Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
4
DISCUSSION
0
null
null
17,426,122
null
Our ChIP data suggested that the acetylation level of histone H3 tails was decreased in both cells in response to 1α,25(OH)2D3 (Figure 5).
null
138
2,300
0
false
null
null
Our ChIP data suggested that the acetylation level of histone H3 tails was decreased in both cells in response to 1α,25(OH)2D3 (Figure 5).
true
true
true
true
true
396
4
DISCUSSION
0
null
null
17,426,122
null
Interestingly, although the histone H3 acetylation levels decreased, the chromatin did not change to completely non-permissive form, because the acetylation status of the histone H4 at all regions remained constant or even increased after the addition of 1α,25(OH)2D3.
null
268
2,301
0
false
null
null
Interestingly, although the histone H3 acetylation levels decreased, the chromatin did not change to completely non-permissive form, because the acetylation status of the histone H4 at all regions remained constant or even increased after the addition of 1α,25(OH)2D3.
true
true
true
true
true
396
4
DISCUSSION
0
null
null
17,426,122
null
The acetylation level of histone H3 at control region remained constantly high and acetylation level of histone H4 increased.
null
125
2,302
0
false
null
null
The acetylation level of histone H3 at control region remained constantly high and acetylation level of histone H4 increased.
true
true
true
true
true
396
4
DISCUSSION
0
null
null
17,426,122
null
This suggests that a wide area of chromatin of distal CYP27B1 promoter is permissive in both cells in the absence of ligand, which may be related to the high basal activity of CYP27B1 gene.
null
189
2,303
0
false
null
null
This suggests that a wide area of chromatin of distal CYP27B1 promoter is permissive in both cells in the absence of ligand, which may be related to the high basal activity of CYP27B1 gene.
true
true
true
true
true
396
4
DISCUSSION
0
null
null
17,426,122
null
Addition of ligand results in local deacetylation of regions 7 and 9 together with region 2 thus leading to repression.
null
119
2,304
0
false
null
null
Addition of ligand results in local deacetylation of regions 7 and 9 together with region 2 thus leading to repression.
true
true
true
true
true
396
4
DISCUSSION
0
null
null
17,426,122
null
Neither of these histone acetylation patterns is able to describe the cell-type-selective repression described here.
null
116
2,305
0
false
null
null
Neither of these histone acetylation patterns is able to describe the cell-type-selective repression described here.
true
true
true
true
true
396
4
DISCUSSION
0
null
null
17,426,122
null
However, it is possible that other forms of histone marking such as methylation, acting alone or in combination with the histone acetylation may be involved.
null
157
2,306
0
false
null
null
However, it is possible that other forms of histone marking such as methylation, acting alone or in combination with the histone acetylation may be involved.
true
true
true
true
true
396
4
DISCUSSION
0
null
null
17,426,122
null
It is also possible that tissue-selective factors may have to be present.
null
73
2,307
0
false
null
null
It is also possible that tissue-selective factors may have to be present.
true
true
true
true
true
396
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
In both cell types, different transcription factors were associated with the nVDRE in a very similar fashion (Figure 5).
[ "35" ]
120
2,308
0
false
In both cell types, different transcription factors were associated with the nVDRE in a very similar fashion (Figure 5).
[]
In both cell types, different transcription factors were associated with the nVDRE in a very similar fashion.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
Significant differences could be observed in the recruitment of pPolII, the CoAs SRC-1 and SRC-3 and the CoR NCoR.
[ "35" ]
114
2,309
0
false
Significant differences could be observed in the recruitment of pPolII, the CoAs SRC-1 and SRC-3 and the CoR NCoR.
[]
Significant differences could be observed in the recruitment of pPolII, the CoAs SRC-1 and SRC-3 and the CoR NCoR.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
In MCF-7 cells, the VDRE1-containing region seemed to favor interactions with CoAs more than in HEK-293 cells.
[ "35" ]
110
2,310
0
false
In MCF-7 cells, the VDRE1-containing region seemed to favor interactions with CoAs more than in HEK-293 cells.
[]
In MCF-7 cells, the VDRE1-containing region seemed to favor interactions with CoAs more than in HEK-293 cells.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
Contrary to this, the region containing VDRE2/3 seemed to recruit CoRs more efficiently in HEK-293 cells than in MCF-7 cells.
[ "35" ]
125
2,311
0
false
Contrary to this, the region containing VDRE2/3 seemed to recruit CoRs more efficiently in HEK-293 cells than in MCF-7 cells.
[]
Contrary to this, the region containing VDRE2/3 seemed to recruit CoRs more efficiently in HEK-293 cells than in MCF-7 cells.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
One possible explanation is that the different cell lines possess differing levels of distinct cofactors.
[ "35" ]
105
2,312
0
false
One possible explanation is that the different cell lines possess differing levels of distinct cofactors.
[]
One possible explanation is that the different cell lines possess differing levels of distinct cofactors.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
According to the GNF SymAtlas database (35), MCF-7 and HEK-293 cells differ significantly from each other with respect to expression of SRC-1, SRC-3, NCoR1 and HDAC2, where the respective CoAs are expressed more in MCF-7 cells, whilst NCoR1 and HDAC2 are more abundant in HEK-293 cells.
[ "35" ]
286
2,313
1
false
According to the GNF SymAtlas database, MCF-7 and HEK-293 cells differ significantly from each other with respect to expression of SRC-1, SRC-3, NCoR1 and HDAC2, where the respective CoAs are expressed more in MCF-7 cells, whilst NCoR1 and HDAC2 are more abundant in HEK-293 cells.
[ "35" ]
According to the GNF SymAtlas database, MCF-7 and HEK-293 cells differ significantly from each other with respect to expression of SRC-1, SRC-3, NCoR1 and HDAC2, where the respective CoAs are expressed more in MCF-7 cells, whilst NCoR1 and HDAC2 are more abundant in HEK-293 cells.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
Thus it is possible that, although the CYP27B1 promoter is similarly permissive in both cell types, concerning the binding of transcription factors, the repression of the gene is reached only in HEK-293 cells, because some important transcription factors are missing in MCF-7 cells.
[ "35" ]
282
2,314
0
false
Thus it is possible that, although the CYP27B1 promoter is similarly permissive in both cell types, concerning the binding of transcription factors, the repression of the gene is reached only in HEK-293 cells, because some important transcription factors are missing in MCF-7 cells.
[]
Thus it is possible that, although the CYP27B1 promoter is similarly permissive in both cell types, concerning the binding of transcription factors, the repression of the gene is reached only in HEK-293 cells, because some important transcription factors are missing in MCF-7 cells.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
This could explain, at least in part, our ChIP data.
[ "35" ]
52
2,315
0
false
This could explain, at least in part, our ChIP data.
[]
This could explain, at least in part, our ChIP data.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
Interestingly, the binding profiles of transcription factors at different regions were very similar, especially in HEK-293 cells.
[ "35" ]
129
2,316
0
false
Interestingly, the binding profiles of transcription factors at different regions were very similar, especially in HEK-293 cells.
