Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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5
DISCUSSION
1
40
[ "ref40", "ref33", "ref34" ]
18,614,536
pmid-8662797|NA|pmid-17018293
This suggests that Ubr1 may also be a therapeutic target during retinal inflammation.
[ "40", "33", "34" ]
86
40,216
0
false
This suggests that Ubr1 may also be a therapeutic target during retinal inflammation.
[]
This suggests that Ubr1 may also be a therapeutic target during retinal inflammation.
true
true
true
true
true
6,942
6
DISCUSSION
1
44
[ "ref44", "ref45" ]
18,614,536
pmid-11121744|pmid-16401721
An alternative role of STAT3 activation on accelerating UPS may be as follows.
[ "44", "45" ]
79
40,217
0
false
An alternative role of STAT3 activation on accelerating UPS may be as follows.
[]
An alternative role of STAT3 activation on accelerating UPS may be as follows.
true
true
true
true
true
6,943
6
DISCUSSION
1
44
[ "ref44", "ref45" ]
18,614,536
pmid-11121744|pmid-16401721
Polarized microtubules, which promote the accumulation of misfolded proteins into aggresomes (44), are stabilized by STAT3 activation (45).
[ "44", "45" ]
142
40,218
1
false
Polarized microtubules, which promote the accumulation of misfolded proteins into aggresomes, are stabilized by STAT3 activation.
[ "44", "45" ]
Polarized microtubules, which promote the accumulation of misfolded proteins into aggresomes, are stabilized by STAT3 activation.
true
true
true
true
true
6,943
6
DISCUSSION
1
44
[ "ref44", "ref45" ]
18,614,536
pmid-11121744|pmid-16401721
Therefore, the intracellular conditions during inflammation would promote the aggregation of misfolded rhodopsin.
[ "44", "45" ]
115
40,219
0
false
Therefore, the intracellular conditions during inflammation would promote the aggregation of misfolded rhodopsin.
[]
Therefore, the intracellular conditions during inflammation would promote the aggregation of misfolded rhodopsin.
true
true
true
true
true
6,943
7
DISCUSSION
1
46
[ "ref46", "ref12" ]
18,614,536
pmid-1710212|pmid-17192435
In addition to direct induction of the UPS, some other mechanisms could be involved in the post-transcriptional inhibition of rhodopsin expression.
[ "46", "12" ]
148
40,220
0
false
In addition to direct induction of the UPS, some other mechanisms could be involved in the post-transcriptional inhibition of rhodopsin expression.
[]
In addition to direct induction of the UPS, some other mechanisms could be involved in the post-transcriptional inhibition of rhodopsin expression.
true
true
true
true
true
6,944
7
DISCUSSION
1
46
[ "ref46", "ref12" ]
18,614,536
pmid-1710212|pmid-17192435
SOCS3 was expressed not only in photoreceptor cells but also in Müller glial cells during inflammation.
[ "46", "12" ]
105
40,221
0
false
SOCS3 was expressed not only in photoreceptor cells but also in Müller glial cells during inflammation.
[]
SOCS3 was expressed not only in photoreceptor cells but also in Müller glial cells during inflammation.
true
true
true
true
true
6,944
7
DISCUSSION
1
46
[ "ref46", "ref12" ]
18,614,536
pmid-1710212|pmid-17192435
It is possible that excessive STAT3 activation could induce the release of cytokines by the Müller glial cells that secondarily up-regulated the UPS and/or other post-transcriptional mechanisms in the photoreceptor cells, especially in those of the α-Cre SOCS3flox/flox mice.
[ "46", "12" ]
279
40,222
0
false
It is possible that excessive STAT3 activation could induce the release of cytokines by the Müller glial cells that secondarily up-regulated the UPS and/or other post-transcriptional mechanisms in the photoreceptor cells, especially in those of the α-Cre SOCS3flox/flox mice.
[]
It is possible that excessive STAT3 activation could induce the release of cytokines by the Müller glial cells that secondarily up-regulated the UPS and/or other post-transcriptional mechanisms in the photoreceptor cells, especially in those of the α-Cre SOCS3flox/flox mice.
true
true
true
true
true
6,944
7
DISCUSSION
1
46
[ "ref46", "ref12" ]
18,614,536
pmid-1710212|pmid-17192435
Otherwise, expression of rhodopsin kinase, which is involved in rhodopsin turnover under normal conditions (46), was up-regulated 8 h after LPS injection in α-Cre SOCS3flox/flox mice, although its level trended downward at 48 h following the decrease in rhodopsin (data not shown).
[ "46", "12" ]
286
40,223
1
false
Otherwise, expression of rhodopsin kinase, which is involved in rhodopsin turnover under normal conditions, was up-regulated 8 h after LPS injection in α-Cre SOCS3flox/flox mice, although its level trended downward at 48 h following the decrease in rhodopsin (data not shown).
[ "46" ]
Otherwise, expression of rhodopsin kinase, which is involved in rhodopsin turnover under normal conditions, was up-regulated 8 h after LPS injection in α-Cre SOCS3flox/flox mice, although its level trended downward at 48 h following the decrease in rhodopsin (data not shown).
true
true
true
true
true
6,944
7
DISCUSSION
1
12
[ "ref46", "ref12" ]
18,614,536
pmid-1710212|pmid-17192435
Therefore, up-regulation of the general pathway for rhodopsin degradation could also contribute to its reduced levels (12).
[ "46", "12" ]
125
40,224
1
false
Therefore, up-regulation of the general pathway for rhodopsin degradation could also contribute to its reduced levels.
[ "12" ]
Therefore, up-regulation of the general pathway for rhodopsin degradation could also contribute to its reduced levels.
true
true
true
true
true
6,944
7
DISCUSSION
1
46
[ "ref46", "ref12" ]
18,614,536
pmid-1710212|pmid-17192435
In LPS-induced retinal inflammation, various kinds of cytokines could also be involved, causing either cell-autonomous or non-cell-autonomous effects on rhodopsin expression with or without STAT3-dependent mechanism.
[ "46", "12" ]
219
40,225
0
false
In LPS-induced retinal inflammation, various kinds of cytokines could also be involved, causing either cell-autonomous or non-cell-autonomous effects on rhodopsin expression with or without STAT3-dependent mechanism.
[]
In LPS-induced retinal inflammation, various kinds of cytokines could also be involved, causing either cell-autonomous or non-cell-autonomous effects on rhodopsin expression with or without STAT3-dependent mechanism.
true
true
true
true
true
6,944
7
DISCUSSION
1
46
[ "ref46", "ref12" ]
18,614,536
pmid-1710212|pmid-17192435
Further investigation should be continued to clarify the detailed mechanisms.
