Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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2
DISCUSSION
1
24
[ "b24", "b25", "b26" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
Our data suggest that S18 is an essential component of the plastid ribosome and translation in the absence of S18 is unlikely to be possible.
[ "24", "25", "26" ]
141
1,700
0
false
Our data suggest that S18 is an essential component of the plastid ribosome and translation in the absence of S18 is unlikely to be possible.
[]
Our data suggest that S18 is an essential component of the plastid ribosome and translation in the absence of S18 is unlikely to be possible.
true
true
true
true
true
296
2
DISCUSSION
1
24
[ "b24", "b25", "b26" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
As sucrose was present in all our selection media and, therefore, photosynthesis is dispensable under in vitro culture conditions (24,25), it seems also unlikely that S18 could be dispensable in non-photosynthetic tissues.
[ "24", "25", "26" ]
222
1,701
0
false
As sucrose was present in all our selection media and, therefore, photosynthesis is dispensable under in vitro culture conditions, it seems also unlikely that S18 could be dispensable in non-photosynthetic tissues.
[ "24,25" ]
As sucrose was present in all our selection media and, therefore, photosynthesis is dispensable under in vitro culture conditions, it seems also unlikely that S18 could be dispensable in non-photosynthetic tissues.
true
true
true
true
true
296
2
DISCUSSION
1
24
[ "b24", "b25", "b26" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
The strict requirement for S18 for plastid ribosome function and the absence of rps18 genes from the plastid genomes of E.longa and protozoans may indicate that the gene was transferred to the nucleus in these species.
[ "24", "25", "26" ]
218
1,702
0
false
The strict requirement for S18 for plastid ribosome function and the absence of rps18 genes from the plastid genomes of E.longa and protozoans may indicate that the gene was transferred to the nucleus in these species.
[]
The strict requirement for S18 for plastid ribosome function and the absence of rps18 genes from the plastid genomes of E.longa and protozoans may indicate that the gene was transferred to the nucleus in these species.
true
true
true
true
true
296
2
DISCUSSION
1
26
[ "b24", "b25", "b26" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
Precedence for the repeated transfer of a plastid gene to the nucleus is the gene for the translation initiation factor infA which was transferred to the nucleus many times independently during angiosperm evolution (26).
[ "24", "25", "26" ]
220
1,703
1
false
Precedence for the repeated transfer of a plastid gene to the nucleus is the gene for the translation initiation factor infA which was transferred to the nucleus many times independently during angiosperm evolution.
[ "26" ]
Precedence for the repeated transfer of a plastid gene to the nucleus is the gene for the translation initiation factor infA which was transferred to the nucleus many times independently during angiosperm evolution.
true
true
true
true
true
296
2
DISCUSSION
1
24
[ "b24", "b25", "b26" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
However, whether or not this is also the case for rps18 in the protozoan lineage, remains to be investigated experimentally.
[ "24", "25", "26" ]
124
1,704
0
false
However, whether or not this is also the case for rps18 in the protozoan lineage, remains to be investigated experimentally.
[]
However, whether or not this is also the case for rps18 in the protozoan lineage, remains to be investigated experimentally.
true
true
true
true
true
296
3
DISCUSSION
1
13
[ "b13", "b10", "b11", "b12", "b8", "b27" ]
16,945,948
pmid-14660796|pmid-7994178|pmid-8440246|pmid-9721684|pmid-16212603|pmid-7666415
Supporting earlier results obtained from loss of plastid antibiotic resistance by loop-out recombination (13), our data on the targeted inactivation of rps18 demonstrate directly an essential role of plastid translation for cell survival in tobacco.
[ "13", "10", "11", "12", "8", "27" ]
249
1,705
1
false
Supporting earlier results obtained from loss of plastid antibiotic resistance by loop-out recombination, our data on the targeted inactivation of rps18 demonstrate directly an essential role of plastid translation for cell survival in tobacco.
[ "13" ]
Supporting earlier results obtained from loss of plastid antibiotic resistance by loop-out recombination, our data on the targeted inactivation of rps18 demonstrate directly an essential role of plastid translation for cell survival in tobacco.
true
true
true
true
true
297
3
DISCUSSION
1
12
[ "b13", "b10", "b11", "b12", "b8", "b27" ]
16,945,948
pmid-14660796|pmid-7994178|pmid-8440246|pmid-9721684|pmid-16212603|pmid-7666415
Interestingly, this contrasts the situation in barley (10,11) and Brassica (12) where plastid translation appears to be dispensable under heterotrophic growth conditions.
[ "13", "10", "11", "12", "8", "27" ]
170
1,706
1
false
Interestingly, this contrasts the situation in barley and Brassica where plastid translation appears to be dispensable under heterotrophic growth conditions.
[ "10,11", "12" ]
Interestingly, this contrasts the situation in barley and Brassica where plastid translation appears to be dispensable under heterotrophic growth conditions.
true
true
true
true
true
297
3
DISCUSSION
1
8
[ "b13", "b10", "b11", "b12", "b8", "b27" ]
16,945,948
pmid-14660796|pmid-7994178|pmid-8440246|pmid-9721684|pmid-16212603|pmid-7666415
In Brassica, it has been suggested that the presence of a second, nuclear-encoded acetyl-CoA carboxylase (ACCase) makes plastid translation non-essential by compensating the loss of expression of the plastid-encoded accD gene (8).
[ "13", "10", "11", "12", "8", "27" ]
230
1,707
1
false
In Brassica, it has been suggested that the presence of a second, nuclear-encoded acetyl-CoA carboxylase (ACCase) makes plastid translation non-essential by compensating the loss of expression of the plastid-encoded accD gene.
[ "8" ]
In Brassica, it has been suggested that the presence of a second, nuclear-encoded acetyl-CoA carboxylase (ACCase) makes plastid translation non-essential by compensating the loss of expression of the plastid-encoded accD gene.
true
true
true
true
true
297
3
DISCUSSION
1
27
[ "b13", "b10", "b11", "b12", "b8", "b27" ]
16,945,948
pmid-14660796|pmid-7994178|pmid-8440246|pmid-9721684|pmid-16212603|pmid-7666415
This explanation would be compatible with the non-essentiality of plastid translation in barley, because accD is not encoded in the chloroplast genome of cereals which, instead, have a eukaryotic-type ACCase encoded in their nuclear genome (27).
[ "13", "10", "11", "12", "8", "27" ]
245
1,708
1
false
This explanation would be compatible with the non-essentiality of plastid translation in barley, because accD is not encoded in the chloroplast genome of cereals which, instead, have a eukaryotic-type ACCase encoded in their nuclear genome.
[ "27" ]
This explanation would be compatible with the non-essentiality of plastid translation in barley, because accD is not encoded in the chloroplast genome of cereals which, instead, have a eukaryotic-type ACCase encoded in their nuclear genome.
true
true
true
true
true
297
3
DISCUSSION
1
13
[ "b13", "b10", "b11", "b12", "b8", "b27" ]
16,945,948
pmid-14660796|pmid-7994178|pmid-8440246|pmid-9721684|pmid-16212603|pmid-7666415
However, whether accD is the only truly essential gene in the tobacco chloroplast genome and thus can indeed explain the differences in the essentiality of plastid translation between different plant species, remains to be established.
[ "13", "10", "11", "12", "8", "27" ]
235
1,709
0
false
However, whether accD is the only truly essential gene in the tobacco chloroplast genome and thus can indeed explain the differences in the essentiality of plastid translation between different plant species, remains to be established.
[]
However, whether accD is the only truly essential gene in the tobacco chloroplast genome and thus can indeed explain the differences in the essentiality of plastid translation between different plant species, remains to be established.
true
true
true
true
true
297
4
DISCUSSION
1
28
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
Another interesting observation made in this study was the appearance of unexpected genome conformations which could be explained by flip-flop recombination on the psbA 3′-UTR which occurs twice in the transplastomes.
