7,277
0
false
Additionally, multiple protein or biomarker targets could be simultaneously identified from a biological sample by a unique adsorption pattern onto an RNA aptamer microarray.
[]
Additionally, multiple protein or biomarker targets could be simultaneously identified from a biological sample by a unique adsorption pattern onto an RNA aptamer microarray.
true
true
true
true
true
1,180
1
INTRODUCTION
1
11
[ "b11", "b14" ]
17,130,155
pmid-14997484|pmid-15253644
Moreover, any proteins bound to an RNA aptamer microarray can be easily removed from the surface by denaturing the aptamer microarray either for re-use of the microarray, or for further protein analysis with additional methods such as mass spectrometry.
[ "11", "14" ]
253
7,278
0
false
Moreover, any proteins bound to an RNA aptamer microarray can be easily removed from the surface by denaturing the aptamer microarray either for re-use of the microarray, or for further protein analysis with additional methods such as mass spectrometry.
[]
Moreover, any proteins bound to an RNA aptamer microarray can be easily removed from the surface by denaturing the aptamer microarray either for re-use of the microarray, or for further protein analysis with additional methods such as mass spectrometry.
true
true
true
true
true
1,180
2
INTRODUCTION
1
12
[ "b12", "b13", "b15", "b16", "b17", "b18" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
Despite the many potential benefits of RNA microarrays, they are not yet widely used.
[ "12", "13", "15", "16", "17", "18" ]
85
7,279
0
false
Despite the many potential benefits of RNA microarrays, they are not yet widely used.
[]
Despite the many potential benefits of RNA microarrays, they are not yet widely used.
true
true
true
true
true
1,181
2
INTRODUCTION
1
12
[ "b12", "b13", "b15", "b16", "b17", "b18" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
This is most likely due to the difficulty of reproducibly fabricating and maintaining stable and uniform RNA microarrays.
[ "12", "13", "15", "16", "17", "18" ]
121
7,280
0
false
This is most likely due to the difficulty of reproducibly fabricating and maintaining stable and uniform RNA microarrays.
[]
This is most likely due to the difficulty of reproducibly fabricating and maintaining stable and uniform RNA microarrays.
true
true
true
true
true
1,181
2
INTRODUCTION
1
12
[ "b12", "b13", "b15", "b16", "b17", "b18" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
Since RNA molecules are more susceptible to enzymatic and chemical degradation as compared with DNA, many of surface attachment chemistries developed for DNA microarrays cannot be directly transferred to RNA microarray fabrication.
[ "12", "13", "15", "16", "17", "18" ]
231
7,281
0
false
Since RNA molecules are more susceptible to enzymatic and chemical degradation as compared with DNA, many of surface attachment chemistries developed for DNA microarrays cannot be directly transferred to RNA microarray fabrication.
[]
Since RNA molecules are more susceptible to enzymatic and chemical degradation as compared with DNA, many of surface attachment chemistries developed for DNA microarrays cannot be directly transferred to RNA microarray fabrication.
true
true
true
true
true
1,181
2
INTRODUCTION
1
16
[ "b12", "b13", "b15", "b16", "b17", "b18" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
Currently, most RNA microarray fabrication methods typically employ modified RNA sequences such as biotinylated RNA for immobilization on streptavidin-coated surface (12,13,15), or thiol-modified RNA for covalent attachment onto a maleimide-modified monolayer (16).
[ "12", "13", "15", "16", "17", "18" ]
265
7,282
1
false
Currently, most RNA microarray fabrication methods typically employ modified RNA sequences such as biotinylated RNA for immobilization on streptavidin-coated surface, or thiol-modified RNA for covalent attachment onto a maleimide-modified monolayer.
[ "12,13,15", "16" ]
Currently, most RNA microarray fabrication methods typically employ modified RNA sequences such as biotinylated RNA for immobilization on streptavidin-coated surface, or thiol-modified RNA for covalent attachment onto a maleimide-modified monolayer.
true
true
true
true
true
1,181
2
INTRODUCTION
1
12
[ "b12", "b13", "b15", "b16", "b17", "b18" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
These modifications can be time-consuming, difficult or costly, and can potentially lead to either cross reaction of RNA aptamers during the fabrication process or the introduction of additional proteins into the microarray.
[ "12", "13", "15", "16", "17", "18" ]
224
7,283
0
false
These modifications can be time-consuming, difficult or costly, and can potentially lead to either cross reaction of RNA aptamers during the fabrication process or the introduction of additional proteins into the microarray.
[]
These modifications can be time-consuming, difficult or costly, and can potentially lead to either cross reaction of RNA aptamers during the fabrication process or the introduction of additional proteins into the microarray.
true
true
true
true
true
1,181
2
INTRODUCTION
1
12
[ "b12", "b13", "b15", "b16", "b17", "b18" ]
17,130,155
pmid-12871718|NA|pmid-12954786|pmid-15516107|pmid-15913532|pmid-15562003|NA|pmid-11158560|pmid-16316195
Some researchers have attached unmodified RNA to surfaces by hybridization onto immobilized DNA probes (17,18); RNA microarrays formed by this method cannot endure any rigorous washing or buffer conditions that lead to denaturation of the RNA–DNA heteroduplex.