[ "46", "12" ]
78
40,226
0
false
Further investigation should be continued to clarify the detailed mechanisms.
[]
Further investigation should be continued to clarify the detailed mechanisms.
true
true
true
true
true
6,944
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
Distinct Regulation of Rhodopsin Expression between the Developing and Adult Retina—We reported previously that STAT3 activation inhibits rhodopsin expression at transcriptional levels in the developing retina.
[ "10", "8", "10", "47", "48" ]
212
40,227
0
false
Distinct Regulation of Rhodopsin Expression between the Developing and Adult Retina—We reported previously that STAT3 activation inhibits rhodopsin expression at transcriptional levels in the developing retina.
[]
Distinct Regulation of Rhodopsin Expression between the Developing and Adult Retina—We reported previously that STAT3 activation inhibits rhodopsin expression at transcriptional levels in the developing retina.
true
true
true
true
true
6,945
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
SOCS3 is required to initiate the transcription of rhodopsin and crx, inhibiting STAT3 activation in the perinatal period (10).
[ "10", "8", "10", "47", "48" ]
130
40,228
1
false
SOCS3 is required to initiate the transcription of rhodopsin and crx, inhibiting STAT3 activation in the perinatal period.
[ "10" ]
SOCS3 is required to initiate the transcription of rhodopsin and crx, inhibiting STAT3 activation in the perinatal period.
true
true
true
true
true
6,945
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
This situation resembles that in the adult retina during inflammation.
[ "10", "8", "10", "47", "48" ]
71
40,229
0
false
This situation resembles that in the adult retina during inflammation.
[]
This situation resembles that in the adult retina during inflammation.
true
true
true
true
true
6,945
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
However, unexpectedly, the amounts of rhodopsin and crx transcripts did not decrease with STAT3 activation during inflammation or after IL-6 exposure.
[ "10", "8", "10", "47", "48" ]
152
40,230
0
false
However, unexpectedly, the amounts of rhodopsin and crx transcripts did not decrease with STAT3 activation during inflammation or after IL-6 exposure.
[]
However, unexpectedly, the amounts of rhodopsin and crx transcripts did not decrease with STAT3 activation during inflammation or after IL-6 exposure.
true
true
true
true
true
6,945
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
These results suggest that the underlying mechanisms for regulating the transcription and/or RNA stability of rhodopsin and crx are different in the inflamed adult retina than in the developing retina (8, 10).
[ "10", "8", "10", "47", "48" ]
214
40,231
0
false
These results suggest that the underlying mechanisms for regulating the transcription and/or RNA stability of rhodopsin and crx are different in the inflamed adult retina than in the developing retina.
[ "8,\n 10" ]
These results suggest that the underlying mechanisms for regulating the transcription and/or RNA stability of rhodopsin and crx are different in the inflamed adult retina than in the developing retina.
true
true
true
true
true
6,945
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
One explanation for this finding is that rhodopsin is a part of a negative feedback loop controlling its own transcription, and the loss of rhodopsin protein therefore rather induces the mRNAs, even in the presence of high levels of STAT3 activation.
[ "10", "8", "10", "47", "48" ]
253
40,232
0
false
One explanation for this finding is that rhodopsin is a part of a negative feedback loop controlling its own transcription, and the loss of rhodopsin protein therefore rather induces the mRNAs, even in the presence of high levels of STAT3 activation.
[]
One explanation for this finding is that rhodopsin is a part of a negative feedback loop controlling its own transcription, and the loss of rhodopsin protein therefore rather induces the mRNAs, even in the presence of high levels of STAT3 activation.
true
true
true
true
true
6,945
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
This is consistent with the fact that the level of crx mRNA increases with new rhodopsin production during development and then is somewhat down-regulated after rhodopsin reaches its plateau level (47, 48).
[ "10", "8", "10", "47", "48" ]
210
40,233
0
false
This is consistent with the fact that the level of crx mRNA increases with new rhodopsin production during development and then is somewhat down-regulated after rhodopsin reaches its plateau level.
[ "47,\n 48" ]
This is consistent with the fact that the level of crx mRNA increases with new rhodopsin production during development and then is somewhat down-regulated after rhodopsin reaches its plateau level.
true
true
true
true
true
6,945
8
DISCUSSION
1
10
[ "ref10", "ref8", "ref10", "ref47", "ref48" ]
18,614,536
pmid-17198696|pmid-15207851|pmid-17198696|pmid-11880494|pmid-9390562
Alternatively, the effect of STAT3 activation in the surrounding retinal cells, such as Müller glial cells, rather than a direct action in photoreceptor cells, may be one of the pathways for the present observation.
[ "10", "8", "10", "47", "48" ]
218
40,234
0
false
Alternatively, the effect of STAT3 activation in the surrounding retinal cells, such as Müller glial cells, rather than a direct action in photoreceptor cells, may be one of the pathways for the present observation.
[]
Alternatively, the effect of STAT3 activation in the surrounding retinal cells, such as Müller glial cells, rather than a direct action in photoreceptor cells, may be one of the pathways for the present observation.
true
true
true
true
true
6,945
9
DISCUSSION
0
null
null
18,614,536
null
As regards transcription under normal condition, the same mechanism as in the developing retina may be also applicable in the adult, since mRNA expression of rhodopsin and crx tended to be down-regulated in α-Cre SOCS3flox/flox mice in which STAT3 is more activated.
null
270
40,235
0
false
null
null
As regards transcription under normal condition, the same mechanism as in the developing retina may be also applicable in the adult, since mRNA expression of rhodopsin and crx tended to be down-regulated in α-Cre SOCS3flox/flox mice in which STAT3 is more activated.
true
true
true
true
true
6,946
9
DISCUSSION
0
null
null
18,614,536
null
But redundant regulatory mechanisms should be present given that rhodopsin protein levels in the α-Cre SOCS3flox/flox mice caught up with those in wild-type mice and the a-wave in ERG was normal in the adult mutants.
null
219
40,236
0
false
null
null
But redundant regulatory mechanisms should be present given that rhodopsin protein levels in the α-Cre SOCS3flox/flox mice caught up with those in wild-type mice and the a-wave in ERG was normal in the adult mutants.
true
true
true
true
true
6,946
10
DISCUSSION
0
null
null
18,614,536
null
Therefore, rhodopsin protein was down-regulated in a post-transcriptional fashion, which involves protein degradation through the UPS, most probably activated by STAT3-dependent E3 ubiquitin ligase, Ubr1.
null
206
40,237
0
false
null
null
Therefore, rhodopsin protein was down-regulated in a post-transcriptional fashion, which involves protein degradation through the UPS, most probably activated by STAT3-dependent E3 ubiquitin ligase, Ubr1.
true
true
true
true
true
6,947
10
DISCUSSION
0
null
null
18,614,536
null
SOCS3 minimizes and promotes recovery from this influence of inflammatory signaling by inhibiting STAT3 activation, thereby contributing to the preservation of rhodopsin expression and visual function.
null
204
40,238
0
false
null
null
SOCS3 minimizes and promotes recovery from this influence of inflammatory signaling by inhibiting STAT3 activation, thereby contributing to the preservation of rhodopsin expression and visual function.
true
true
true
true
true
6,947
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5 B6" ]
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
Gene transcription is regulated, in large part, by transcription factor (TF) proteins that bind to the relative vicinity of the target gene in a sequence-specific fashion.