[]
Interestingly, the binding profiles of transcription factors at different regions were very similar, especially in HEK-293 cells.
true
true
true
true
true
397
5
DISCUSSION
1
35
[ "B35" ]
17,426,122
pmid-11904358
This suggests that it is possible that different regions may be connected with each other via chromatin looping and therefore the output of single antibody ChIP analysis of the distal and proximal regions actually represents the same super complex of transcription factors.
[ "35" ]
273
2,317
0
false
This suggests that it is possible that different regions may be connected with each other via chromatin looping and therefore the output of single antibody ChIP analysis of the distal and proximal regions actually represents the same super complex of transcription factors.
[]
This suggests that it is possible that different regions may be connected with each other via chromatin looping and therefore the output of single antibody ChIP analysis of the distal and proximal regions actually represents the same super complex of transcription factors.
true
true
true
true
true
397
6
DISCUSSION
0
null
null
17,426,122
null
This hypothesis is supported by the fact that our 3C analysis confirmed that the proximal and distal regions of the human CYP27B1 gene promoter are in contact with each other (Figure 6).
null
186
2,318
0
false
null
null
This hypothesis is supported by the fact that our 3C analysis confirmed that the proximal and distal regions of the human CYP27B1 gene promoter are in contact with each other (Figure 6).
true
true
true
true
true
398
6
DISCUSSION
0
null
null
17,426,122
null
From the results, it can be observed that in MCF-7 cells region 7 (containing VDRE1) is connected to the region containing the TSS in a ligand-dependent manner, but the region containing VDRE2/3 does not form any similar connections.
null
233
2,319
0
false
null
null
From the results, it can be observed that in MCF-7 cells region 7 (containing VDRE1) is connected to the region containing the TSS in a ligand-dependent manner, but the region containing VDRE2/3 does not form any similar connections.
true
true
true
true
true
398
6
DISCUSSION
0
null
null
17,426,122
null
In contrast to this, in HEK-293 cells, regions encompassing both VDRE1 and VDRE2/3 were connected with a region containing the TSS of the CYP27B1 gene.
null
151
2,320
0
false
null
null
In contrast to this, in HEK-293 cells, regions encompassing both VDRE1 and VDRE2/3 were connected with a region containing the TSS of the CYP27B1 gene.
true
true
true
true
true
398
6
DISCUSSION
0
null
null
17,426,122
null
The connection between the VDRE1-containing region and the proximal promoter was present both in the absence and in the presence of ligand.
null
139
2,321
0
false
null
null
The connection between the VDRE1-containing region and the proximal promoter was present both in the absence and in the presence of ligand.
true
true
true
true
true
398
6
DISCUSSION
0
null
null
17,426,122
null
However, the most striking result was that VDRE2/3-containing region was only in contact with the proximal promoter when 1α,25(OH)2D3 was present.
null
146
2,322
0
false
null
null
However, the most striking result was that VDRE2/3-containing region was only in contact with the proximal promoter when 1α,25(OH)2D3 was present.
true
true
true
true
true
398
6
DISCUSSION
0
null
null
17,426,122
null
This suggests that VDRE1-containing region seems to be related more with basal (positive) transcriptional activity and that the VDRE2/3-containing region may have an important role in transcriptional repression.
null
211
2,323
0
false
null
null
This suggests that VDRE1-containing region seems to be related more with basal (positive) transcriptional activity and that the VDRE2/3-containing region may have an important role in transcriptional repression.
true
true
true
true
true
398
6
DISCUSSION
0
null
null
17,426,122
null
Please note that because there were no restriction-enzyme-cutting sites between the nVDRE and the TSS, it was impossible to determine exactly if VDRE1 or VDRE2/3 are connected to the nVDRE or TSS or both.
null
204
2,324
0
false
null
null
Please note that because there were no restriction-enzyme-cutting sites between the nVDRE and the TSS, it was impossible to determine exactly if VDRE1 or VDRE2/3 are connected to the nVDRE or TSS or both.
true
true
true
true
true
398
6
DISCUSSION
0
null
null
17,426,122
null
In this case, the 3C analysis only reveals that the distal regions are connected with the proximal region that contains both the nVDRE and TSS.
null
143
2,325
0
false
null
null
In this case, the 3C analysis only reveals that the distal regions are connected with the proximal region that contains both the nVDRE and TSS.
true
true
true
true
true
398
7
DISCUSSION
0
null
null
17,426,122
null
In the light of our results presented here, we propose a model that may explain the role of distal VDREs in the transcriptional regulation of CYP27B1 gene in HEK-293 cells (Figure 7).
null
183
2,326
0
false
null
null
In the light of our results presented here, we propose a model that may explain the role of distal VDREs in the transcriptional regulation of CYP27B1 gene in HEK-293 cells (Figure 7).
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
When the gene is active, chromatin looping brings the distal region, which includes VDRE1, close to the proximal promoter.
null
122
2,327
0
false
null
null
When the gene is active, chromatin looping brings the distal region, which includes VDRE1, close to the proximal promoter.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
Both regions associate with a common super complex of transcription factors that is broadly transcriptionally positive and includes CoAs such as SRC-1, SRC-2, SRC-3 and CBP.
null
173
2,328
0
false
null
null
Both regions associate with a common super complex of transcription factors that is broadly transcriptionally positive and includes CoAs such as SRC-1, SRC-2, SRC-3 and CBP.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
The nVDRE is connected via VDIR, but the anchoring transcription factor at VDRE1 is presently unknown.
null
102
2,329
0
false
null
null
The nVDRE is connected via VDIR, but the anchoring transcription factor at VDRE1 is presently unknown.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
We cannot either exclude the possibility that the ligand-independent looping happens via some other element that locates close to VDRE1.
null
136
2,330
0
false
null
null
We cannot either exclude the possibility that the ligand-independent looping happens via some other element that locates close to VDRE1.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
The HAT activity of CBP acetylates the histone H3 tails and thus keeps the chromatin at proximal promoter permissive for basal transcriptional machinery including pPolII.
null
170
2,331
0
false
null
null
The HAT activity of CBP acetylates the histone H3 tails and thus keeps the chromatin at proximal promoter permissive for basal transcriptional machinery including pPolII.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
The region containing VDRE2/3 on the other hand is not involved in the transcriptional activation of the CYP27B1 gene as can be inferred from its non-connectedness to the TSS-containing region in MCF-7 cells.
null
208
2,332
0
false
null
null
The region containing VDRE2/3 on the other hand is not involved in the transcriptional activation of the CYP27B1 gene as can be inferred from its non-connectedness to the TSS-containing region in MCF-7 cells.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
However, it seems to recruit several transcription factors including repressive proteins, which are missing from the super complex associated with the nVDRE- and VDRE1-containing chromatin regions, selectively in HEK-293 cells.
null
227
2,333
0
false
null
null
However, it seems to recruit several transcription factors including repressive proteins, which are missing from the super complex associated with the nVDRE- and VDRE1-containing chromatin regions, selectively in HEK-293 cells.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
This suggests that a different complex is bound to this region, but the purpose of this complex is presently unknown as well as how the protein complex is associated with the region containing VDRE2/3.