[ "28", "29", "16", "16", "30" ]
217
1,710
0
false
Another interesting observation made in this study was the appearance of unexpected genome conformations which could be explained by flip-flop recombination on the psbA 3′-UTR which occurs twice in the transplastomes.
[]
Another interesting observation made in this study was the appearance of unexpected genome conformations which could be explained by flip-flop recombination on the psbA 3′-UTR which occurs twice in the transplastomes.
true
true
true
true
true
298
4
DISCUSSION
1
28
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
It is well established that the two large inverted repeat regions of the chloroplast genome, which contain, for example, the ribosomal RNA operon, constantly undergo homologous recombination, thus producing two isoforms of the chloroplast genome (28,29).
[ "28", "29", "16", "16", "30" ]
254
1,711
0
false
It is well established that the two large inverted repeat regions of the chloroplast genome, which contain, for example, the ribosomal RNA operon, constantly undergo homologous recombination, thus producing two isoforms of the chloroplast genome.
[ "28,29" ]
It is well established that the two large inverted repeat regions of the chloroplast genome, which contain, for example, the ribosomal RNA operon, constantly undergo homologous recombination, thus producing two isoforms of the chloroplast genome.
true
true
true
true
true
298
4
DISCUSSION
1
28
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
However, flip-flop recombination on inverted repeats as short as the psbA 3′-UTR (∼200 bp) has not been directly demonstrated before.
[ "28", "29", "16", "16", "30" ]
133
1,712
0
false
However, flip-flop recombination on inverted repeats as short as the psbA 3′-UTR (∼200 bp) has not been directly demonstrated before.
[]
However, flip-flop recombination on inverted repeats as short as the psbA 3′-UTR has not been directly demonstrated before.
true
true
true
true
true
298
4
DISCUSSION
1
28
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
Is this a peculiarity of the rps18 knockout lines or a more common phenomenon in chloroplast transformation experiments that has been overlooked before?
[ "28", "29", "16", "16", "30" ]
152
1,713
0
false
Is this a peculiarity of the rps18 knockout lines or a more common phenomenon in chloroplast transformation experiments that has been overlooked before?
[]
Is this a peculiarity of the rps18 knockout lines or a more common phenomenon in chloroplast transformation experiments that has been overlooked before?
true
true
true
true
true
298
4
DISCUSSION
1
16
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
Interestingly, already the very first chloroplast transformation experiments with chimeric selectable marker genes reported in 1993 produced several lines that showed rearranged plastid genomes (16).
[ "28", "29", "16", "16", "30" ]
199
1,714
1
false
Interestingly, already the very first chloroplast transformation experiments with chimeric selectable marker genes reported in 1993 produced several lines that showed rearranged plastid genomes.
[ "16" ]
Interestingly, already the very first chloroplast transformation experiments with chimeric selectable marker genes reported in 1993 produced several lines that showed rearranged plastid genomes.
true
true
true
true
true
298
4
DISCUSSION
1
16
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
Although involvement of the 3′-UTR of the aadA marker in the rearrangements was demonstrated, the mechanisms generating the rearranged genomes could not be fully explained (16).
[ "28", "29", "16", "16", "30" ]
177
1,715
1
false
Although involvement of the 3′-UTR of the aadA marker in the rearrangements was demonstrated, the mechanisms generating the rearranged genomes could not be fully explained.
[ "16" ]
Although involvement of the 3′-UTR of the aadA marker in the rearrangements was demonstrated, the mechanisms generating the rearranged genomes could not be fully explained.
true
true
true
true
true
298
4
DISCUSSION
1
28
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
We therefore re-analyzed the data and tested whether flip-flop recombination could explain the rearrangements.
[ "28", "29", "16", "16", "30" ]
110
1,716
0
false
We therefore re-analyzed the data and tested whether flip-flop recombination could explain the rearrangements.
[]
We therefore re-analyzed the data and tested whether flip-flop recombination could explain the rearrangements.
true
true
true
true
true
298
4
DISCUSSION
1
28
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
This was indeed the case, although the fact that the recombined clones could not be brought to homoplasmy could indicate that, in these lines, additional rearrangements (e.g.
[ "28", "29", "16", "16", "30" ]
174
1,717
0
false
This was indeed the case, although the fact that the recombined clones could not be brought to homoplasmy could indicate that, in these lines, additional rearrangements (e.g.
[]
This was indeed the case, although the fact that the recombined clones could not be brought to homoplasmy could indicate that, in these lines, additional rearrangements (e.g.
true
true
true
true
true
298
4
DISCUSSION
1
28
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
deletions) had occurred.
[ "28", "29", "16", "16", "30" ]
24
1,718
0
false
deletions) had occurred.
[]
deletions) had occurred.
false
true
true
true
false
298
4
DISCUSSION
1
30
[ "b28", "b29", "b16", "b16", "b30" ]
16,945,948
NA|NA|pmid-8381537|pmid-8381537|pmid-15561145
Whether or not such possible deletions could be explained by genome multimerization and/or template switching during chloroplast DNA replication (30), which could bring short repeats in directly repeated orientation, remains to be investigated.
[ "28", "29", "16", "16", "30" ]
244
1,719
1
false
Whether or not such possible deletions could be explained by genome multimerization and/or template switching during chloroplast DNA replication, which could bring short repeats in directly repeated orientation, remains to be investigated.
[ "30" ]
Whether or not such possible deletions could be explained by genome multimerization and/or template switching during chloroplast DNA replication, which could bring short repeats in directly repeated orientation, remains to be investigated.
true
true
true
true
true
298
5
DISCUSSION
0
null
null
16,945,948
null
Taken together, these data indicate that the occurrence of flip-flop recombination could be a common phenomenon in chloroplast transformation experiments and, as plastome-derived 3′-UTRs are required to stabilize mRNAs made from plastid transgenes, probably cannot be avoided entirely.
null
285
1,720
0
false
null
null
Taken together, these data indicate that the occurrence of flip-flop recombination could be a common phenomenon in chloroplast transformation experiments and, as plastome-derived 3′-UTRs are required to stabilize mRNAs made from plastid transgenes, probably cannot be avoided entirely.
true
true
true
true
true
299
5
DISCUSSION
0
null
null
16,945,948
null
Being aware of this type of recombination occurring in transgenic chloroplast genomes is important for the interpretation of RFLP analyses which are commonly conducted to demonstrate transgene integration and homoplasmy of transplastomic plants.
null
245
1,721
0
false
null
null
Being aware of this type of recombination occurring in transgenic chloroplast genomes is important for the interpretation of RFLP analyses which are commonly conducted to demonstrate transgene integration and homoplasmy of transplastomic plants.
true
true
true
true
true
299
5
DISCUSSION
0
null
null
16,945,948
null
It is also important to know that flip-flop recombination might result in genome instability when, for example, a selectable marker gene cassette with the psbA 3′-UTR is integrated into the small single copy region of the plastid genome.
null
237
1,722
0
false
null
null
It is also important to know that flip-flop recombination might result in genome instability when, for example, a selectable marker gene cassette with the psbA 3′-UTR is integrated into the small single copy region of the plastid genome.
true
true
true
true
true
299
5
DISCUSSION
0
null
null
16,945,948
null
In this case, flip-flop recombination between the two psbA 3′-UTRs (one in the large single copy region and one in the small single-copy region) would invert one of the inverted repeat regions of the chloroplast genome (Figure 4).
null
230
1,723
0
false
null
null
In this case, flip-flop recombination between the two psbA 3′-UTRs (one in the large single copy region and one in the small single-copy region) would invert one of the inverted repeat regions of the chloroplast genome (Figure 4).