[ "1", "2", "3–6" ]
171
40,239
0
false
Gene transcription is regulated, in large part, by transcription factor (TF) proteins that bind to the relative vicinity of the target gene in a sequence-specific fashion.
[]
Gene transcription is regulated, in large part, by transcription factor (TF) proteins that bind to the relative vicinity of the target gene in a sequence-specific fashion.
true
true
true
true
true
6,948
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5 B6" ]
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
The activities of the TFs themselves are often regulated through one or more posttranslational modifications (PTMs).
[ "1", "2", "3–6" ]
116
40,240
0
false
The activities of the TFs themselves are often regulated through one or more posttranslational modifications (PTMs).
[]
The activities of the TFs themselves are often regulated through one or more posttranslational modifications (PTMs).
true
true
true
true
true
6,948
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5 B6" ]
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
PTMs constitute covalent chemical changes—e.g.
[ "1", "2", "3–6" ]
46
40,241
0
false
PTMs constitute covalent chemical changes—e.g.
[]
PTMs constitute covalent chemical changes—e.g.
true
true
true
true
true
6,948
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5 B6" ]
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
phosphorylation, acetylation, methylation or glycosylation—to the residues in the protein sequence.
[ "1", "2", "3–6" ]
99
40,242
0
false
phosphorylation, acetylation, methylation or glycosylation—to the residues in the protein sequence.
[]
phosphorylation, acetylation, methylation or glycosylation—to the residues in the protein sequence.
false
true
true
true
false
6,948
0
INTRODUCTION
1
3–6
[ "B1", "B2", "B3 B4 B5 B6" ]
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
Hundreds of distinct types of PTMs have been reported (1,2), at least a dozen of which regulate TF activities (3–6).
[ "1", "2", "3–6" ]
116
40,243
1
false
Hundreds of distinct types of PTMs have been reported, at least a dozen of which regulate TF activities.
[ "1,2", "3–6" ]
Hundreds of distinct types of PTMs have been reported, at least a dozen of which regulate TF activities.
true
true
true
true
true
6,948
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
TF-PTMs modulate, through mechanisms that are not completely known, the activity of TFs and the downstream regulation of the target genes, thus acting as ‘molecular switchboards’ that map inputs from cell signaling pathways to gene transcripts (3,4).
[ "3", "4", "7", "8" ]
250
40,244
0
false
TF-PTMs modulate, through mechanisms that are not completely known, the activity of TFs and the downstream regulation of the target genes, thus acting as ‘molecular switchboards’ that map inputs from cell signaling pathways to gene transcripts.
[ "3,4" ]
TF-PTMs modulate, through mechanisms that are not completely known, the activity of TFs and the downstream regulation of the target genes, thus acting as ‘molecular switchboards’ that map inputs from cell signaling pathways to gene transcripts.
true
true
true
true
true
6,949
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
On one extreme, such regulation can be simple and binary—i.e.
[ "3", "4", "7", "8" ]
61
40,245
0
false
On one extreme, such regulation can be simple and binary—i.e.
[]
On one extreme, such regulation can be simple and binary—i.e.
true
true
true
true
true
6,949
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
PTMs that serve as ‘on/off’ switches for TFs.
[ "3", "4", "7", "8" ]
45
40,246
0
false
PTMs that serve as ‘on/off’ switches for TFs.
[]
PTMs that serve as ‘on/off’ switches for TFs.
true
true
true
true
true
6,949
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
More often, however, this regulation is highly complex, with multiple signaling inputs integrated into tightly regulated transcript levels.
[ "3", "4", "7", "8" ]
139
40,247
0
false
More often, however, this regulation is highly complex, with multiple signaling inputs integrated into tightly regulated transcript levels.
[]
More often, however, this regulation is highly complex, with multiple signaling inputs integrated into tightly regulated transcript levels.
true
true
true
true
true
6,949
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
Furthermore, the relative concentrations of many PTMs at steady state are dynamically maintained by opposing forces catalyzing the addition or removal of a chemical group.
[ "3", "4", "7", "8" ]
171
40,248
0
false
Furthermore, the relative concentrations of many PTMs at steady state are dynamically maintained by opposing forces catalyzing the addition or removal of a chemical group.
[]
Furthermore, the relative concentrations of many PTMs at steady state are dynamically maintained by opposing forces catalyzing the addition or removal of a chemical group.
true
true
true
true
true
6,949
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
To fully understand the complexity of TF-PTM-mediated regulation of gene transcription, we first need to map the connectivity between signaling molecules, PTMs, TFs and target genes, and such a map currently does not exist.
[ "3", "4", "7", "8" ]
223
40,249
0
false
To fully understand the complexity of TF-PTM-mediated regulation of gene transcription, we first need to map the connectivity between signaling molecules, PTMs, TFs and target genes, and such a map currently does not exist.
[]
To fully understand the complexity of TF-PTM-mediated regulation of gene transcription, we first need to map the connectivity between signaling molecules, PTMs, TFs and target genes, and such a map currently does not exist.
true
true
true
true
true
6,949
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
The characterized instances of TF-PTMs are biased largely towards well-characterized TFs, e.g.
[ "3", "4", "7", "8" ]
94
40,250
0
false
The characterized instances of TF-PTMs are biased largely towards well-characterized TFs, e.g.
[]
The characterized instances of TF-PTMs are biased largely towards well-characterized TFs, e.g.
true
true
true
true
true
6,949
1
INTRODUCTION
1
7
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
the cAMP-response element binding protein (CREB) (7), and PTM types, e.g.
[ "3", "4", "7", "8" ]
73
40,251
1
false
the cAMP-response element binding protein (CREB), and PTM types, e.g.
[ "7" ]
the cAMP-response element binding protein (CREB), and PTM types, e.g.
false
true
true
true
false
6,949
1
INTRODUCTION
1
8
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
phosphorylation (8).
[ "3", "4", "7", "8" ]
20
40,252
1
false
phosphorylation.