null
201
2,334
0
false
null
null
This suggests that a different complex is bound to this region, but the purpose of this complex is presently unknown as well as how the protein complex is associated with the region containing VDRE2/3.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
The addition of 1α,25(OH)2D3 results in the modulation of the super complex where activating transcription factors are replaced with repressing proteins.
null
153
2,335
0
false
null
null
The addition of 1α,25(OH)2D3 results in the modulation of the super complex where activating transcription factors are replaced with repressing proteins.
true
true
true
true
true
399
7
DISCUSSION
0
null
null
17,426,122
null
At the same time, the chromatin architecture changes and chromatin looping locates VDRE2/3
null
90
2,336
0
false
null
null
At the same time, the chromatin architecture changes and chromatin looping locates VDRE2/3
true
true
false
true
false
399
7
DISCUSSION
0
null
null
17,426,122
null
close to proximal promoter allowing it to associate with a common repressive super complex together with nVDRE and VDRE1.
null
121
2,337
0
false
null
null
close to proximal promoter allowing it to associate with a common repressive super complex together with nVDRE and VDRE1.
false
true
true
true
false
399
7
DISCUSSION
0
null
null
17,426,122
null
Figure 7.A model representing the crosstalk of distal and proximal promoter regions during the transcriptional regulation of the CYP27B1 gene.
null
142
2,338
0
false
null
null
Figure 7.A model representing the crosstalk of distal and proximal promoter regions during the transcriptional regulation of the CYP27B1 gene.
true
true
true
true
true
399
8
DISCUSSION
0
null
null
17,426,122
null
A model representing the crosstalk of distal and proximal promoter regions during the transcriptional regulation of the CYP27B1 gene.
null
133
2,339
0
false
null
null
A model representing the crosstalk of distal and proximal promoter regions during the transcriptional regulation of the CYP27B1 gene.
true
true
true
true
true
400
9
DISCUSSION
0
null
null
17,426,122
null
In conclusion, we have revealed that the responsiveness of the CYP27B1 gene to 1α,25(OH)2D3 is a cell-type-selective event that involves different combinations of multiple VDREs that act to recruit and interact with protein super complexes of differing transcriptional abilities.
null
279
2,340
0
false
null
null
In conclusion, we have revealed that the responsiveness of the CYP27B1 gene to 1α,25(OH)2D3 is a cell-type-selective event that involves different combinations of multiple VDREs that act to recruit and interact with protein super complexes of differing transcriptional abilities.
true
true
true
true
true
401
9
DISCUSSION
0
null
null
17,426,122
null
It is hoped that this work will allow us to understand better gene repression by nuclear receptors in general and the tissue-selective nature of the CYP27B1 gene repression by 1α,25(OH)2D3 specifically.
null
202
2,341
0
false
null
null
It is hoped that this work will allow us to understand better gene repression by nuclear receptors in general and the tissue-selective nature of the CYP27B1 gene repression by 1α,25(OH)2D3 specifically.
true
true
true
true
true
401
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B5", "B6", "B7" ]
17,576,670
pmid-15556037|pmid-16845074|pmid-16845069|pmid-17094254|pmid-11741530|pmid-15146492|pmid-12784359
The high-throughput functional identification and structural characterization of transcriptional networks are major objectives of post-genomic research (1–4).
[ "1–4", "5", "6", "7" ]
158
2,342
1
false
The high-throughput functional identification and structural characterization of transcriptional networks are major objectives of post-genomic research.
[ "1–4" ]
The high-throughput functional identification and structural characterization of transcriptional networks are major objectives of post-genomic research.
true
true
true
true
true
402
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B5", "B6", "B7" ]
17,576,670
pmid-15556037|pmid-16845074|pmid-16845069|pmid-17094254|pmid-11741530|pmid-15146492|pmid-12784359
Predictive methods have an important role to play in this endeavor since the large number of protein/DNA and protein/protein interactions involved in transcriptional regulation precludes their systematic study by X-ray crystallography or NMR.
[ "1–4", "5", "6", "7" ]
242
2,343
0
false
Predictive methods have an important role to play in this endeavor since the large number of protein/DNA and protein/protein interactions involved in transcriptional regulation precludes their systematic study by X-ray crystallography or NMR.
[]
Predictive methods have an important role to play in this endeavor since the large number of protein/DNA and protein/protein interactions involved in transcriptional regulation precludes their systematic study by X-ray crystallography or NMR.
true
true
true
true
true
402
0
INTRODUCTION
1
5
[ "B1 B2 B3 B4", "B5", "B6", "B7" ]
17,576,670
pmid-15556037|pmid-16845074|pmid-16845069|pmid-17094254|pmid-11741530|pmid-15146492|pmid-12784359
Since transcription factor families are generally specified by highly conserved consensus DNA-binding domains (DBD) as well as common strategies of interaction with target DNA (5) DBD homology modeling is a particularly relevant approach (see (6) and references herein).
[ "1–4", "5", "6", "7" ]
270
2,344
1
false
Since transcription factor families are generally specified by highly conserved consensus DNA-binding domains (DBD) as well as common strategies of interaction with target DNA DBD homology modeling is a particularly relevant approach and references herein).
[ "5", "see (6" ]
Since transcription factor families are generally specified by highly conserved consensus DNA-binding domains (DBD) as well as common strategies of interaction with target DNA DBD homology modeling is a particularly relevant approach and references herein).
true
true
true
true
true
402
0
INTRODUCTION
1
7
[ "B1 B2 B3 B4", "B5", "B6", "B7" ]
17,576,670
pmid-15556037|pmid-16845074|pmid-16845069|pmid-17094254|pmid-11741530|pmid-15146492|pmid-12784359
Equally, the prepositioning of a DBD within its DNA-binding site can often be inferred by homology, a step that most docking programs cannot yet address ab initio (7).
[ "1–4", "5", "6", "7" ]
167
2,345
1
false
Equally, the prepositioning of a DBD within its DNA-binding site can often be inferred by homology, a step that most docking programs cannot yet address ab initio.
[ "7" ]
Equally, the prepositioning of a DBD within its DNA-binding site can often be inferred by homology, a step that most docking programs cannot yet address ab initio.
true
true
true
true
true
402
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B5", "B6", "B7" ]
17,576,670
pmid-15556037|pmid-16845074|pmid-16845069|pmid-17094254|pmid-11741530|pmid-15146492|pmid-12784359
However, despite these advantages, the prediction of DBD/DNA complex 3D structures is by no means straightforward, as exemplified by complexes involving the POU DBD.
[ "1–4", "5", "6", "7" ]
165
2,346
0
false
However, despite these advantages, the prediction of DBD/DNA complex 3D structures is by no means straightforward, as exemplified by complexes involving the POU DBD.