true
true
true
true
true
299
5
DISCUSSION
0
null
null
16,945,948
null
This, in turn, would result in the two inverted repeat regions now being direct repeats which can recombine with each other producing a large deletion in the genome.
null
165
1,724
0
false
null
null
This, in turn, would result in the two inverted repeat regions now being direct repeats which can recombine with each other producing a large deletion in the genome.
true
true
true
true
true
299
5
DISCUSSION
0
null
null
16,945,948
null
Thus, the occurrence of flip-flop recombination has important implications for the design of optimum chloroplast transformation vectors that are suitable to produce genetically stable transplastomic plants.
null
206
1,725
0
false
null
null
Thus, the occurrence of flip-flop recombination has important implications for the design of optimum chloroplast transformation vectors that are suitable to produce genetically stable transplastomic plants.
true
true
true
true
true
299
0
INTRODUCTION
0
null
null
17,135,202
null
The annotation of conserved domain footprints on protein sequences often serves as the first step toward characterizing protein function in silico.
null
147
1,726
0
false
null
null
The annotation of conserved domain footprints on protein sequences often serves as the first step toward characterizing protein function in silico.
true
true
true
true
true
300
0
INTRODUCTION
0
null
null
17,135,202
null
Protein domains may be viewed as units in the molecular evolution of proteins and can be organized into an evolutionary classification.
null
135
1,727
0
false
null
null
Protein domains may be viewed as units in the molecular evolution of proteins and can be organized into an evolutionary classification.
true
true
true
true
true
300
0
INTRODUCTION
0
null
null
17,135,202
null
The set of protein domains characterized so far appears to describe no more than a few thousand superfamilies, where members of each superfamily are related to each other by common descent.
null
189
1,728
0
false
null
null
The set of protein domains characterized so far appears to describe no more than a few thousand superfamilies, where members of each superfamily are related to each other by common descent.
true
true
true
true
true
300
0
INTRODUCTION
0
null
null
17,135,202
null
NCBI's conserved domain database (CDD) attempts to collate that set and to organize related domain models in a hierarchical fashion, meant to reflect major ancient gene duplication events and subsequent functional diversification.
null
230
1,729
0
false
null
null
NCBI's conserved domain database (CDD) attempts to collate that set and to organize related domain models in a hierarchical fashion, meant to reflect major ancient gene duplication events and subsequent functional diversification.
true
true
true
true
true
300
1
INTRODUCTION
0
null
null
17,135,202
null
Computational annotation of protein function is generally obtained via sequence similarity: once a close neighbor with known function has been identified, its annotation is copied to the sequence with unknown function.
null
218
1,730
0
false
null
null
Computational annotation of protein function is generally obtained via sequence similarity: once a close neighbor with known function has been identified, its annotation is copied to the sequence with unknown function.
true
true
true
true
true
301
1
INTRODUCTION
0
null
null
17,135,202
null
This strategy may work very well in functionally homogeneous families and when applied only for very close neighbors or suspected orthologs, but it is doomed to fail often when domain or protein families are sufficiently diverse and when no close neighbors with known function are available.
null
291
1,731
0
false
null
null
This strategy may work very well in functionally homogeneous families and when applied only for very close neighbors or suspected orthologs, but it is doomed to fail often when domain or protein families are sufficiently diverse and when no close neighbors with known function are available.
true
true
true
true
true
301
2
INTRODUCTION
1
1
[ "b1", "b2" ]
17,135,202
pmid-15608175|pmid-16846248
To this end, the CDD (1) provides a strategy toward a more accurate assessment of such neighbor relationships, similar to approaches termed ‘phylogenomic inference’ (2).
[ "1", "2" ]
169
1,732
1
false
To this end, the CDD provides a strategy toward a more accurate assessment of such neighbor relationships, similar to approaches termed ‘phylogenomic inference’.
[ "1", "2" ]
To this end, the CDD provides a strategy toward a more accurate assessment of such neighbor relationships, similar to approaches termed ‘phylogenomic inference’.
true
true
true
true
true
302
2
INTRODUCTION
1
1
[ "b1", "b2" ]
17,135,202
pmid-15608175|pmid-16846248
CDD acknowledges that protein domain families may be very diverse and that they may contain sets of related subfamilies.
[ "1", "2" ]
120
1,733
0
false
CDD acknowledges that protein domain families may be very diverse and that they may contain sets of related subfamilies.
[]
CDD acknowledges that protein domain families may be very diverse and that they may contain sets of related subfamilies.
true
true
true
true
true
302
2
INTRODUCTION
1
1
[ "b1", "b2" ]
17,135,202
pmid-15608175|pmid-16846248
Of these, only few may have been characterized experimentally, and within this set function may have diverged considerably.
[ "1", "2" ]
123
1,734
0
false
Of these, only few may have been characterized experimentally, and within this set function may have diverged considerably.
[]
Of these, only few may have been characterized experimentally, and within this set function may have diverged considerably.
true
true
true
true
true
302
2
INTRODUCTION
1
1
[ "b1", "b2" ]
17,135,202
pmid-15608175|pmid-16846248
While it may be possible, and certainly efficient, to represent such a set of subfamilies with just a single family model, that model could only provide very generic annotation.
[ "1", "2" ]
177
1,735
0
false
While it may be possible, and certainly efficient, to represent such a set of subfamilies with just a single family model, that model could only provide very generic annotation.
[]
While it may be possible, and certainly efficient, to represent such a set of subfamilies with just a single family model, that model could only provide very generic annotation.
true
true
true
true
true
302
2
INTRODUCTION
1
1
[ "b1", "b2" ]
17,135,202
pmid-15608175|pmid-16846248
In CDD curation, we attempt to detect evidence for duplication and functional divergence in domain families by means of phylogenetic analysis.
[ "1", "2" ]
142
1,736
0
false
In CDD curation, we attempt to detect evidence for duplication and functional divergence in domain families by means of phylogenetic analysis.
[]
In CDD curation, we attempt to detect evidence for duplication and functional divergence in domain families by means of phylogenetic analysis.
true
true
true
true
true
302
2
INTRODUCTION
1
1
[ "b1", "b2" ]
17,135,202
pmid-15608175|pmid-16846248
We record the resulting subfamily structure as a set of explicit models, but limit the analysis to ancient duplication events—several hundred million years in the past, as judged by the taxonomic distribution of protein sequences with particular domain subfamily footprints.
[ "1", "2" ]
274
1,737
0
false
We record the resulting subfamily structure as a set of explicit models, but limit the analysis to ancient duplication events—several hundred million years in the past, as judged by the taxonomic distribution of protein sequences with particular domain subfamily footprints.
[]
We record the resulting subfamily structure as a set of explicit models, but limit the analysis to ancient duplication events—several hundred million years in the past, as judged by the taxonomic distribution of protein sequences with particular domain subfamily footprints.
true
true
true
true
true
302
3
INTRODUCTION
1
3
[ "b3" ]
17,135,202
pmid-9254694
CDD provides a search tool employing reverse position-specific BLAST (RPS–BLAST), where query sequences are compared to databases of position-specific score matrices (PSSMs), and E-values are obtained in much the same way as in the widely used PSI-BLAST application (3).
[ "3" ]
270
1,738
1
false
CDD provides a search tool employing reverse position-specific BLAST (RPS–BLAST), where query sequences are compared to databases of position-specific score matrices (PSSMs), and E-values are obtained in much the same way as in the widely used PSI-BLAST application.