[ "12", "13", "15", "16", "17", "18" ]
260
7,284
0
false
Some researchers have attached unmodified RNA to surfaces by hybridization onto immobilized DNA probes ; RNA microarrays formed by this method cannot endure any rigorous washing or buffer conditions that lead to denaturation of the RNA–DNA heteroduplex.
[ "17,18" ]
Some researchers have attached unmodified RNA to surfaces by hybridization onto immobilized DNA probes ; RNA microarrays formed by this method cannot endure any rigorous washing or buffer conditions that lead to denaturation of the RNA–DNA heteroduplex.
true
true
true
true
true
1,181
3
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
Recently, we have demonstrated that stable RNA microarrays can be created using unmodified single-stranded RNA (ssRNA) by a covalent enzymatic ligation reaction with ssDNA immobilized onto a surface (19).
[ "19", "20", "21" ]
204
7,285
1
false
Recently, we have demonstrated that stable RNA microarrays can be created using unmodified single-stranded RNA (ssRNA) by a covalent enzymatic ligation reaction with ssDNA immobilized onto a surface.
[ "19" ]
Recently, we have demonstrated that stable RNA microarrays can be created using unmodified single-stranded RNA (ssRNA) by a covalent enzymatic ligation reaction with ssDNA immobilized onto a surface.
true
true
true
true
true
1,182
3
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
Our initial experiments utilized T4 DNA ligase for the surface ligation reaction; this enzyme unfortunately requires the use of a DNA template that can complicate the fabrication process and limit the surface ligation efficiency.
[ "19", "20", "21" ]
229
7,286
0
false
Our initial experiments utilized T4 DNA ligase for the surface ligation reaction; this enzyme unfortunately requires the use of a DNA template that can complicate the fabrication process and limit the surface ligation efficiency.
[]
Our initial experiments utilized T4 DNA ligase for the surface ligation reaction; this enzyme unfortunately requires the use of a DNA template that can complicate the fabrication process and limit the surface ligation efficiency.
true
true
true
true
true
1,182
3
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
In contrast, the enzyme T4 RNA ligase does not require a template for DNA–RNA ligation in solution (20,21).
[ "19", "20", "21" ]
107
7,287
0
false
In contrast, the enzyme T4 RNA ligase does not require a template for DNA–RNA ligation in solution.
[ "20,21" ]
In contrast, the enzyme T4 RNA ligase does not require a template for DNA–RNA ligation in solution.
true
true
true
true
true
1,182
3
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
Can we use this enzyme instead of T4 DNA ligase to simplify the RNA microarray fabrication process?
[ "19", "20", "21" ]
99
7,288
0
false
Can we use this enzyme instead of T4 DNA ligase to simplify the RNA microarray fabrication process?
[]
Can we use this enzyme instead of T4 DNA ligase to simplify the RNA microarray fabrication process?
true
true
true
true
true
1,182
3
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
In this paper, we demonstrate the successful fabrication of RNA aptamer microarrays using T4 RNA ligase to catalyze surface RNA–DNA ligation reactions.
[ "19", "20", "21" ]
151
7,289
0
false
In this paper, we demonstrate the successful fabrication of RNA aptamer microarrays using T4 RNA ligase to catalyze surface RNA–DNA ligation reactions.
[]
In this paper, we demonstrate the successful fabrication of RNA aptamer microarrays using T4 RNA ligase to catalyze surface RNA–DNA ligation reactions.
true
true
true
true
true
1,182
3
INTRODUCTION
1
19
[ "b19", "b20", "b21" ]
17,130,155
pmid-16316195|pmid-3799962|pmid-6353144
Although T4 RNA ligase has been widely applied in solution reactions, it is the first time that this enzyme has been used to ligate RNA to DNA in a surface format.
[ "19", "20", "21" ]
163
7,290
0
false
Although T4 RNA ligase has been widely applied in solution reactions, it is the first time that this enzyme has been used to ligate RNA to DNA in a surface format.
[]
Although T4 RNA ligase has been widely applied in solution reactions, it is the first time that this enzyme has been used to ligate RNA to DNA in a surface format.
true
true
true
true
true
1,182
4
INTRODUCTION
1
22
[ "b22", "b23", "b28", "b29", "b30" ]
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
The formation of a stable RNA microarray with the surface ligation chemistry is verified with surface plasmon resonance imaging (SPRI) measurements.
[ "22", "23", "28", "29", "30" ]
148
7,291
0
false
The formation of a stable RNA microarray with the surface ligation chemistry is verified with surface plasmon resonance imaging (SPRI) measurements.
[]
The formation of a stable RNA microarray with the surface ligation chemistry is verified with surface plasmon resonance imaging (SPRI) measurements.
true
true
true
true
true
1,183
4
INTRODUCTION
1
22
[ "b22", "b23", "b28", "b29", "b30" ]
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
SPRI is a multiplexed, surface-sensitive optical technique that uses changes in the local refractive index to detect adsorption onto microarrays (22).