[ "8" ]
phosphorylation.
false
true
true
true
false
6,949
1
INTRODUCTION
1
3
[ "B3", "B4", "B7", "B8" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
Therefore, we cannot begin to explore the more complex problems of molecular kinetics or network topologies surrounding TF-PTMs on a systematic basis.
[ "3", "4", "7", "8" ]
150
40,253
0
false
Therefore, we cannot begin to explore the more complex problems of molecular kinetics or network topologies surrounding TF-PTMs on a systematic basis.
[]
Therefore, we cannot begin to explore the more complex problems of molecular kinetics or network topologies surrounding TF-PTMs on a systematic basis.
true
true
true
true
true
6,949
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
A canonical example of a regulatory TF-PTM is Ser133 phosphorylation of CREB in mammals (Figure 1).
[ "3" ]
99
40,254
0
false
A canonical example of a regulatory TF-PTM is Ser133 phosphorylation of CREB in mammals (Figure 1).
[]
A canonical example of a regulatory TF-PTM is Ser133 phosphorylation of CREB in mammals (Figure 1).
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
This TF-PTM has long been characterized as a key event in protein kinase A (PKA) signaling that results in the activation of target genes.
[ "3" ]
138
40,255
0
false
This TF-PTM has long been characterized as a key event in protein kinase A (PKA) signaling that results in the activation of target genes.
[]
This TF-PTM has long been characterized as a key event in protein kinase A (PKA) signaling that results in the activation of target genes.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
The primary serine phosphorylation allows CREB to interact with its co-activator, CBP, thereby recruiting the core transcriptional machinery.
[ "3" ]
141
40,256
0
false
The primary serine phosphorylation allows CREB to interact with its co-activator, CBP, thereby recruiting the core transcriptional machinery.
[]
The primary serine phosphorylation allows CREB to interact with its co-activator, CBP, thereby recruiting the core transcriptional machinery.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
Other kinases have since been discovered to also activate downstream genes through this same TF-PTM.
[ "3" ]
100
40,257
0
false
Other kinases have since been discovered to also activate downstream genes through this same TF-PTM.
[]
Other kinases have since been discovered to also activate downstream genes through this same TF-PTM.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
Other PTMs that alter CREB activity have also been discovered, including additional phosphorylations, acetylations and interestingly, an O-linked N-acetyl glycosylation (O-GlcNAc) that antagonizes the primary activating phosphorylation.
[ "3" ]
236
40,258
0
false
Other PTMs that alter CREB activity have also been discovered, including additional phosphorylations, acetylations and interestingly, an O-linked N-acetyl glycosylation (O-GlcNAc) that antagonizes the primary activating phosphorylation.
[]
Other PTMs that alter CREB activity have also been discovered, including additional phosphorylations, acetylations and interestingly, an O-linked N-acetyl glycosylation (O-GlcNAc) that antagonizes the primary activating phosphorylation.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
These modifications are reviewed in further detail in ref.
[ "3" ]
58
40,259
0
false
These modifications are reviewed in further detail in ref.
[]
These modifications are reviewed in further detail in ref.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
CREB exemplifies the potential complexity of TF-PTM regulatory programs beyond simple ‘on/off’ switches, and the emerging appreciation for modifications other than phosphorylation.
[ "3" ]
180
40,260
0
false
CREB exemplifies the potential complexity of TF-PTM regulatory programs beyond simple ‘on/off’ switches, and the emerging appreciation for modifications other than phosphorylation.
[]
CREB exemplifies the potential complexity of TF-PTM regulatory programs beyond simple ‘on/off’ switches, and the emerging appreciation for modifications other than phosphorylation.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
Figure 1.cAMP-response element binding protein (CREB) Regulation.
[ "3" ]
65
40,261
0
false
Figure 1.cAMP-response element binding protein (CREB) Regulation.
[]
Figure 1.cAMP-response element binding protein (CREB) Regulation.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
CREB is a well-studied TF that exemplifies the complexity of TF-PTM regulatory circuits.
[ "3" ]
88
40,262
0
false
CREB is a well-studied TF that exemplifies the complexity of TF-PTM regulatory circuits.
[]
CREB is a well-studied TF that exemplifies the complexity of TF-PTM regulatory circuits.
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
Canonical CREB regulation begins with phosphorylation of Ser133 by Protein Kinase A (PKA), which facilitates interaction with CREB-binding protein (CBP) to recruit RNA Polymerase II (RNAPII) and promote transcription of target genes such as Somatostatin (SST).
[ "3" ]
260
40,263
0
false
Canonical CREB regulation begins with phosphorylation of Ser133 by Protein Kinase A (PKA), which facilitates interaction with CREB-binding protein (CBP) to recruit RNA Polymerase II (RNAPII) and promote transcription of target genes such as Somatostatin (SST).
[]
Canonical CREB regulation begins with phosphorylation of Ser133 by Protein Kinase A (PKA), which facilitates interaction with CREB-binding protein (CBP) to recruit RNA Polymerase II (RNAPII) and promote transcription of target genes such as Somatostatin (SST).
true
true
true
true
true
6,950
2
INTRODUCTION
1
3
[ "B3" ]
18,927,104
pmid-14737652
Other kinases can also regulate CREB through Ser133 and other phosphorylations, CBP can further regulate CREB activity through multiple acetylations, and glycosylation can disrupt the activating effect of the Ser133 phosphorylation.
[ "3" ]
232
40,264
0
false
Other kinases can also regulate CREB through Ser133 and other phosphorylations, CBP can further regulate CREB activity through multiple acetylations, and glycosylation can disrupt the activating effect of the Ser133 phosphorylation.
[]
Other kinases can also regulate CREB through Ser133 and other phosphorylations, CBP can further regulate CREB activity through multiple acetylations, and glycosylation can disrupt the activating effect of the Ser133 phosphorylation.
true
true
true
true
true
6,950
3
INTRODUCTION
0
null
null
18,927,104
NA|pmid-17921496|pmid-12740579
cAMP-response element binding protein (CREB) Regulation.
null
56
40,265
0
false
null
null
cAMP-response element binding protein (CREB) Regulation.
false
true
true
true
false
6,951
3
INTRODUCTION
0
null
null
18,927,104
NA|pmid-17921496|pmid-12740579
CREB is a well-studied TF that exemplifies the complexity of TF-PTM regulatory circuits.
null
88
40,266
0
false
null
null
CREB is a well-studied TF that exemplifies the complexity of TF-PTM regulatory circuits.