[]
However, despite these advantages, the prediction of DBD/DNA complex 3D structures is by no means straightforward, as exemplified by complexes involving the POU DBD.
true
true
true
true
true
402
1
INTRODUCTION
1
8
[ "B8", "B9" ]
17,576,670
pmid-10199551|pmid-8156594
The ‘POU’ (acronym of Pit, Oct, Unc) family of transcription factors is defined on the basis of a common DBD of approximately 160 residues, first identified in the mammalian proteins Pit-1 and Oct-1 and the nematode factor Unc-86
[ "8", "9" ]
229
2,347
0
false
The ‘POU’ (acronym of Pit, Oct, Unc) family of transcription factors is defined on the basis of a common DBD of approximately 160 residues, first identified in the mammalian proteins Pit-1 and Oct-1 and the nematode factor Unc-86
[]
The ‘POU’ (acronym of Pit, Oct, Unc) family of transcription factors is defined on the basis of a common DBD of approximately 160 residues, first identified in the mammalian proteins Pit-1 and Oct-1 and the nematode factor Unc-86
true
true
false
true
false
403
1
INTRODUCTION
1
8
[ "B8", "B9" ]
17,576,670
pmid-10199551|pmid-8156594
[for a review, see (8)].
[ "8", "9" ]
24
2,348
0
false
.
[ "for a review, see (8)" ]
.
false
false
true
true
false
403
1
INTRODUCTION
1
8
[ "B8", "B9" ]
17,576,670
pmid-10199551|pmid-8156594
The POU DBD comprises two distinct, highly conserved sub-domains, termed ‘POUs’ and ‘POUh’, which contain respectively four and three α-helices and are connected by a flexible linker, variable in sequence and length.
[ "8", "9" ]
216
2,349
0
false
The POU DBD comprises two distinct, highly conserved sub-domains, termed ‘POUs’ and ‘POUh’, which contain respectively four and three α-helices and are connected by a flexible linker, variable in sequence and length.
[]
The POU DBD comprises two distinct, highly conserved sub-domains, termed ‘POUs’ and ‘POUh’, which contain respectively four and three α-helices and are connected by a flexible linker, variable in sequence and length.
true
true
true
true
true
403
1
INTRODUCTION
1
9
[ "B8", "B9" ]
17,576,670
pmid-10199551|pmid-8156594
The crystallographic structure of the complex between the POU domain of the ubiquitous protein Oct-1 and the octamer ATGCAAAT has revealed that POUs interacts with the tetramer ATGC in a similar fashion to the phage repressors, whereas the POUh interaction with the tretramer AAAT resembles that of a homeodomain (9).
[ "8", "9" ]
317
2,350
1
false
The crystallographic structure of the complex between the POU domain of the ubiquitous protein Oct-1 and the octamer ATGCAAAT has revealed that POUs interacts with the tetramer ATGC in a similar fashion to the phage repressors, whereas the POUh interaction with the tretramer AAAT resembles that of a homeodomain.
[ "9" ]
The crystallographic structure of the complex between the POU domain of the ubiquitous protein Oct-1 and the octamer ATGCAAAT has revealed that POUs interacts with the tetramer ATGC in a similar fashion to the phage repressors, whereas the POUh interaction with the tretramer AAAT resembles that of a homeodomain.
true
true
true
true
true
403
2
INTRODUCTION
1
10
[ "B10", "B11 B12 B13" ]
17,576,670
pmid-7622033|pmid-9009203|pmid-11583619|pmid-11073444
If all the POU domains can bind to the prototypic octamer ATGCAAAT, they also recognize numerous other AT-rich sequences due to the flexibility of the linker joining the two sub-domains (10).
[ "10", "11–13" ]
191
2,351
1
false
If all the POU domains can bind to the prototypic octamer ATGCAAAT, they also recognize numerous other AT-rich sequences due to the flexibility of the linker joining the two sub-domains.
[ "10" ]
If all the POU domains can bind to the prototypic octamer ATGCAAAT, they also recognize numerous other AT-rich sequences due to the flexibility of the linker joining the two sub-domains.
true
true
true
true
true
404
2
INTRODUCTION
1
11–13
[ "B10", "B11 B12 B13" ]
17,576,670
pmid-7622033|pmid-9009203|pmid-11583619|pmid-11073444
Remarkably, crystallographic structures of various Pit-1 or Oct-1 POU/DNA complexes have shown that the cis elements of a DNA target recognized respectively by POUs and POUh neither have to be contiguous nor even to belong to the same DNA strand (11–13).
[ "10", "11–13" ]
254
2,352
1
false
Remarkably, crystallographic structures of various Pit-1 or Oct-1 POU/DNA complexes have shown that the cis elements of a DNA target recognized respectively by POUs and POUh neither have to be contiguous nor even to belong to the same DNA strand.
[ "11–13" ]
Remarkably, crystallographic structures of various Pit-1 or Oct-1 POU/DNA complexes have shown that the cis elements of a DNA target recognized respectively by POUs and POUh neither have to be contiguous nor even to belong to the same DNA strand.
true
true
true
true
true
404
2
INTRODUCTION
1
10
[ "B10", "B11 B12 B13" ]
17,576,670
pmid-7622033|pmid-9009203|pmid-11583619|pmid-11073444
Taken together, these structures have revealed two distinct patterns of POU homodimerization, based on different relative positionings of POUs and POUh, and depending on the type of DNA target.
[ "10", "11–13" ]
193
2,353
0
false
Taken together, these structures have revealed two distinct patterns of POU homodimerization, based on different relative positionings of POUs and POUh, and depending on the type of DNA target.
[]
Taken together, these structures have revealed two distinct patterns of POU homodimerization, based on different relative positionings of POUs and POUh, and depending on the type of DNA target.
true
true
true
true
true
404
2
INTRODUCTION
1
10
[ "B10", "B11 B12 B13" ]
17,576,670
pmid-7622033|pmid-9009203|pmid-11583619|pmid-11073444
The ‘PORE’ (Palindromic Oct-1 Responsive Elements) DNA motifs induce a POU conformation similar to that found in the initial Oct-1 POU/octamer complex.
[ "10", "11–13" ]
151
2,354
0
false
The ‘PORE’ (Palindromic Oct-1 Responsive Elements) DNA motifs induce a POU conformation similar to that found in the initial Oct-1 POU/octamer complex.
[]
The ‘PORE’ DNA motifs induce a POU conformation similar to that found in the initial Oct-1 POU/octamer complex.
true
true
true
true
true
404
2
INTRODUCTION
1
10
[ "B10", "B11 B12 B13" ]
17,576,670
pmid-7622033|pmid-9009203|pmid-11583619|pmid-11073444
By contrast, the ‘MORE’ (More palindromic Oct-1 Responsive Element) DNA motifs elicit a POU conformation analogous to that first discovered in Pit-1 POU/DNA complexes.
[ "10", "11–13" ]
167
2,355
0
false
By contrast, the ‘MORE’ (More palindromic Oct-1 Responsive Element) DNA motifs elicit a POU conformation analogous to that first discovered in Pit-1 POU/DNA complexes.