[ "22", "23", "28", "29", "30" ]
150
7,292
1
false
SPRI is a multiplexed, surface-sensitive optical technique that uses changes in the local refractive index to detect adsorption onto microarrays.
[ "22" ]
SPRI is a multiplexed, surface-sensitive optical technique that uses changes in the local refractive index to detect adsorption onto microarrays.
true
true
true
true
true
1,183
4
INTRODUCTION
1
22
[ "b22", "b23", "b28", "b29", "b30" ]
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
SPRI measurements of microarrays have been used extensively for the study of DNA–protein, peptide–protein, protein–carbohydrate and protein–antibody interactions (23–28).
[ "22", "23", "28", "29", "30" ]
170
7,293
0
false
SPRI measurements of microarrays have been used extensively for the study of DNA–protein, peptide–protein, protein–carbohydrate and protein–antibody interactions.
[ "23–28" ]
SPRI measurements of microarrays have been used extensively for the study of DNA–protein, peptide–protein, protein–carbohydrate and protein–antibody interactions.
true
true
true
true
true
1,183
4
INTRODUCTION
1
22
[ "b22", "b23", "b28", "b29", "b30" ]
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
We have employed SPRI previously to quantitatively monitor the adsorption of DNA and RNA onto DNA microarrays (29,30).
[ "22", "23", "28", "29", "30" ]
118
7,294
0
false
We have employed SPRI previously to quantitatively monitor the adsorption of DNA and RNA onto DNA microarrays.
[ "29,30" ]
We have employed SPRI previously to quantitatively monitor the adsorption of DNA and RNA onto DNA microarrays.
true
true
true
true
true
1,183
4
INTRODUCTION
1
22
[ "b22", "b23", "b28", "b29", "b30" ]
17,130,155
pmid-11031275|pmid-16332097|pmid-12403566|pmid-11195491|pmid-16097744
Additional ex situ polarization modulation FTIR (PM-FTIR) experiments are used to further confirm the formation of an RNA monolayer.
[ "22", "23", "28", "29", "30" ]
132
7,295
0
false
Additional ex situ polarization modulation FTIR (PM-FTIR) experiments are used to further confirm the formation of an RNA monolayer.
[]
Additional ex situ polarization modulation FTIR (PM-FTIR) experiments are used to further confirm the formation of an RNA monolayer.
true
true
true
true
true
1,183
5
INTRODUCTION
1
31
[ "b31" ]
17,130,155
pmid-15053580
In addition to the fabrication of ssRNA microarrays with T4 RNA ligase, we have developed a second surface enzyme reaction for the determination of the relative surface densities of the RNA microarray elements.
[ "31" ]
210
7,296
0
false
In addition to the fabrication of ssRNA microarrays with T4 RNA ligase, we have developed a second surface enzyme reaction for the determination of the relative surface densities of the RNA microarray elements.
[]
In addition to the fabrication of ssRNA microarrays with T4 RNA ligase, we have developed a second surface enzyme reaction for the determination of the relative surface densities of the RNA microarray elements.
true
true
true
true
true
1,184
5
INTRODUCTION
1
31
[ "b31" ]
17,130,155
pmid-15053580
This second characterization reaction utilizes the enzyme RNase H to completely remove the ligated RNA from all of the microarray elements via the hydrolysis of RNA–DNA heteroduplexes on the surface.
[ "31" ]
199
7,297
0
false
This second characterization reaction utilizes the enzyme RNase H to completely remove the ligated RNA from all of the microarray elements via the hydrolysis of RNA–DNA heteroduplexes on the surface.
[]
This second characterization reaction utilizes the enzyme RNase H to completely remove the ligated RNA from all of the microarray elements via the hydrolysis of RNA–DNA heteroduplexes on the surface.
true
true
true
true
true
1,184
5
INTRODUCTION
1
31
[ "b31" ]
17,130,155
pmid-15053580
We have used RNase H previously for the ultrasensitive detection of DNA with SPRI measurements of RNA microarrays (31).
[ "31" ]
119
7,298
1
false
We have used RNase H previously for the ultrasensitive detection of DNA with SPRI measurements of RNA microarrays.
[ "31" ]
We have used RNase H previously for the ultrasensitive detection of DNA with SPRI measurements of RNA microarrays.
true
true
true
true
true
1,184
5
INTRODUCTION
1
31
[ "b31" ]
17,130,155
pmid-15053580
In this work, we use SPRI in conjunction with RNase H to measure relative surface densities by the amount of SPRI signal loss at each aptamer array element.
[ "31" ]
156
7,299
0
false
In this work, we use SPRI in conjunction with RNase H to measure relative surface densities by the amount of SPRI signal loss at each aptamer array element.
[]
In this work, we use SPRI in conjunction with RNase H to measure relative surface densities by the amount of SPRI signal loss at each aptamer array element.
true
true
true
true
true
1,184