true
true
true
true
true
6,951
3
INTRODUCTION
0
null
null
18,927,104
NA|pmid-17921496|pmid-12740579
Canonical CREB regulation begins with phosphorylation of Ser133 by Protein Kinase A (PKA), which facilitates interaction with CREB-binding protein (CBP) to recruit RNA Polymerase II (RNAPII) and promote transcription of target genes such as Somatostatin (SST).
null
260
40,267
0
false
null
null
Canonical CREB regulation begins with phosphorylation of Ser133 by Protein Kinase A (PKA), which facilitates interaction with CREB-binding protein (CBP) to recruit RNA Polymerase II (RNAPII) and promote transcription of target genes such as Somatostatin (SST).
true
true
true
true
true
6,951
3
INTRODUCTION
0
null
null
18,927,104
NA|pmid-17921496|pmid-12740579
Other kinases can also regulate CREB through Ser133 and other phosphorylations, CBP can further regulate CREB activity through multiple acetylations, and glycosylation can disrupt the activating effect of the Ser133 phosphorylation.
null
232
40,268
0
false
null
null
Other kinases can also regulate CREB through Ser133 and other phosphorylations, CBP can further regulate CREB activity through multiple acetylations, and glycosylation can disrupt the activating effect of the Ser133 phosphorylation.
true
true
true
true
true
6,951
4
INTRODUCTION
0
null
null
18,927,104
null
Few TFs have been studied as extensively as CREB, and numerous TF-PTMs remain to be discovered.
null
95
40,269
0
false
null
null
Few TFs have been studied as extensively as CREB, and numerous TF-PTMs remain to be discovered.
true
true
true
true
true
6,952
4
INTRODUCTION
0
null
null
18,927,104
null
To investigate TF-PTM-mediated gene regulation at the level of systems biology, we first need to identify the key regulatory connectivity between modifying enzymes, TFs and target genes, as well as the specific TF-PTMs involved in transducing these signals.
null
257
40,270
0
false
null
null
To investigate TF-PTM-mediated gene regulation at the level of systems biology, we first need to identify the key regulatory connectivity between modifying enzymes, TFs and target genes, as well as the specific TF-PTMs involved in transducing these signals.
true
true
true
true
true
6,952
4
INTRODUCTION
0
null
null
18,927,104
null
The potential combinations of modifying enzymes, TFs, and target genes, even in simple organisms such as S. cerevisiae, are overwhelming.
null
137
40,271
0
false
null
null
The potential combinations of modifying enzymes, TFs, and target genes, even in simple organisms such as S. cerevisiae, are overwhelming.
true
true
true
true
true
6,952
4
INTRODUCTION
0
null
null
18,927,104
null
However, only a miniscule portion of these combinations are relevant to gene regulation, and prioritizing them for further study is a key step towards modeling this complex form of regulation.
null
192
40,272
0
false
null
null
However, only a miniscule portion of these combinations are relevant to gene regulation, and prioritizing them for further study is a key step towards modeling this complex form of regulation.
true
true
true
true
true
6,952
5
INTRODUCTION
1
9
[ "B9", "B10 B11 B12" ]
18,927,104
pmid-15952883|NA|pmid-17921496|pmid-12740579
A comprehensive view of the TF-PTM landscape could provide clues to broader biological questions, for instance: (i) the process-specific roles of individual types of PTMs, especially the types that are not as well studied as phosphorylation, such as hydroxylation (9), and (ii) the common mechanisms and principles by wh...
[ "9", "10–12" ]
360
40,273
1
false
A comprehensive view of the TF-PTM landscape could provide clues to broader biological questions, for instance: (i) the process-specific roles of individual types of PTMs, especially the types that are not as well studied as phosphorylation, such as hydroxylation, and (ii) the common mechanisms and principles by which ...
[ "9" ]
A comprehensive view of the TF-PTM landscape could provide clues to broader biological questions, for instance: (i) the process-specific roles of individual types of PTMs, especially the types that are not as well studied as phosphorylation, such as hydroxylation, and (ii) the common mechanisms and principles by which ...
true
true
true
true
true
6,953
5
INTRODUCTION
1
9
[ "B9", "B10 B11 B12" ]
18,927,104
pmid-15952883|NA|pmid-17921496|pmid-12740579
Our ability to approach these questions is limited by our knowledge of experimentally determined TF-PTMs and their effect on the transcription of individual genes.
[ "9", "10–12" ]
163
40,274
0
false
Our ability to approach these questions is limited by our knowledge of experimentally determined TF-PTMs and their effect on the transcription of individual genes.
[]
Our ability to approach these questions is limited by our knowledge of experimentally determined TF-PTMs and their effect on the transcription of individual genes.
true
true
true
true
true
6,953
5
INTRODUCTION
1
10–12
[ "B9", "B10 B11 B12" ]
18,927,104
pmid-15952883|NA|pmid-17921496|pmid-12740579
Predictive approaches have been proposed to identify cases where the regulatory interaction between a TF and a target gene is dependent on the expression of a modifier gene (10–12).
[ "9", "10–12" ]
181
40,275
1
false
Predictive approaches have been proposed to identify cases where the regulatory interaction between a TF and a target gene is dependent on the expression of a modifier gene.
[ "10–12" ]
Predictive approaches have been proposed to identify cases where the regulatory interaction between a TF and a target gene is dependent on the expression of a modifier gene.
true
true
true
true
true
6,953
5
INTRODUCTION
1
9
[ "B9", "B10 B11 B12" ]
18,927,104
pmid-15952883|NA|pmid-17921496|pmid-12740579
Such genome-scale predictions could be used to construct a ‘rough map’ of the TF-PTM landscape to begin to answer the questions above.
[ "9", "10–12" ]
134
40,276
0
false
Such genome-scale predictions could be used to construct a ‘rough map’ of the TF-PTM landscape to begin to answer the questions above.
[]
Such genome-scale predictions could be used to construct a ‘rough map’ of the TF-PTM landscape to begin to answer the questions above.
true
true
true
true
true
6,953
5
INTRODUCTION
1
9
[ "B9", "B10 B11 B12" ]
18,927,104
pmid-15952883|NA|pmid-17921496|pmid-12740579
However, these predictive methods are in their infancy and lack a ‘gold set’ by which to gauge their performance.
[ "9", "10–12" ]
113
40,277
0
false
However, these predictive methods are in their infancy and lack a ‘gold set’ by which to gauge their performance.
[]
However, these predictive methods are in their infancy and lack a ‘gold set’ by which to gauge their performance.
true
true
true
true
true
6,953
5
INTRODUCTION
1
9
[ "B9", "B10 B11 B12" ]
18,927,104
pmid-15952883|NA|pmid-17921496|pmid-12740579
As one of its goals, PTM-Switchboard will provide a benchmark set for predictive methods.