[]
By contrast, the ‘MORE’ DNA motifs elicit a POU conformation analogous to that first discovered in Pit-1 POU/DNA complexes.
true
true
true
true
true
404
3
INTRODUCTION
1
14
[ "B14", "B15 B16 B17 B18", "B19" ]
17,576,670
pmid-8274283|pmid-7478537|pmid-8873046|pmid-7651733|pmid-15024080|pmid-15767276
N-Oct-3, the human equivalent of the mouse Brn-2 protein, is widely expressed in the developing central nervous system, and necessary to maintain neural cell differentiation (14).
[ "14", "15–18", "19" ]
179
2,356
1
false
N-Oct-3, the human equivalent of the mouse Brn-2 protein, is widely expressed in the developing central nervous system, and necessary to maintain neural cell differentiation.
[ "14" ]
N-Oct-3, the human equivalent of the mouse Brn-2 protein, is widely expressed in the developing central nervous system, and necessary to maintain neural cell differentiation.
true
true
true
true
true
405
3
INTRODUCTION
1
15–18
[ "B14", "B15 B16 B17 B18", "B19" ]
17,576,670
pmid-8274283|pmid-7478537|pmid-8873046|pmid-7651733|pmid-15024080|pmid-15767276
It is also implicated in the development of the neural-crest-derived melanocytic lineage and its over-expression in melanocytes leads to tumorigenesis via the dysregulation of a number of genes (15–18).
[ "14", "15–18", "19" ]
202
2,357
1
false
It is also implicated in the development of the neural-crest-derived melanocytic lineage and its over-expression in melanocytes leads to tumorigenesis via the dysregulation of a number of genes.
[ "15–18" ]
It is also implicated in the development of the neural-crest-derived melanocytic lineage and its over-expression in melanocytes leads to tumorigenesis via the dysregulation of a number of genes.
true
true
true
true
true
405
3
INTRODUCTION
1
14
[ "B14", "B15 B16 B17 B18", "B19" ]
17,576,670
pmid-8274283|pmid-7478537|pmid-8873046|pmid-7651733|pmid-15024080|pmid-15767276
The fact that N-Oct-3 can interact with such a variety of targets is due to the structural plasticity of its POU domain.
[ "14", "15–18", "19" ]
120
2,358
0
false
The fact that N-Oct-3 can interact with such a variety of targets is due to the structural plasticity of its POU domain.
[]
The fact that N-Oct-3 can interact with such a variety of targets is due to the structural plasticity of its POU domain.
true
true
true
true
true
405
3
INTRODUCTION
1
19
[ "B14", "B15 B16 B17 B18", "B19" ]
17,576,670
pmid-8274283|pmid-7478537|pmid-8873046|pmid-7651733|pmid-15024080|pmid-15767276
In a previous report (19), we have shown that the N-Oct-3 DBD, in addition to forming the classical homodimers in association with PORE and MORE sequences, can also adopt a novel mode of homodimerization when bound to a set of neuronal promoters, including the CRH (corticotropin-releasing hormone) gene promoter.
[ "14", "15–18", "19" ]
313
2,359
1
false
In a previous report, we have shown that the N-Oct-3 DBD, in addition to forming the classical homodimers in association with PORE and MORE sequences, can also adopt a novel mode of homodimerization when bound to a set of neuronal promoters, including the CRH (corticotropin-releasing hormone) gene promoter.
[ "19" ]
In a previous report, we have shown that the N-Oct-3 DBD, in addition to forming the classical homodimers in association with PORE and MORE sequences, can also adopt a novel mode of homodimerization when bound to a set of neuronal promoters, including the CRH (corticotropin-releasing hormone) gene promoter.
true
true
true
true
true
405
3
INTRODUCTION
1
14
[ "B14", "B15 B16 B17 B18", "B19" ]
17,576,670
pmid-8274283|pmid-7478537|pmid-8873046|pmid-7651733|pmid-15024080|pmid-15767276
We have demonstrated that this pattern is induced by a structural motif that we have termed ‘NORE’ (N-Oct-3 Responsive Element).
[ "14", "15–18", "19" ]
128
2,360
0
false
We have demonstrated that this pattern is induced by a structural motif that we have termed ‘NORE’ (N-Oct-3 Responsive Element).
[]
We have demonstrated that this pattern is induced by a structural motif that we have termed ‘NORE’ (N-Oct-3 Responsive Element).
true
true
true
true
true
405
4
INTRODUCTION
0
null
null
17,576,670
null
In the current study, we have used a combination of hydrodynamic methods, DNA footprinting experiments, molecular modeling and small angle X-ray scattering (SAXS) to address the following questions: (i) How should the N-Oct-3-binding site within the HLA DRα promoter be read structurally and translated into a new POU do...
null
349
2,361
0
false
null
null
In the current study, we have used a combination of hydrodynamic methods, DNA footprinting experiments, molecular modeling and small angle X-ray scattering (SAXS) to address the following questions: (i) How should the N-Oct-3-binding site within the HLA DRα promoter be read structurally and translated into a new POU do...
true
true
true
true
true
406
4
INTRODUCTION
0
null
null
17,576,670
null
(ii) How do transitions between free and bound conformations occur and what are the molecular mechanisms involved?
null
114
2,362
0
false
null
null
(ii) How do transitions between free and bound conformations occur and what are the molecular mechanisms involved?
false
false
true
true
false
406
4
INTRODUCTION
0
null
null
17,576,670
null
Our results lead us to conclude that there might exist a continuous spectrum of free and ‘pre-bound’ N-Oct-3 POU conformations.
null
127
2,363
0
false
null
null
Our results lead us to conclude that there might exist a continuous spectrum of free and ‘pre-bound’ N-Oct-3 POU conformations.
true
true
true
true
true
406
4
INTRODUCTION
0
null
null
17,576,670
null
In addition, a specific pair of glycine residues in the linker likely acts as a major conformational switch.
null
108
2,364
0
false
null
null
In addition, a specific pair of glycine residues in the linker likely acts as a major conformational switch.
true
true
true
true
true
406
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,612
pmid-9023104|pmid-14704338|pmid-17071718
The vast majority of new tRNA gene sequence data accumulates today from analysis of genome sequences.
[ "1", "2", "3" ]
101
2,365
0
false
The vast majority of new tRNA gene sequence data accumulates today from analysis of genome sequences.
[]
The vast majority of new tRNA gene sequence data accumulates today from analysis of genome sequences.
true
true
true
true
true
407
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,612
pmid-9023104|pmid-14704338|pmid-17071718
The major tRNA gene-finders in use today, tRNAscan-SE (1) and ARAGORN (2), classify the functions of predicted tRNA genes by structurally locating and decoding their inferred anticodons according to an assumed genetic code.
[ "1", "2", "3" ]
223
2,366
1
false
The major tRNA gene-finders in use today, tRNAscan-SE and ARAGORN, classify the functions of predicted tRNA genes by structurally locating and decoding their inferred anticodons according to an assumed genetic code.