[ "3" ]
CDD provides a search tool employing reverse position-specific BLAST (RPS–BLAST), where query sequences are compared to databases of position-specific score matrices (PSSMs), and E-values are obtained in much the same way as in the widely used PSI-BLAST application.
true
true
true
true
true
303
3
INTRODUCTION
1
3
[ "b3" ]
17,135,202
pmid-9254694
When CDD is scanned with protein query sequences, a region on a query may pick up more than one overlapping footprint from a set of related models.
[ "3" ]
147
1,739
0
false
When CDD is scanned with protein query sequences, a region on a query may pick up more than one overlapping footprint from a set of related models.
[]
When CDD is scanned with protein query sequences, a region on a query may pick up more than one overlapping footprint from a set of related models.
true
true
true
true
true
303
3
INTRODUCTION
1
3
[ "b3" ]
17,135,202
pmid-9254694
One of those models provides the best score or lowest E-value, but that alone may not be sufficient to indicate that the query sequence is a bona fide member of the corresponding subfamily.
[ "3" ]
189
1,740
0
false
One of those models provides the best score or lowest E-value, but that alone may not be sufficient to indicate that the query sequence is a bona fide member of the corresponding subfamily.
[]
One of those models provides the best score or lowest E-value, but that alone may not be sufficient to indicate that the query sequence is a bona fide member of the corresponding subfamily.
true
true
true
true
true
303
3
INTRODUCTION
1
3
[ "b3" ]
17,135,202
pmid-9254694
Since the CDD collection also contains imported models, which have not been curated at NCBI, search results may present a mixture of curated models (accessions starting with ‘cd..’) and un-curated models (accessions starting with ‘pfam’, ‘smart’ or ‘COG’).
[ "3" ]
256
1,741
0
false
Since the CDD collection also contains imported models, which have not been curated at NCBI, search results may present a mixture of curated models (accessions starting with ‘cd..’) and un-curated models (accessions starting with ‘pfam’, ‘smart’ or ‘COG’).
[]
Since the CDD collection also contains imported models, which have not been curated at NCBI, search results may present a mixture of curated models (accessions starting with ‘cd..’) and un-curated models (accessions starting with ‘pfam’, ‘smart’ or ‘COG’).
true
true
true
true
true
303
3
INTRODUCTION
1
3
[ "b3" ]
17,135,202
pmid-9254694
By default, overlapping domain hits are sorted by E-value, but curated models are listed first, if their E-values exceed a secondary significance threshold of 1e-05.
[ "3" ]
165
1,742
0
false
By default, overlapping domain hits are sorted by E-value, but curated models are listed first, if their E-values exceed a secondary significance threshold of 1e-05.
[]
By default, overlapping domain hits are sorted by E-value, but curated models are listed first, if their E-values exceed a secondary significance threshold of 1e-05.
true
true
true
true
true
303
3
INTRODUCTION
1
3
[ "b3" ]
17,135,202
pmid-9254694
Default displays are presented in a concise fashion, where domain hits that overlap with the top-ranked domain hits are hidden.
[ "3" ]
127
1,743
0
false
Default displays are presented in a concise fashion, where domain hits that overlap with the top-ranked domain hits are hidden.
[]
Default displays are presented in a concise fashion, where domain hits that overlap with the top-ranked domain hits are hidden.
true
true
true
true
true
303
4
INTRODUCTION
0
null
null
17,135,202
null
We have started to distribute CDTree, a helper application for the web browser.
null
79
1,744
0
false
null
null
We have started to distribute CDTree, a helper application for the web browser.
true
true
true
true
true
304
4
INTRODUCTION
0
null
null
17,135,202
null
CDTree allows users to examine the results of simple phylogenetic analysis on the sequences from a curated domain hierarchy, and view their query sequence in the context of such a phylogenetic sequence tree.
null
207
1,745
0
false
null
null
CDTree allows users to examine the results of simple phylogenetic analysis on the sequences from a curated domain hierarchy, and view their query sequence in the context of such a phylogenetic sequence tree.
true
true
true
true
true
304
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
Visualization of site-specific labels in long linear or circular DNA allows unambiguous identification of various local DNA structures, such as bent DNA (1–3), as well as the protein binding sites (4–6) at predicted distances from the labels.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
242
1,746
0
false
Visualization of site-specific labels in long linear or circular DNA allows unambiguous identification of various local DNA structures, such as bent DNA, as well as the protein binding sites at predicted distances from the labels.
[ "1–3", "4–6" ]
Visualization of site-specific labels in long linear or circular DNA allows unambiguous identification of various local DNA structures, such as bent DNA, as well as the protein binding sites at predicted distances from the labels.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
The formation and stability of local structures, as well as protein functions, depend on the level of superhelical tension in DNA, therefore there is a great demand for a simple labeling procedure that does not change the DNA topology.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
235
1,747
0
false
The formation and stability of local structures, as well as protein functions, depend on the level of superhelical tension in DNA, therefore there is a great demand for a simple labeling procedure that does not change the DNA topology.
[]
The formation and stability of local structures, as well as protein functions, depend on the level of superhelical tension in DNA, therefore there is a great demand for a simple labeling procedure that does not change the DNA topology.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
Different approaches have been proposed for the sequence-specific DNA labeling.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
79
1,748
0
false
Different approaches have been proposed for the sequence-specific DNA labeling.
[]
Different approaches have been proposed for the sequence-specific DNA labeling.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
Some of them utilize the site-specific binding of oligonucleotides (7–9) or PNA fragments (10–12).
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
98
1,749
0
false
Some of them utilize the site-specific binding of oligonucleotides or PNA fragments.
[ "7–9", "10–12" ]
Some of them utilize the site-specific binding of oligonucleotides or PNA fragments.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
The major drawbacks of these approaches are the complexity of their designs and the involvement of multiple experimental steps, and/or their dependence on DNA supercoiling.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
172
1,750
0
false
The major drawbacks of these approaches are the complexity of their designs and the involvement of multiple experimental steps, and/or their dependence on DNA supercoiling.
[]
The major drawbacks of these approaches are the complexity of their designs and the involvement of multiple experimental steps, and/or their dependence on DNA supercoiling.
true
true
true
true
true
305
0
INTRODUCTION
1
13
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
Restriction enzymes and methylases rendered inactive by mutations have been suggested for direct DNA labeling (13), however moderate specific affinities of 10−7 to 10−9 M limit their use for routine labeling.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
208
1,751
1
false
Restriction enzymes and methylases rendered inactive by mutations have been suggested for direct DNA labeling, however moderate specific affinities of 10−7 to 10−9 M limit their use for routine labeling.
[ "13" ]
Restriction enzymes and methylases rendered inactive by mutations have been suggested for direct DNA labeling, however moderate specific affinities of 10−7 to 10−9 M limit their use for routine labeling.
true
true
true
true
true
305
0
INTRODUCTION
1
14
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
We have recently used AFM to study very stable complexes of the restriction enzyme SfiI with DNA which was kept undigested by replacing Mg2+ cations in the buffer with Ca2+ (14).
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
178
1,752
1
false
We have recently used AFM to study very stable complexes of the restriction enzyme SfiI with DNA which was kept undigested by replacing Mg2+ cations in the buffer with Ca2+.
[ "14" ]
We have recently used AFM to study very stable complexes of the restriction enzyme SfiI with DNA which was kept undigested by replacing Mg2+ cations in the buffer with Ca2+.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
SfiI binds as a tetramer (total molecular weight of 124 kDa), which is easily identified in the AFM images.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
107
1,753
0
false
SfiI binds as a tetramer, which is easily identified in the AFM images.
[ "total molecular weight of 124 kDa" ]
SfiI binds as a tetramer, which is easily identified in the AFM images.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
Thus, SfiI appears to be an excellent candidate label of specific sites in circular DNA.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
88
1,754
0
false
Thus, SfiI appears to be an excellent candidate label of specific sites in circular DNA.