[ "9", "10–12" ]
89
40,278
0
false
As one of its goals, PTM-Switchboard will provide a benchmark set for predictive methods.
[]
As one of its goals, PTM-Switchboard will provide a benchmark set for predictive methods.
true
true
true
true
true
6,953
6
INTRODUCTION
1
13–15
[ "B13 B14 B15" ]
18,927,104
pmid-10592173|pmid-12438188|pmid-18629064
PTM-Switchboard differs from existing molecular pathway databases (13–15).
[ "13–15" ]
74
40,279
1
false
PTM-Switchboard differs from existing molecular pathway databases.
[ "13–15" ]
PTM-Switchboard differs from existing molecular pathway databases.
true
true
true
true
true
6,954
6
INTRODUCTION
1
13–15
[ "B13 B14 B15" ]
18,927,104
pmid-10592173|pmid-12438188|pmid-18629064
Instead of using pair-wise interactions as a primary data type, PTM-Switchboard stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on a third gene (the modifying enzyme).
[ "13–15" ]
226
40,280
0
false
Instead of using pair-wise interactions as a primary data type, PTM-Switchboard stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on a third gene (the modifying enzyme).
[]
Instead of using pair-wise interactions as a primary data type, PTM-Switchboard stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on a third gene (the modifying enzyme).
true
true
true
true
true
6,954
6
INTRODUCTION
1
13–15
[ "B13 B14 B15" ]
18,927,104
pmid-10592173|pmid-12438188|pmid-18629064
We refer to this as the Modifier-Transcription Factor-Gene triplet, or in short, the ‘MFG triplet’ (Figure 2).
[ "13–15" ]
110
40,281
0
false
We refer to this as the Modifier-Transcription Factor-Gene triplet, or in short, the ‘MFG triplet’ (Figure 2).
[]
We refer to this as the Modifier-Transcription Factor-Gene triplet, or in short, the ‘MFG triplet’ (Figure 2).
true
true
true
true
true
6,954
6
INTRODUCTION
1
13–15
[ "B13 B14 B15" ]
18,927,104
pmid-10592173|pmid-12438188|pmid-18629064
The database currently contains 116 experimentally validated instances covering 13 modifying enzymes, 11 TFs and 91 target genes—a sufficient set to evaluate computational approaches and seed further cataloging efforts.
[ "13–15" ]
219
40,282
0
false
The database currently contains 116 experimentally validated instances covering 13 modifying enzymes, 11 TFs and 91 target genes—a sufficient set to evaluate computational approaches and seed further cataloging efforts.
[]
The database currently contains 116 experimentally validated instances covering 13 modifying enzymes, 11 TFs and 91 target genes—a sufficient set to evaluate computational approaches and seed further cataloging efforts.
true
true
true
true
true
6,954
6
INTRODUCTION
1
13–15
[ "B13 B14 B15" ]
18,927,104
pmid-10592173|pmid-12438188|pmid-18629064
Figure 2.Example MFG Triplet.
[ "13–15" ]
29
40,283
0
false
Figure 2.Example MFG Triplet.
[]
Figure 2.Example MFG Triplet.
true
true
true
true
true
6,954
6
INTRODUCTION
1
13–15
[ "B13 B14 B15" ]
18,927,104
pmid-10592173|pmid-12438188|pmid-18629064
In this simple example, a factor (F) is unable to regulate the target gene (G) in its initial state.
[ "13–15" ]
100
40,284
0
false
In this simple example, a factor (F) is unable to regulate the target gene (G) in its initial state.
[]
In this simple example, a factor (F) is unable to regulate the target gene (G) in its initial state.
true
true
true
true
true
6,954
6
INTRODUCTION
1
13–15
[ "B13 B14 B15" ]
18,927,104
pmid-10592173|pmid-12438188|pmid-18629064
Modification catalyzed by the enzyme (M) transitions F to a new state (marked by *) at which point it is able to regulate G.
[ "13–15" ]
124
40,285
0
false
Modification catalyzed by the enzyme (M) transitions F to a new state (marked by *) at which point it is able to regulate G.
[]
Modification catalyzed by the enzyme (M) transitions F to a new state (marked by *) at which point it is able to regulate G.
true
true
true
true
true
6,954
7
INTRODUCTION
0
null
null
18,927,104
null
Example MFG Triplet.
null
20
40,286
0
false
null
null
Example MFG Triplet.
true
true
true
true
true
6,955
7
INTRODUCTION
0
null
null
18,927,104
null
In this simple example, a factor (F) is unable to regulate the target gene (G) in its initial state.
null
100
40,287
0
false
null
null
In this simple example, a factor (F) is unable to regulate the target gene (G) in its initial state.
true
true
true
true
true
6,955
7
INTRODUCTION
0
null
null
18,927,104
null
Modification catalyzed by the enzyme (M) transitions F to a new state (marked by *) at which point it is able to regulate G.
null
124
40,288
0
false
null
null
Modification catalyzed by the enzyme (M) transitions F to a new state (marked by *) at which point it is able to regulate G.
true
true
true
true
true
6,955
8
INTRODUCTION
1
16
[ "B16", "B17" ]
18,927,104
pmid-16644790|pmid-16046493
PTM-Switchboard is also intended to seed a larger community effort to build a more comprehensive database of MFG triplets, as they are extremely laborious to search and curate from the literature.
[ "16", "17" ]
196
40,289
0
false
PTM-Switchboard is also intended to seed a larger community effort to build a more comprehensive database of MFG triplets, as they are extremely laborious to search and curate from the literature.
[]
PTM-Switchboard is also intended to seed a larger community effort to build a more comprehensive database of MFG triplets, as they are extremely laborious to search and curate from the literature.
true
true
true
true
true
6,956
8
INTRODUCTION
1
16
[ "B16", "B17" ]
18,927,104
pmid-16644790|pmid-16046493
Text-mining approaches (16,17) are currently limited to identifying pair-wise interactions, and MFG triplets are rarely studied together as part of a single paper.
[ "16", "17" ]
163
40,290
0
false
Text-mining approaches are currently limited to identifying pair-wise interactions, and MFG triplets are rarely studied together as part of a single paper.
[ "16,17" ]
Text-mining approaches are currently limited to identifying pair-wise interactions, and MFG triplets are rarely studied together as part of a single paper.
true
true
true
true
true
6,956
8
INTRODUCTION
1
16
[ "B16", "B17" ]
18,927,104
pmid-16644790|pmid-16046493
More commonly, the overall effects of a PTM on a TF's cellular localization, degradation or DNA-binding activity are studied in one reference, while the gene targets of the TF are studied independent of any PTMs in another reference.