[ "1", "2" ]
The major tRNA gene-finders in use today, tRNAscan-SE and ARAGORN, classify the functions of predicted tRNA genes by structurally locating and decoding their inferred anticodons according to an assumed genetic code.
true
true
true
true
true
407
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,612
pmid-9023104|pmid-14704338|pmid-17071718
As a result, genome projects regularly misclassify initiator tRNAs in genomes from all three phylogenetic domains and lysylated isoleucine tRNA (kIle) genes from bacteria (described further below).
[ "1", "2", "3" ]
197
2,367
0
false
As a result, genome projects regularly misclassify initiator tRNAs in genomes from all three phylogenetic domains and lysylated isoleucine tRNA (kIle) genes from bacteria (described further below).
[]
As a result, genome projects regularly misclassify initiator tRNAs in genomes from all three phylogenetic domains and lysylated isoleucine tRNA (kIle) genes from bacteria (described further below).
true
true
true
true
true
407
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,612
pmid-9023104|pmid-14704338|pmid-17071718
These two types of tRNAs carry the same genetically templated anticodons as methionine elongators and hence cannot be distinguished from them by anticodon-based tRNA classifiers.
[ "1", "2", "3" ]
178
2,368
0
false
These two types of tRNAs carry the same genetically templated anticodons as methionine elongators and hence cannot be distinguished from them by anticodon-based tRNA classifiers.
[]
These two types of tRNAs carry the same genetically templated anticodons as methionine elongators and hence cannot be distinguished from them by anticodon-based tRNA classifiers.
true
true
true
true
true
407
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,612
pmid-9023104|pmid-14704338|pmid-17071718
It may also happen that these genes are entirely missing in the annotation of a complete genome.
[ "1", "2", "3" ]
96
2,369
0
false
It may also happen that these genes are entirely missing in the annotation of a complete genome.
[]
It may also happen that these genes are entirely missing in the annotation of a complete genome.
true
true
true
true
true
407
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,612
pmid-9023104|pmid-14704338|pmid-17071718
Because genome projects regularly verify the completion of their assemblies by checking for the presence of a complete set of tRNA gene classes in their genome data, the ability to identify these two additional classes of tRNA genes provides additional power for this important task [although in very rare cases the lysy...
[ "1", "2", "3" ]
402
2,370
0
false
Because genome projects regularly verify the completion of their assemblies by checking for the presence of a complete set of tRNA gene classes in their genome data, the ability to identify these two additional classes of tRNA genes provides additional power for this important task.
[ "although in very rare cases the lysylated isoacceptor may be missing along with corresponding metabolic pathways (3)" ]
Because genome projects regularly verify the completion of their assemblies by checking for the presence of a complete set of tRNA gene classes in their genome data, the ability to identify these two additional classes of tRNA genes provides additional power for this important task.
true
true
true
true
true
407
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,612
pmid-9023104|pmid-14704338|pmid-17071718
Furthermore, a method that uses entire sequence information to classify tRNA gene function is more robust to sequencing error, can correctly predict tRNA charging specificity in organisms with altered genetic codes, can predict the identity of suppressors, and can predict the potential or former charging identity of tR...
[ "1", "2", "3" ]
437
2,371
0
false
Furthermore, a method that uses entire sequence information to classify tRNA gene function is more robust to sequencing error, can correctly predict tRNA charging specificity in organisms with altered genetic codes, can predict the identity of suppressors, and can predict the potential or former charging identity of tR...
[]
Furthermore, a method that uses entire sequence information to classify tRNA gene function is more robust to sequencing error, can correctly predict tRNA charging specificity in organisms with altered genetic codes, can predict the identity of suppressors, and can predict the potential or former charging identity of tR...
true
true
true
true
true
407
1
INTRODUCTION
1
4
[ "B4" ]
17,591,612
pmid-16473847
We present here a new version (1.0) of such a method—an update to the TFAM statistical classifier of tRNA function published earlier (4).
[ "4" ]
137
2,372
1
false
We present here a new version (1.0) of such a method—an update to the TFAM statistical classifier of tRNA function published earlier.
[ "4" ]
We present here a new version (1.0) of such a method—an update to the TFAM statistical classifier of tRNA function published earlier.
true
true
true
true
true
408
1
INTRODUCTION
1
4
[ "B4" ]
17,591,612
pmid-16473847
TFAM 1.0 is now available online as a Web Server requiring no installation.
[ "4" ]
75
2,373
0
false
TFAM 1.0 is now available online as a Web Server requiring no installation.
[]
TFAM 1.0 is now available online as a Web Server requiring no installation.
true
true
true
true
true
408
1
INTRODUCTION
1
4
[ "B4" ]
17,591,612
pmid-16473847
Version 1.0 of TFAM also provides eukaryotic and archaeal tRNA functional models for the purpose of identifying initiator tRNAs, and an expanded bacterial model that can predict some kIle tRNAs.
[ "4" ]
194
2,374
0
false
Version 1.0 of TFAM also provides eukaryotic and archaeal tRNA functional models for the purpose of identifying initiator tRNAs, and an expanded bacterial model that can predict some kIle tRNAs.
[]
Version 1.0 of TFAM also provides eukaryotic and archaeal tRNA functional models for the purpose of identifying initiator tRNAs, and an expanded bacterial model that can predict some kIle tRNAs.
true
true
true
true
true
408
1
INTRODUCTION
1
4
[ "B4" ]
17,591,612
pmid-16473847
For certain bacterial species such as proteobacteria and gram-positive bacteria, TFAM 1.0 can be expected to correctly annotate the function of all tRNAs with good confidence.
[ "4" ]
175
2,375
0
false
For certain bacterial species such as proteobacteria and gram-positive bacteria, TFAM 1.0 can be expected to correctly annotate the function of all tRNAs with good confidence.
[]
For certain bacterial species such as proteobacteria and gram-positive bacteria, TFAM 1.0 can be expected to correctly annotate the function of all tRNAs with good confidence.
true
true
true
true
true
408
2
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
In bacteria, the cytidine in the CAU anticodons of lysylated isoleucine tRNAs are post-transcriptionally modified to lysidine (5).
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
130
2,376
1
false
In bacteria, the cytidine in the CAU anticodons of lysylated isoleucine tRNAs are post-transcriptionally modified to lysidine.
[ "5" ]
In bacteria, the cytidine in the CAU anticodons of lysylated isoleucine tRNAs are post-transcriptionally modified to lysidine.
true
true
true
true
true
409
2
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
This modification simultaneously changes the codon reading specificity of this usually minor isoacceptor from AUG to AUA and its amino acid charging specificity from methionine to isoleucine in keeping with the genetic code.
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
224
2,377
0
false
This modification simultaneously changes the codon reading specificity of this usually minor isoacceptor from AUG to AUA and its amino acid charging specificity from methionine to isoleucine in keeping with the genetic code.