[]
Thus, SfiI appears to be an excellent candidate label of specific sites in circular DNA.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
However, the requirement of two DNA recognition sites for the stable complex formation complicates the use of SfiI for site-specific labeling: (i) SfiI poorly binds to an isolated recognition site; (ii) SfiI binding to DNA molecules with more than one recognition site results in DNA looping that changes the overall DNA...
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
443
1,755
0
false
However, the requirement of two DNA recognition sites for the stable complex formation complicates the use of SfiI for site-specific labeling: (i) SfiI poorly binds to an isolated recognition site; (ii) SfiI binding to DNA molecules with more than one recognition site results in DNA looping that changes the overall DNA...
[]
However, the requirement of two DNA recognition sites for the stable complex formation complicates the use of SfiI for site-specific labeling: (i) SfiI poorly binds to an isolated recognition site; (ii) SfiI binding to DNA molecules with more than one recognition site results in DNA looping that changes the overall DNA...
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
Here we show that these complications can be overcome by inducing stable SfiI binding to its target site in DNA with the help of a short DNA duplex that provides the second SfiI recognition site.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
195
1,756
0
false
Here we show that these complications can be overcome by inducing stable SfiI binding to its target site in DNA with the help of a short DNA duplex that provides the second SfiI recognition site.
[]
Here we show that these complications can be overcome by inducing stable SfiI binding to its target site in DNA with the help of a short DNA duplex that provides the second SfiI recognition site.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
Using the oligonucleotide duplex in excess to target DNA preferentially drives the formation of an intermolecular (trans) synaptic complexes which contain SfiI, long DNA molecule and the oligonucleotide duplex, rather than the trans complex formed by SfiI-mediated bridging of two recognition sites in two long DNA fragm...
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
443
1,757
0
false
Using the oligonucleotide duplex in excess to target DNA preferentially drives the formation of an intermolecular (trans) synaptic complexes which contain SfiI, long DNA molecule and the oligonucleotide duplex, rather than the trans complex formed by SfiI-mediated bridging of two recognition sites in two long DNA fragm...
[]
Using the oligonucleotide duplex in excess to target DNA preferentially drives the formation of an intermolecular (trans) synaptic complexes which contain SfiI, long DNA molecule and the oligonucleotide duplex, rather than the trans complex formed by SfiI-mediated bridging of two recognition sites in two long DNA fragm...
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
This labeling procedure does not interfere with cruciform formation and has very low dependence on the DNA supercoiling.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
120
1,758
0
false
This labeling procedure does not interfere with cruciform formation and has very low dependence on the DNA supercoiling.
[]
This labeling procedure does not interfere with cruciform formation and has very low dependence on the DNA supercoiling.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b6", "b7", "b9", "b10", "b12", "b13", "b14" ]
16,963,492
pmid-9466934|pmid-15311927|pmid-15342791|pmid-15790303|pmid-12403621|pmid-8464052|pmid-15102432|pmid-9576914|pmid-8799111|pmid-16388590
In addition, the complex dissociates slowly in moderately acidic (pH 5) or alkaline (pH 9) media.
[ "1", "3", "4", "6", "7", "9", "10", "12", "13", "14" ]
97
1,759
0
false
In addition, the complex dissociates slowly in moderately acidic (pH 5) or alkaline media.
[ "pH 9" ]
In addition, the complex dissociates slowly in moderately acidic (pH 5) or alkaline media.
true
true
true
true
true
305
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
Alternative pre-mRNA splicing is a critical mechanism for regulating gene expression in metazoan organisms, and leads to tremendous protein diversity from a relatively small number of genes.
[ "1", "2–6", "7–13", "14–16", "17" ]
190
1,760
0
false
Alternative pre-mRNA splicing is a critical mechanism for regulating gene expression in metazoan organisms, and leads to tremendous protein diversity from a relatively small number of genes.
[]
Alternative pre-mRNA splicing is a critical mechanism for regulating gene expression in metazoan organisms, and leads to tremendous protein diversity from a relatively small number of genes.
true
true
true
true
true
306
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
A majority of human genes exhibit some form of alternative splicing.
[ "1", "2–6", "7–13", "14–16", "17" ]
68
1,761
0
false
A majority of human genes exhibit some form of alternative splicing.
[]
A majority of human genes exhibit some form of alternative splicing.
true
true
true
true
true
306
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
In particular, the human genome encodes a complex alternative splicing program that switches alternative exons on and off according to the needs of individual differentiated cell types.
[ "1", "2–6", "7–13", "14–16", "17" ]
185
1,762
0
false
In particular, the human genome encodes a complex alternative splicing program that switches alternative exons on and off according to the needs of individual differentiated cell types.
[]
In particular, the human genome encodes a complex alternative splicing program that switches alternative exons on and off according to the needs of individual differentiated cell types.
true
true
true
true
true
306
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
Despite intensive study in recent years, the mechanisms regulating the human alternative splicing program are not yet well understood.
[ "1", "2–6", "7–13", "14–16", "17" ]
134
1,763
0
false
Despite intensive study in recent years, the mechanisms regulating the human alternative splicing program are not yet well understood.
[]
Despite intensive study in recent years, the mechanisms regulating the human alternative splicing program are not yet well understood.
true
true
true
true
true
306
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
The complex decision process, involving which subset of exons on the primary RNA transcript (henceforth, pre-mRNA) will get spliced into the mature mRNA isoform, is mediated by a combination of cis-regulatory elements organized across exons and introns (1), quite analogous to the cis-regulation of transcription.
[ "1", "2–6", "7–13", "14–16", "17" ]
313
1,764
1
false
The complex decision process, involving which subset of exons on the primary RNA transcript (henceforth, pre-mRNA) will get spliced into the mature mRNA isoform, is mediated by a combination of cis-regulatory elements organized across exons and introns, quite analogous to the cis-regulation of transcription.
[ "1" ]
The complex decision process, involving which subset of exons on the primary RNA transcript (henceforth, pre-mRNA) will get spliced into the mature mRNA isoform, is mediated by a combination of cis-regulatory elements organized across exons and introns, quite analogous to the cis-regulation of transcription.
true
true
true
true
true
306
0
INTRODUCTION
1
2–6
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
Global identification of splicing regulatory elements has been difficult and has been primarily restricted to exonic elements (2–6), while limited computational information is available on intronic elements (7–13).
[ "1", "2–6", "7–13", "14–16", "17" ]
214
1,765
1
false
Global identification of splicing regulatory elements has been difficult and has been primarily restricted to exonic elements, while limited computational information is available on intronic elements.
[ "2–6", "7–13" ]
Global identification of splicing regulatory elements has been difficult and has been primarily restricted to exonic elements, while limited computational information is available on intronic elements.
true
true
true
true
true
306
0
INTRODUCTION
1
14–16
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
However, availability of splicing microarrays (14–16), which can interrogate expression levels of exons genome-wide under any particular biological condition, has opened up new possibilities.
[ "1", "2–6", "7–13", "14–16", "17" ]
191
1,766
1
false
However, availability of splicing microarrays, which can interrogate expression levels of exons genome-wide under any particular biological condition, has opened up new possibilities.
[ "14–16" ]
However, availability of splicing microarrays, which can interrogate expression levels of exons genome-wide under any particular biological condition, has opened up new possibilities.
true
true
true
true
true
306
0
INTRODUCTION
1
17
[ "B1", "B2 B3 B4 B5 B6", "B7 B8 B9 B10 B11 B12 B13", "B14 B15 B16", "B17" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
In this work, we demonstrate that one can now apply analogous computational approaches used for dissecting transcriptional regulation (17) to decipher the splicing regulatory elements, with genes replaced by exons and promoters by pre-mRNA regions proximal to the splice sites.