[ "16", "17" ]
233
40,291
0
false
More commonly, the overall effects of a PTM on a TF's cellular localization, degradation or DNA-binding activity are studied in one reference, while the gene targets of the TF are studied independent of any PTMs in another reference.
[]
More commonly, the overall effects of a PTM on a TF's cellular localization, degradation or DNA-binding activity are studied in one reference, while the gene targets of the TF are studied independent of any PTMs in another reference.
true
true
true
true
true
6,956
8
INTRODUCTION
1
16
[ "B16", "B17" ]
18,927,104
pmid-16644790|pmid-16046493
In some cases, MFG triplets can be inferred from these references together, but only with careful consideration of the molecular mechanisms involved—a task clearly beyond current text-mining methods.
[ "16", "17" ]
199
40,292
0
false
In some cases, MFG triplets can be inferred from these references together, but only with careful consideration of the molecular mechanisms involved—a task clearly beyond current text-mining methods.
[]
In some cases, MFG triplets can be inferred from these references together, but only with careful consideration of the molecular mechanisms involved—a task clearly beyond current text-mining methods.
true
true
true
true
true
6,956
8
INTRODUCTION
1
16
[ "B16", "B17" ]
18,927,104
pmid-16644790|pmid-16046493
PTM-Switchboard links the two fields of cell signaling and transcriptional regulation, and provides substantial opportunity to leverage the existing knowledge bases in these fields.
[ "16", "17" ]
181
40,293
0
false
PTM-Switchboard links the two fields of cell signaling and transcriptional regulation, and provides substantial opportunity to leverage the existing knowledge bases in these fields.
[]
PTM-Switchboard links the two fields of cell signaling and transcriptional regulation, and provides substantial opportunity to leverage the existing knowledge bases in these fields.
true
true
true
true
true
6,956
0
DISCUSSION
0
null
null
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
Here, we report the development of a new kind of database—PTM-Switchboard—to catalog TF-PTM mediated regulation of gene transcription.
null
134
40,294
0
false
null
null
Here, we report the development of a new kind of database—PTM-Switchboard—to catalog TF-PTM mediated regulation of gene transcription.
true
true
true
true
true
6,957
0
DISCUSSION
0
null
null
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
As illustrated by the cases of CREB and the FUS3/STE12/FUS1 triplet, curating known MFG triplets requires an expert examination of literature.
null
142
40,295
0
false
null
null
As illustrated by the cases of CREB and the FUS3/STE12/FUS1 triplet, curating known MFG triplets requires an expert examination of literature.
true
true
true
true
true
6,957
0
DISCUSSION
0
null
null
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
We have curated over 100 complete MFG triplets, thus establishing the groundwork for continued efforts.
null
103
40,296
0
false
null
null
We have curated over 100 complete MFG triplets, thus establishing the groundwork for continued efforts.
true
true
true
true
true
6,957
0
DISCUSSION
0
null
null
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
The database provides a focused and structured platform to leverage other regulatory network and signaling pathway resources for this multi-faceted task.
null
153
40,297
0
false
null
null
The database provides a focused and structured platform to leverage other regulatory network and signaling pathway resources for this multi-faceted task.
true
true
true
true
true
6,957
0
DISCUSSION
0
null
null
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
In the future, we plan to extend this framework to other organisms and explore modeling and text-mining approaches to expand the collection.
null
140
40,298
0
false
null
null
In the future, we plan to extend this framework to other organisms and explore modeling and text-mining approaches to expand the collection.
true
true
true
true
true
6,957
0
DISCUSSION
0
null
null
18,927,104
pmid-15174123|pmid-15174122|pmid-14737652|pmid-11823631|pmid-15714552|pmid-12526789
We have also made an effort to facilitate community involvement by allowing user submission of additional MFG triplets.
null
119
40,299
0
false
null
null
We have also made an effort to facilitate community involvement by allowing user submission of additional MFG triplets.
true
true
true
true
true
6,957
1
DISCUSSION
1
34
[ "B34", "B35", "B36", "B10", "B11" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
The first version of PTM-Switchboard is meant as the starting point towards a comprehensive database, but can also serve several more immediate purposes.
[ "34", "35", "36", "10", "11" ]
153
40,300
0
false
The first version of PTM-Switchboard is meant as the starting point towards a comprehensive database, but can also serve several more immediate purposes.
[]
The first version of PTM-Switchboard is meant as the starting point towards a comprehensive database, but can also serve several more immediate purposes.
true
true
true
true
true
6,958
1
DISCUSSION
1
34
[ "B34", "B35", "B36", "B10", "B11" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
For the molecular biologist studying a particular gene or pathway, PTM-Switchboard is available as a repository of structured MFG triplet data that is otherwise tedious to extract from the literature.
[ "34", "35", "36", "10", "11" ]
200
40,301
0
false
For the molecular biologist studying a particular gene or pathway, PTM-Switchboard is available as a repository of structured MFG triplet data that is otherwise tedious to extract from the literature.
[]
For the molecular biologist studying a particular gene or pathway, PTM-Switchboard is available as a repository of structured MFG triplet data that is otherwise tedious to extract from the literature.
true
true
true
true
true
6,958
1
DISCUSSION
1
34
[ "B34", "B35", "B36", "B10", "B11" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
Indeed, specific protein and transcription factor databases such as UniProt (34), TRANSFAC (35), and dbPTM (36) include information relevant to MFG-triplet.
[ "34", "35", "36", "10", "11" ]
156
40,302
1
false
Indeed, specific protein and transcription factor databases such as UniProt, TRANSFAC, and dbPTM include information relevant to MFG-triplet.
[ "34", "35", "36" ]
Indeed, specific protein and transcription factor databases such as UniProt, TRANSFAC, and dbPTM include information relevant to MFG-triplet.
true
true
true
true
true
6,958
1
DISCUSSION
1
34
[ "B34", "B35", "B36", "B10", "B11" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
However, integration of these resources to extract consistent information needed for MFG-triplet ascertainment is not straightforward.
[ "34", "35", "36", "10", "11" ]
134
40,303
0
false
However, integration of these resources to extract consistent information needed for MFG-triplet ascertainment is not straightforward.
[]
However, integration of these resources to extract consistent information needed for MFG-triplet ascertainment is not straightforward.
true
true
true
true
true
6,958
1
DISCUSSION
1
34
[ "B34", "B35", "B36", "B10", "B11" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
For the computational biologist, the entirety of the database (or a subset filtered by an appropriate evidence code) can serve as an ideal gold set for training and testing models of three-way regulatory interactions (10,11).
[ "34", "35", "36", "10", "11" ]
225
40,304
0
false
For the computational biologist, the entirety of the database (or a subset filtered by an appropriate evidence code) can serve as an ideal gold set for training and testing models of three-way regulatory interactions.