[]
This modification simultaneously changes the codon reading specificity of this usually minor isoacceptor from AUG to AUA and its amino acid charging specificity from methionine to isoleucine in keeping with the genetic code.
true
true
true
true
true
409
2
INTRODUCTION
1
6
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
Because the unmodified (CAU) tRNA is charged with methionine (6) it cannot be expected that TFAM would recognize this tRNA as an isoleucine tRNA.
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
145
2,378
1
false
Because the unmodified (CAU) tRNA is charged with methionine it cannot be expected that TFAM would recognize this tRNA as an isoleucine tRNA.
[ "6" ]
Because the unmodified (CAU) tRNA is charged with methionine it cannot be expected that TFAM would recognize this tRNA as an isoleucine tRNA.
true
true
true
true
true
409
2
INTRODUCTION
1
3
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
However, the determinants that target this tRNA for post-transcriptional modification are themselves genetically templated in the tRNA gene (7,8), and it is possible for TFAM to distinguish this class of tRNA with fairly good confidence when suitably trained (3).
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
263
2,379
1
false
However, the determinants that target this tRNA for post-transcriptional modification are themselves genetically templated in the tRNA gene, and it is possible for TFAM to distinguish this class of tRNA with fairly good confidence when suitably trained.
[ "7,8", "3" ]
However, the determinants that target this tRNA for post-transcriptional modification are themselves genetically templated in the tRNA gene, and it is possible for TFAM to distinguish this class of tRNA with fairly good confidence when suitably trained.
true
true
true
true
true
409
2
INTRODUCTION
1
8
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
Nonetheless, both experimental (8) and bioinformatic (3) evidence suggest that the determinants for this class have diverged in bacteria.
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
137
2,380
1
false
Nonetheless, both experimental and bioinformatic evidence suggest that the determinants for this class have diverged in bacteria.
[ "8", "3" ]
Nonetheless, both experimental and bioinformatic evidence suggest that the determinants for this class have diverged in bacteria.
true
true
true
true
true
409
2
INTRODUCTION
1
3
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
Rather than iteratively accreting all divergent sequences of the same apparent type into one model class (3), we have taken a different, perhaps more conservative approach of making smaller, more phylogenetically restricted models, in the hopes that this will allow us to study the evolution and diversification of tRNA ...
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
342
2,381
1
false
Rather than iteratively accreting all divergent sequences of the same apparent type into one model class, we have taken a different, perhaps more conservative approach of making smaller, more phylogenetically restricted models, in the hopes that this will allow us to study the evolution and diversification of tRNA iden...
[ "3" ]
Rather than iteratively accreting all divergent sequences of the same apparent type into one model class, we have taken a different, perhaps more conservative approach of making smaller, more phylogenetically restricted models, in the hopes that this will allow us to study the evolution and diversification of tRNA iden...
true
true
true
true
true
409
2
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
Our ultimate aim is to model and understand the constellation of identity determinants that actually can or could function together in the same cellular context.
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
161
2,382
0
false
Our ultimate aim is to model and understand the constellation of identity determinants that actually can or could function together in the same cellular context.
[]
Our ultimate aim is to model and understand the constellation of identity determinants that actually can or could function together in the same cellular context.
true
true
true
true
true
409
2
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B3", "B8", "B3", "B3" ]
17,591,612
pmid-15124629|pmid-3054566|pmid-16039592|pmid-15894617|pmid-17071718|pmid-15894617|pmid-17071718|pmid-17071718
In TFAM 1.0 we release a model of lysylated isoleucine tRNAs based only on proteobacterial data.
[ "5", "6", "7", "8", "3", "8", "3", "3" ]
96
2,383
0
false
In TFAM 1.0 we release a model of lysylated isoleucine tRNAs based only on proteobacterial data.
[]
In TFAM 1.0 we release a model of lysylated isoleucine tRNAs based only on proteobacterial data.
true
true
true
true
true
409
3
INTRODUCTION
0
null
null
17,591,612
null
Earlier versions of TFAM were only available for standalone compilation and installation on UNIX-like platforms and required complicated installations of prerequisites.
null
168
2,384
0
false
null
null
Earlier versions of TFAM were only available for standalone compilation and installation on UNIX-like platforms and required complicated installations of prerequisites.
true
true
true
true
true
410
3
INTRODUCTION
0
null
null
17,591,612
null
The new web-based interface, besides obviating the installation burden, provides additional functionality over the standalone interface including color visualization and sorting of TFAM scores.
null
193
2,385
0
false
null
null
The new web-based interface, besides obviating the installation burden, provides additional functionality over the standalone interface including color visualization and sorting of TFAM scores.
true
true
true
true
true
410
3
INTRODUCTION
0
null
null
17,591,612
null
Installation of the standalone version has also been simplified by the removal of dependencies.
null
95
2,386
0
false
null
null
Installation of the standalone version has also been simplified by the removal of dependencies.
true
true
true
true
true
410
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7" ]
17,317,683
pmid-12127448|pmid-15860776|pmid-8781229|pmid-15963891|pmid-15745998|pmid-15604402|pmid-16713707
Recently, RNA X-ray crystal structures revealed, in the context of their biologically active hosts, several RNA motifs that were previously studied experimentally as individual fragments.
[ "1", "2", "3", "4–7" ]
187
2,387
0
false
Recently, RNA X-ray crystal structures revealed, in the context of their biologically active hosts, several RNA motifs that were previously studied experimentally as individual fragments.
[]
Recently, RNA X-ray crystal structures revealed, in the context of their biologically active hosts, several RNA motifs that were previously studied experimentally as individual fragments.
true
true
true
true
true
411
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7" ]
17,317,683
pmid-12127448|pmid-15860776|pmid-8781229|pmid-15963891|pmid-15745998|pmid-15604402|pmid-16713707
Many of these motifs have been predicted from comparative sequence analysis (1), indicating the existence of a relationship between their sequence and structure.
[ "1", "2", "3", "4–7" ]
161
2,388
1
false
Many of these motifs have been predicted from comparative sequence analysis, indicating the existence of a relationship between their sequence and structure.
[ "1" ]
Many of these motifs have been predicted from comparative sequence analysis, indicating the existence of a relationship between their sequence and structure.
true
true
true
true
true
411
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7" ]
17,317,683
pmid-12127448|pmid-15860776|pmid-8781229|pmid-15963891|pmid-15745998|pmid-15604402|pmid-16713707
The recent structures confirmed that these RNA motifs fold in stable conformations, and are involved in important intra- and inter-molecular stabilization interactions, as well as in catalytic domains (2,3).
[ "1", "2", "3", "4–7" ]
207
2,389
0
false
The recent structures confirmed that these RNA motifs fold in stable conformations, and are involved in important intra- and inter-molecular stabilization interactions, as well as in catalytic domains.
[ "2,3" ]
The recent structures confirmed that these RNA motifs fold in stable conformations, and are involved in important intra- and inter-molecular stabilization interactions, as well as in catalytic domains.
true
true
true
true
true
411
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7" ]
17,317,683
pmid-12127448|pmid-15860776|pmid-8781229|pmid-15963891|pmid-15745998|pmid-15604402|pmid-16713707
Consequently, it is now largely recognized that RNA motifs are crucial elements of RNA tertiary structure (The tertiary structure of an RNA is defined by all its nucleotide interactions: base pairs (canonical and non-canonical) and stacking.)