[ "1", "2–6", "7–13", "14–16", "17" ]
277
1,767
1
false
In this work, we demonstrate that one can now apply analogous computational approaches used for dissecting transcriptional regulation to decipher the splicing regulatory elements, with genes replaced by exons and promoters by pre-mRNA regions proximal to the splice sites.
[ "17" ]
In this work, we demonstrate that one can now apply analogous computational approaches used for dissecting transcriptional regulation to decipher the splicing regulatory elements, with genes replaced by exons and promoters by pre-mRNA regions proximal to the splice sites.
true
true
true
true
true
306
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
A new set of approaches based on correlation with expression has been particularly successful in identifying cis-regulatory elements governing transcription (18–21).
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
165
1,768
1
false
A new set of approaches based on correlation with expression has been particularly successful in identifying cis-regulatory elements governing transcription.
[ "18–21" ]
A new set of approaches based on correlation with expression has been particularly successful in identifying cis-regulatory elements governing transcription.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Here, the premise is that gene expression results from integration of multiple signals within the promoter region, as mediated by binding of trans-factors to the cis-elements.
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
175
1,769
0
false
Here, the premise is that gene expression results from integration of multiple signals within the promoter region, as mediated by binding of trans-factors to the cis-elements.
[]
Here, the premise is that gene expression results from integration of multiple signals within the promoter region, as mediated by binding of trans-factors to the cis-elements.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
This implies that for an active cis-regulatory motif, its parameters [occurrence frequencies and position weight matrix (PWM) scores] must be significantly correlated with the expression levels across genes under any specific biological condition.
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
247
1,770
0
false
This implies that for an active cis-regulatory motif, its parameters [occurrence frequencies and position weight matrix (PWM) scores] must be significantly correlated with the expression levels across genes under any specific biological condition.
[]
This implies that for an active cis-regulatory motif, its parameters [occurrence frequencies and position weight matrix (PWM) scores] must be significantly correlated with the expression levels across genes under any specific biological condition.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Multiple studies have eseished that, using this strategy, one can identify the motifs that are functional under the tested condition.
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
133
1,771
0
false
Multiple studies have eseished that, using this strategy, one can identify the motifs that are functional under the tested condition.
[]
Multiple studies have eseished that, using this strategy, one can identify the motifs that are functional under the tested condition.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Furthermore, expression data from a single test condition and a reference condition are often sufficient for the analysis.
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
122
1,772
0
false
Furthermore, expression data from a single test condition and a reference condition are often sufficient for the analysis.
[]
Furthermore, expression data from a single test condition and a reference condition are often sufficient for the analysis.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
In addition, unlike clustering-based approaches, interacting combinations of motifs can be inferred with high confidence (19,22).
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
129
1,773
0
false
In addition, unlike clustering-based approaches, interacting combinations of motifs can be inferred with high confidence.
[ "19,22" ]
In addition, unlike clustering-based approaches, interacting combinations of motifs can be inferred with high confidence.
true
true
true
true
true
307
1
INTRODUCTION
1
22
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Finally, a recent study based on linear splines, which model the sigmoidal nature of transcriptional response, shows that such approaches can accurately identify direct targets of trans-factors binding to the active motifs, even when the motifs are very degenerate (22).
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
270
1,774
1
false
Finally, a recent study based on linear splines, which model the sigmoidal nature of transcriptional response, shows that such approaches can accurately identify direct targets of trans-factors binding to the active motifs, even when the motifs are very degenerate.
[ "22" ]
Finally, a recent study based on linear splines, which model the sigmoidal nature of transcriptional response, shows that such approaches can accurately identify direct targets of trans-factors binding to the active motifs, even when the motifs are very degenerate.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Target identification in such situations has been quite challenging.
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
68
1,775
0
false
Target identification in such situations has been quite challenging.
[]
Target identification in such situations has been quite challenging.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Thus, one can delineate the key elements of transcriptional regulatory networks using correlation with expression.
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
114
1,776
0
false
Thus, one can delineate the key elements of transcriptional regulatory networks using correlation with expression.
[]
Thus, one can delineate the key elements of transcriptional regulatory networks using correlation with expression.
true
true
true
true
true
307
1
INTRODUCTION
1
18–21
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
This has proven effective in both lower eukaryotes, e.g.
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
56
1,777
0
false
This has proven effective in both lower eukaryotes, e.g.
[]
This has proven effective in both lower eukaryotes, e.g.
true
true
true
true
true
307
1
INTRODUCTION
1
22
[ "B18 B19 B20 B21", "B19", "B22", "B22", "B18", "B19", "B23", "B22" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
yeast (18,19,23), and in mammals (22).
[ "18–21", "19", "22", "22", "18", "19", "23", "22" ]
38
1,778
1
false
yeast, and in mammals.
[ "18,19,23", "22" ]
yeast, and in mammals.
false
true
true
true
false
307
2
INTRODUCTION
1
8
[ "B8", "B24", "B25", "B26", "B18", "B22", "B27 B28 B29 B30 B31 B32 B33", "B34", "B35" ]
17,626,050
pmid-15691898|pmid-12840041|pmid-16839875|pmid-17456239|pmid-11175784|pmid-16760900|pmid-12574126|pmid-15824060|pmid-16260614|pmid-16449636|pmid-16537540|pmid-16839192|pmid-17101796|pmid-11158314|pmid-16403634|pmid-8663598|pmid-16403634|pmid-11313454|pmid-16109373|pmid-12574126|pmid-12150906|pmid-11528389|pmid-12022233...
Here we report the first application, to our knowledge, of the correlation with expression approach for identification of cis-elements that regulate alternative splicing by integrating pre-mRNA sequence information with the exon microarray data.
[ "8", "24", "25", "26", "18", "22", "27–33", "34", "35" ]
245
1,779
0
false
Here we report the first application, to our knowledge, of the correlation with expression approach for identification of cis-elements that regulate alternative splicing by integrating pre-mRNA sequence information with the exon microarray data.
[]
Here we report the first application, to our knowledge, of the correlation with expression approach for identification of cis-elements that regulate alternative splicing by integrating pre-mRNA sequence information with the exon microarray data.
true
true
true
true
true
308
2
INTRODUCTION
1
8
[ "B8", "B24", "B25", "B26", "B18", "B22", "B27 B28 B29 B30 B31 B32 B33", "B34", "B35" ]
17,626,050
pmid-15691898|pmid-12840041|pmid-16839875|pmid-17456239|pmid-11175784|pmid-16760900|pmid-12574126|pmid-15824060|pmid-16260614|pmid-16449636|pmid-16537540|pmid-16839192|pmid-17101796|pmid-11158314|pmid-16403634|pmid-8663598|pmid-16403634|pmid-11313454|pmid-16109373|pmid-12574126|pmid-12150906|pmid-11528389|pmid-12022233...
Specifically, we focused on tissue-specific splicing, as tissue-specific pre-mRNA regions are largely conserved across species (8,24,25), and thus, phylogenetic conservation can be used to evaluate the predictions.
[ "8", "24", "25", "26", "18", "22", "27–33", "34", "35" ]
214
1,780
0
false
Specifically, we focused on tissue-specific splicing, as tissue-specific pre-mRNA regions are largely conserved across species, and thus, phylogenetic conservation can be used to evaluate the predictions.