[ "1", "2", "3", "4–7" ]
242
2,390
0
false
Consequently, it is now largely recognized that RNA motifs are crucial elements of RNA tertiary structure (The tertiary structure of an RNA is defined by all its nucleotide interactions: base pairs (canonical and non-canonical) and stacking.)
[]
Consequently, it is now largely recognized that RNA motifs are crucial elements of RNA tertiary structure (The tertiary structure of an RNA is defined by all its nucleotide interactions: base pairs (canonical and non-canonical) and stacking.)
true
true
false
true
false
411
0
INTRODUCTION
1
4–7
[ "B1", "B2", "B3", "B4 B5 B6 B7" ]
17,317,683
pmid-12127448|pmid-15860776|pmid-8781229|pmid-15963891|pmid-15745998|pmid-15604402|pmid-16713707
and function (4–7).
[ "1", "2", "3", "4–7" ]
19
2,391
1
false
and function.
[ "4–7" ]
and function.
false
true
true
true
false
411
1
INTRODUCTION
1
8
[ "B8", "B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,317,683
pmid-7800507|pmid-8029015|pmid-12520045|pmid-15262817|pmid-15215371|pmid-11700055|pmid-16332715|pmid-1701686|pmid-15095976
During the last decade, RNA motifs have been computationally represented by stochastic context-free grammars (SCFGs) (8), covariance models (9–11), secondary structure profiles (12,13) and constraint networks (14,15).
[ "8", "9–11", "12", "13", "14", "15", "16" ]
217
2,392
1
false
During the last decade, RNA motifs have been computationally represented by stochastic context-free grammars (SCFGs), covariance models, secondary structure profiles and constraint networks.
[ "8", "9–11", "12,13", "14,15" ]
During the last decade, RNA motifs have been computationally represented by stochastic context-free grammars (SCFGs), covariance models, secondary structure profiles and constraint networks.
true
true
true
true
true
412
1
INTRODUCTION
1
8
[ "B8", "B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,317,683
pmid-7800507|pmid-8029015|pmid-12520045|pmid-15262817|pmid-15215371|pmid-11700055|pmid-16332715|pmid-1701686|pmid-15095976
Most of these computational models are inferred from sequence alignments.
[ "8", "9–11", "12", "13", "14", "15", "16" ]
73
2,393
0
false
Most of these computational models are inferred from sequence alignments.
[]
Most of these computational models are inferred from sequence alignments.
true
true
true
true
true
412
1
INTRODUCTION
1
8
[ "B8", "B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,317,683
pmid-7800507|pmid-8029015|pmid-12520045|pmid-15262817|pmid-15215371|pmid-11700055|pmid-16332715|pmid-1701686|pmid-15095976
They allow us to parse, or fit, RNA sequences into their plausible secondary structure (The secondary structure of an RNA is defined by the canonical base pairs of its double-helical regions: Watson-Crick A • U, C • G and G • U.)
[ "8", "9–11", "12", "13", "14", "15", "16" ]
229
2,394
0
false
They allow us to parse, or fit, RNA sequences into their plausible secondary structure (The secondary structure of an RNA is defined by the canonical base pairs of its double-helical regions: Watson-Crick A • U, C • G and G • U.)
[]
They allow us to parse, or fit, RNA sequences into their plausible secondary structure (The secondary structure of an RNA is defined by the canonical base pairs of its double-helical regions: Watson-Crick A • U, C • G and G • U.)
true
true
false
true
false
412
1
INTRODUCTION
1
8
[ "B8", "B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,317,683
pmid-7800507|pmid-8029015|pmid-12520045|pmid-15262817|pmid-15215371|pmid-11700055|pmid-16332715|pmid-1701686|pmid-15095976
and seek for new instances in genomic data.
[ "8", "9–11", "12", "13", "14", "15", "16" ]
43
2,395
0
false
and seek for new instances in genomic data.
[]
and seek for new instances in genomic data.
false
true
true
true
false
412
1
INTRODUCTION
1
16
[ "B8", "B9 B10 B11", "B12", "B13", "B14", "B15", "B16" ]
17,317,683
pmid-7800507|pmid-8029015|pmid-12520045|pmid-15262817|pmid-15215371|pmid-11700055|pmid-16332715|pmid-1701686|pmid-15095976
In addition to parsing RNA sequences, some computational models, such as SCFGs, directly generate a set of sequences that are compatible with the motif they represent, a necessary step towards in silico selection and engineering of RNA sequences with predetermined structure and function (16).
[ "8", "9–11", "12", "13", "14", "15", "16" ]
293
2,396
1
false
In addition to parsing RNA sequences, some computational models, such as SCFGs, directly generate a set of sequences that are compatible with the motif they represent, a necessary step towards in silico selection and engineering of RNA sequences with predetermined structure and function.
[ "16" ]
In addition to parsing RNA sequences, some computational models, such as SCFGs, directly generate a set of sequences that are compatible with the motif they represent, a necessary step towards in silico selection and engineering of RNA sequences with predetermined structure and function.
true
true
true
true
true
412
2
INTRODUCTION
1
2
[ "B2", "B2", "B17", "B2" ]
17,317,683
pmid-15860776|pmid-15860776|pmid-12458088|pmid-15860776
Current computational RNA motif representations are, to some degree, sensitive to their input sequence alignments, which are, unfortunately, not always reliable.
[ "2", "2", "17", "2" ]
161
2,397
0
false
Current computational RNA motif representations are, to some degree, sensitive to their input sequence alignments, which are, unfortunately, not always reliable.
[]
Current computational RNA motif representations are, to some degree, sensitive to their input sequence alignments, which are, unfortunately, not always reliable.
true
true
true
true
true
413
2
INTRODUCTION
1
2
[ "B2", "B2", "B17", "B2" ]
17,317,683
pmid-15860776|pmid-15860776|pmid-12458088|pmid-15860776
They are also limited by the complexity of RNA tertiary structure, which goes beyond secondary structure, co-variations and sequence similarities.
[ "2", "2", "17", "2" ]
146
2,398
0
false
They are also limited by the complexity of RNA tertiary structure, which goes beyond secondary structure, co-variations and sequence similarities.
[]
They are also limited by the complexity of RNA tertiary structure, which goes beyond secondary structure, co-variations and sequence similarities.
true
true
true
true
true
413
2
INTRODUCTION
1
2
[ "B2", "B2", "B17", "B2" ]
17,317,683
pmid-15860776|pmid-15860776|pmid-12458088|pmid-15860776
Aligning RNA sequences involves an iterative process of pattern matching and modeling (2).
[ "2", "2", "17", "2" ]
90
2,399
1
false
Aligning RNA sequences involves an iterative process of pattern matching and modeling.
[ "2" ]
Aligning RNA sequences involves an iterative process of pattern matching and modeling.
true
true
true
true
true
413