[ "8,24,25" ]
Specifically, we focused on tissue-specific splicing, as tissue-specific pre-mRNA regions are largely conserved across species, and thus, phylogenetic conservation can be used to evaluate the predictions.
true
true
true
true
true
308
2
INTRODUCTION
1
26
[ "B8", "B24", "B25", "B26", "B18", "B22", "B27 B28 B29 B30 B31 B32 B33", "B34", "B35" ]
17,626,050
pmid-15691898|pmid-12840041|pmid-16839875|pmid-17456239|pmid-11175784|pmid-16760900|pmid-12574126|pmid-15824060|pmid-16260614|pmid-16449636|pmid-16537540|pmid-16839192|pmid-17101796|pmid-11158314|pmid-16403634|pmid-8663598|pmid-16403634|pmid-11313454|pmid-16109373|pmid-12574126|pmid-12150906|pmid-11528389|pmid-12022233...
We employed an Affymetrix exon microarray (26) to identify 56 muscle-enriched alternative cassette exons, a number of which are predicted to alter the expression of cytoskeletal related genes.
[ "8", "24", "25", "26", "18", "22", "27–33", "34", "35" ]
192
1,781
1
false
We employed an Affymetrix exon microarray to identify 56 muscle-enriched alternative cassette exons, a number of which are predicted to alter the expression of cytoskeletal related genes.
[ "26" ]
We employed an Affymetrix exon microarray to identify 56 muscle-enriched alternative cassette exons, a number of which are predicted to alter the expression of cytoskeletal related genes.
true
true
true
true
true
308
2
INTRODUCTION
1
18
[ "B8", "B24", "B25", "B26", "B18", "B22", "B27 B28 B29 B30 B31 B32 B33", "B34", "B35" ]
17,626,050
pmid-15691898|pmid-12840041|pmid-16839875|pmid-17456239|pmid-11175784|pmid-16760900|pmid-12574126|pmid-15824060|pmid-16260614|pmid-16449636|pmid-16537540|pmid-16839192|pmid-17101796|pmid-11158314|pmid-16403634|pmid-8663598|pmid-16403634|pmid-11313454|pmid-16109373|pmid-12574126|pmid-12150906|pmid-11528389|pmid-12022233...
We used both linear regression (18) and linear splines (22) to examine whether cis-elements in introns adjoining these exons correlate with gene-normalized exon expression in muscle.
[ "8", "24", "25", "26", "18", "22", "27–33", "34", "35" ]
182
1,782
1
false
We used both linear regression and linear splines to examine whether cis-elements in introns adjoining these exons correlate with gene-normalized exon expression in muscle.
[ "18", "22" ]
We used both linear regression and linear splines to examine whether cis-elements in introns adjoining these exons correlate with gene-normalized exon expression in muscle.
true
true
true
true
true
308
2
INTRODUCTION
1
8
[ "B8", "B24", "B25", "B26", "B18", "B22", "B27 B28 B29 B30 B31 B32 B33", "B34", "B35" ]
17,626,050
pmid-15691898|pmid-12840041|pmid-16839875|pmid-17456239|pmid-11175784|pmid-16760900|pmid-12574126|pmid-15824060|pmid-16260614|pmid-16449636|pmid-16537540|pmid-16839192|pmid-17101796|pmid-11158314|pmid-16403634|pmid-8663598|pmid-16403634|pmid-11313454|pmid-16109373|pmid-12574126|pmid-12150906|pmid-11528389|pmid-12022233...
Multiple motifs that demonstrated statistically significant correlation were also found to be conserved in mouse, chicken and frog.
[ "8", "24", "25", "26", "18", "22", "27–33", "34", "35" ]
131
1,783
0
false
Multiple motifs that demonstrated statistically significant correlation were also found to be conserved in mouse, chicken and frog.
[]
Multiple motifs that demonstrated statistically significant correlation were also found to be conserved in mouse, chicken and frog.
true
true
true
true
true
308
2
INTRODUCTION
1
27–33
[ "B8", "B24", "B25", "B26", "B18", "B22", "B27 B28 B29 B30 B31 B32 B33", "B34", "B35" ]
17,626,050
pmid-15691898|pmid-12840041|pmid-16839875|pmid-17456239|pmid-11175784|pmid-16760900|pmid-12574126|pmid-15824060|pmid-16260614|pmid-16449636|pmid-16537540|pmid-16839192|pmid-17101796|pmid-11158314|pmid-16403634|pmid-8663598|pmid-16403634|pmid-11313454|pmid-16109373|pmid-12574126|pmid-12150906|pmid-11528389|pmid-12022233...
In addition, several of these elements have been previously characterized experimentally as regulators of muscle-specific splicing via binding to members of the Fox (27–33), CELF (34) and PTB (35) families of splicing factors.
[ "8", "24", "25", "26", "18", "22", "27–33", "34", "35" ]
226
1,784
1
false
In addition, several of these elements have been previously characterized experimentally as regulators of muscle-specific splicing via binding to members of the Fox, CELF and PTB families of splicing factors.
[ "27–33", "34", "35" ]
In addition, several of these elements have been previously characterized experimentally as regulators of muscle-specific splicing via binding to members of the Fox, CELF and PTB families of splicing factors.
true
true
true
true
true
308
2
INTRODUCTION
1
8
[ "B8", "B24", "B25", "B26", "B18", "B22", "B27 B28 B29 B30 B31 B32 B33", "B34", "B35" ]
17,626,050
pmid-15691898|pmid-12840041|pmid-16839875|pmid-17456239|pmid-11175784|pmid-16760900|pmid-12574126|pmid-15824060|pmid-16260614|pmid-16449636|pmid-16537540|pmid-16839192|pmid-17101796|pmid-11158314|pmid-16403634|pmid-8663598|pmid-16403634|pmid-11313454|pmid-16109373|pmid-12574126|pmid-12150906|pmid-11528389|pmid-12022233...
Taken together, our study shows that correlation with expression is indeed effective in deciphering splicing regulatory elements, and provides the most comprehensive picture yet available of muscle-specific alternative splicing program in humans.
[ "8", "24", "25", "26", "18", "22", "27–33", "34", "35" ]
246
1,785
0
false
Taken together, our study shows that correlation with expression is indeed effective in deciphering splicing regulatory elements, and provides the most comprehensive picture yet available of muscle-specific alternative splicing program in humans.
[]
Taken together, our study shows that correlation with expression is indeed effective in deciphering splicing regulatory elements, and provides the most comprehensive picture yet available of muscle-specific alternative splicing program in humans.
true
true
true
true
true
308
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
In this study we have demonstrated that the correlation with expression approach, applied to global exon expression profiles, represents a powerful new tool for identification of cis-regulatory motifs for alternative splicing.
[ "57" ]
226
1,786
0
false
In this study we have demonstrated that the correlation with expression approach, applied to global exon expression profiles, represents a powerful new tool for identification of cis-regulatory motifs for alternative splicing.
[]
In this study we have demonstrated that the correlation with expression approach, applied to global exon expression profiles, represents a powerful new tool for identification of cis-regulatory motifs for alternative splicing.
true
true
true
true
true
309
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
Using a dataset of high-confidence muscle-enriched alternative exons extracted from human exon microarray data, we correlated motif occurrences in the flanking introns with the splicing index measure of relative muscle enrichment to identify candidate regulatory motifs for the muscle-splicing program.
[ "57" ]
302
1,787
0
false
Using a dataset of high-confidence muscle-enriched alternative exons extracted from human exon microarray data, we correlated motif occurrences in the flanking introns with the splicing index measure of relative muscle enrichment to identify candidate regulatory motifs for the muscle-splicing program.
[]
Using a dataset of high-confidence muscle-enriched alternative exons extracted from human exon microarray data, we correlated motif occurrences in the flanking introns with the splicing index measure of relative muscle enrichment to identify candidate regulatory motifs for the muscle-splicing program.
true
true
true
true
true
309
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
The logic of this strategy is supported by many studies of transcriptional regulation, and a few of splicing regulation (57), showing that functional response often correlates with regulatory motif copy number.
[ "57" ]
210
1,788
1
false
The logic of this strategy is supported by many studies of transcriptional regulation, and a few of splicing regulation, showing that functional response often correlates with regulatory motif copy number.
[ "57" ]
The logic of this strategy is supported by many studies of transcriptional regulation, and a few of splicing regulation, showing that functional response often correlates with regulatory motif copy number.
true
true
true
true
true
309
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
The analysis presented here demonstrates that the number of Fox splicing factor binding sites (ugcaug) correlates strongly with the muscle splicing index (Figure 3A), consistent with previous reports that Fox proteins can regulate various tissue-specific alternative splicing events.
[ "57" ]
283
1,789
0
false
The analysis presented here demonstrates that the number of Fox splicing factor binding sites (ugcaug) correlates strongly with the muscle splicing index (Figure 3A), consistent with previous reports that Fox proteins can regulate various tissue-specific alternative splicing events.
[]
The analysis presented here demonstrates that the number of Fox splicing factor binding sites (ugcaug) correlates strongly with the muscle splicing index (Figure 3A), consistent with previous reports that Fox proteins can regulate various tissue-specific alternative splicing events.
true
true
true
true
true
309
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
The validity of correlation results were further supported by over-representation analysis, by comparative genomics showing that top scoring correlation motifs are phylogenetically conserved among vertebrate genomes, and by previous experimental studies implicating most of the same motifs in regulation of muscle-specif...
[ "57" ]
331
1,790
0
false
The validity of correlation results were further supported by over-representation analysis, by comparative genomics showing that top scoring correlation motifs are phylogenetically conserved among vertebrate genomes, and by previous experimental studies implicating most of the same motifs in regulation of muscle-specif...
[]
The validity of correlation results were further supported by over-representation analysis, by comparative genomics showing that top scoring correlation motifs are phylogenetically conserved among vertebrate genomes, and by previous experimental studies implicating most of the same motifs in regulation of muscle-specif...
true
true
true
true
true
309
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
Since tissue-specific alternative splicing is rarely an all or nothing phenomenon (e.g.
[ "57" ]
87
1,791
0
false
Since tissue-specific alternative splicing is rarely an all or nothing phenomenon (e.g.
[]
Since tissue-specific alternative splicing is rarely an all or nothing phenomenon (e.g.
true
true
true
true
true
309
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
Figure 1), correlation with expression may offer an attractive approach toward understanding complex tissue-specific patterns of alternative splicing.
[ "57" ]
150
1,792
0
false
Figure 1), correlation with expression may offer an attractive approach toward understanding complex tissue-specific patterns of alternative splicing.
[]
Figure 1), correlation with expression may offer an attractive approach toward understanding complex tissue-specific patterns of alternative splicing.
true
true
true
true
true
309
0
DISCUSSION
1
57
[ "B57" ]
17,626,050
pmid-12626338|pmid-12114529|pmid-15607979|pmid-12824367|pmid-8202349|pmid-16055740|pmid-11376152|pmid-15691898|pmid-15889141|pmid-12655015|pmid-16424921|pmid-15505203|pmid-14656968|pmid-11988574|pmid-16127451|pmid-14684825|pmid-15637633|pmid-9671461
This approach may be particularly effective when PWMs are utilized in the splines-based framework to account simultaneously for both relative affinity and number of motif occurrences, providing insight into both the target exons and binding sites associated with a given motif.
[ "57" ]
277
1,793
0
false
This approach may be particularly effective when PWMs are utilized in the splines-based framework to account simultaneously for both relative affinity and number of motif occurrences, providing insight into both the target exons and binding sites associated with a given motif.
[]
This approach may be particularly effective when PWMs are utilized in the splines-based framework to account simultaneously for both relative affinity and number of motif occurrences, providing insight into both the target exons and binding sites associated with a given motif.
true
true
true
true
true
309
1
DISCUSSION
1
51
[ "B51" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Our immediate goal here in this proof of concept study was to examine whether the correlation with expression method can be used to identify splicing regulatory motifs, and consider muscle-specific alternative splicing program as an example of this application.
[ "51" ]
261
1,794
0
false
Our immediate goal here in this proof of concept study was to examine whether the correlation with expression method can be used to identify splicing regulatory motifs, and consider muscle-specific alternative splicing program as an example of this application.
[]
Our immediate goal here in this proof of concept study was to examine whether the correlation with expression method can be used to identify splicing regulatory motifs, and consider muscle-specific alternative splicing program as an example of this application.
true
true
true
true
true
310
1
DISCUSSION
1
51
[ "B51" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
This analysis strongly implicated several classes of known regulatory factors including Fox (ugcaug), CELF (gugugu and ucugug), PTB (cucucu and ucuu) and putative KH-type splicing factor (acuaac) as important mediators of muscle-enriched splicing.
[ "51" ]
247
1,795
0
false
This analysis strongly implicated several classes of known regulatory factors including Fox (ugcaug), CELF (gugugu and ucugug), PTB (cucucu and ucuu) and putative KH-type splicing factor (acuaac) as important mediators of muscle-enriched splicing.
[]
This analysis strongly implicated several classes of known regulatory factors including Fox (ugcaug), CELF (gugugu and ucugug), PTB (cucucu and ucuu) and putative KH-type splicing factor (acuaac) as important mediators of muscle-enriched splicing.
true
true
true
true
true
310
1
DISCUSSION
1
51
[ "B51" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
The current study thus confirms and substantially extends earlier reports that these factors can regulate one or a few muscle-enriched exons by providing significant new computational evidence that they correlate with muscle exons in a much larger dataset.
[ "51" ]
256
1,796
0
false
The current study thus confirms and substantially extends earlier reports that these factors can regulate one or a few muscle-enriched exons by providing significant new computational evidence that they correlate with muscle exons in a much larger dataset.
[]
The current study thus confirms and substantially extends earlier reports that these factors can regulate one or a few muscle-enriched exons by providing significant new computational evidence that they correlate with muscle exons in a much larger dataset.
true
true
true
true
true
310
1
DISCUSSION
1
51
[ "B51" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Interestingly, there was a notable lack of novel cis-elements in the proximal flanking introns that strongly correlate with muscle expression across the entire dataset.
[ "51" ]
168
1,797
0
false
Interestingly, there was a notable lack of novel cis-elements in the proximal flanking introns that strongly correlate with muscle expression across the entire dataset.
[]
Interestingly, there was a notable lack of novel cis-elements in the proximal flanking introns that strongly correlate with muscle expression across the entire dataset.
true
true
true
true
true
310
1
DISCUSSION
1
51
[ "B51" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
This could indicate that much of the fundamental machinery for regulation of generalized muscle-enriched splicing has been identified or, more likely, that additional features need to be incorporated in the algorithms to identify the remaining components.
[ "51" ]
255
1,798
0
false
This could indicate that much of the fundamental machinery for regulation of generalized muscle-enriched splicing has been identified or, more likely, that additional features need to be incorporated in the algorithms to identify the remaining components.
[]
This could indicate that much of the fundamental machinery for regulation of generalized muscle-enriched splicing has been identified or, more likely, that additional features need to be incorporated in the algorithms to identify the remaining components.
true
true
true
true
true
310
1
DISCUSSION
1
51
[ "B51" ]
17,626,050
pmid-11175784|pmid-15534222|pmid-12626739|pmid-12217908|pmid-15534222|pmid-16760900|pmid-16760900|pmid-11175784|pmid-15534222|pmid-12482955|pmid-16760900|pmid-12702209
Such features may include wider motifs and motifs located more distally from the regulated exons.
[ "51" ]
97
1,799
0
false
Such features may include wider motifs and motifs located more distally from the regulated exons.
[]
Such features may include wider motifs and motifs located more distally from the regulated exons.
true
true
true
true
true
310