[ "10,11" ]
For the computational biologist, the entirety of the database (or a subset filtered by an appropriate evidence code) can serve as an ideal gold set for training and testing models of three-way regulatory interactions.
true
true
true
true
true
6,958
1
DISCUSSION
1
34
[ "B34", "B35", "B36", "B10", "B11" ]
18,927,104
pmid-14737652|pmid-11823631|pmid-11483993|pmid-12468231|pmid-14681372|pmid-8594589|pmid-16381945|NA|pmid-17921496
Moreover, the computational predictions can be conveniently compiled in PTM-Switchboard and made accessible to molecular biologists for experimental validation.
[ "34", "35", "36", "10", "11" ]
160
40,305
0
false
Moreover, the computational predictions can be conveniently compiled in PTM-Switchboard and made accessible to molecular biologists for experimental validation.
[]
Moreover, the computational predictions can be conveniently compiled in PTM-Switchboard and made accessible to molecular biologists for experimental validation.
true
true
true
true
true
6,958
2
DISCUSSION
0
null
null
18,927,104
pmid-14737652
The collection is immediately useful to researchers interested in the approximately two-dozen modifying enzymes and transcription factors included in the first version, or as a resource for studying the regulation of over 100 target genes.
null
239
40,306
0
false
null
null
The collection is immediately useful to researchers interested in the approximately two-dozen modifying enzymes and transcription factors included in the first version, or as a resource for studying the regulation of over 100 target genes.
true
true
true
true
true
6,959
2
DISCUSSION
0
null
null
18,927,104
pmid-14737652
PTM-Switchboard provides extensive connectivity to other data repositories, making it an ideal portal for researchers studying transcriptional regulation or cell signaling in Saccharomyces cerevisiae.
null
200
40,307
0
false
null
null
PTM-Switchboard provides extensive connectivity to other data repositories, making it an ideal portal for researchers studying transcriptional regulation or cell signaling in Saccharomyces cerevisiae.
true
true
true
true
true
6,959
2
DISCUSSION
0
null
null
18,927,104
pmid-14737652
Furthermore, transcriptional genomics studies typically reveal TFs potentially mediating the transcriptional control in a biological process of interest, for instance through motif enrichment analyses.
null
201
40,308
0
false
null
null
Furthermore, transcriptional genomics studies typically reveal TFs potentially mediating the transcriptional control in a biological process of interest, for instance through motif enrichment analyses.
true
true
true
true
true
6,959
2
DISCUSSION
0
null
null
18,927,104
pmid-14737652
The knowledge catalogued in PTM-Switchboard will be immediately helpful in designing further validation experiments and to place these experimental observations in a broader context of cell signaling.
null
200
40,309
0
false
null
null
The knowledge catalogued in PTM-Switchboard will be immediately helpful in designing further validation experiments and to place these experimental observations in a broader context of cell signaling.
true
true
true
true
true
6,959
3
DISCUSSION
1
10–12
[ "B10 B11 B12" ]
18,927,104
NA|pmid-17921496|pmid-12740579
Several approaches have been proposed to infer regulatory triplets based on expression data (10–12).
[ "10–12" ]
100
40,310
1
false
Several approaches have been proposed to infer regulatory triplets based on expression data.
[ "10–12" ]
Several approaches have been proposed to infer regulatory triplets based on expression data.
true
true
true
true
true
6,960
3
DISCUSSION
1
10–12
[ "B10 B11 B12" ]
18,927,104
NA|pmid-17921496|pmid-12740579
The experimentally validated cases catalogued in PTM-Switchboard provide an ideal ‘gold set’ for benchmarking the performance of these methods on the more specific task of identifying MFG triplets.
[ "10–12" ]
197
40,311
0
false
The experimentally validated cases catalogued in PTM-Switchboard provide an ideal ‘gold set’ for benchmarking the performance of these methods on the more specific task of identifying MFG triplets.
[]
The experimentally validated cases catalogued in PTM-Switchboard provide an ideal ‘gold set’ for benchmarking the performance of these methods on the more specific task of identifying MFG triplets.
true
true
true
true
true
6,960
3
DISCUSSION
1
10–12
[ "B10 B11 B12" ]
18,927,104
NA|pmid-17921496|pmid-12740579
Furthermore, investigation of transcriptional networks based entirely on genomic and transcriptomic information, as is the current practice, is limited.
[ "10–12" ]
152
40,312
0
false
Furthermore, investigation of transcriptional networks based entirely on genomic and transcriptomic information, as is the current practice, is limited.
[]
Furthermore, investigation of transcriptional networks based entirely on genomic and transcriptomic information, as is the current practice, is limited.
true
true
true
true
true
6,960
3
DISCUSSION
1
10–12
[ "B10 B11 B12" ]
18,927,104
NA|pmid-17921496|pmid-12740579
This collection is designed to encourage more integrative computational approaches based on posttranscriptional data sources.
[ "10–12" ]
125
40,313
0
false
This collection is designed to encourage more integrative computational approaches based on posttranscriptional data sources.
[]
This collection is designed to encourage more integrative computational approaches based on posttranscriptional data sources.
true
true
true
true
true
6,960
3
DISCUSSION
1
10–12
[ "B10 B11 B12" ]
18,927,104
NA|pmid-17921496|pmid-12740579
By cataloging known instances of TF-PTM mediated regulation of gene transcription, PTM-Switchboard bridges the current resources in the fields of cell signaling and transcriptional regulation to facilitate a broader understanding of regulatory networks.
[ "10–12" ]
253
40,314
0
false
By cataloging known instances of TF-PTM mediated regulation of gene transcription, PTM-Switchboard bridges the current resources in the fields of cell signaling and transcriptional regulation to facilitate a broader understanding of regulatory networks.
[]
By cataloging known instances of TF-PTM mediated regulation of gene transcription, PTM-Switchboard bridges the current resources in the fields of cell signaling and transcriptional regulation to facilitate a broader understanding of regulatory networks.
true
true
true
true
true
6,960
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
18,502,774
pmid-11103998|pmid-11733745|pmid-12016301|pmid-10592235|pmid-1384741
Recently, it has become clear that RNA molecules have a variety of important biological functions in cells, including protein synthesis, RNA processing and modification, mRNA translation, gene regulation, chromosome replication and so on (1–3).
[ "1–3", "4", "5" ]
244
40,315
1
false
Recently, it has become clear that RNA molecules have a variety of important biological functions in cells, including protein synthesis, RNA processing and modification, mRNA translation, gene regulation, chromosome replication and so on.
[ "1–3" ]
Recently, it has become clear that RNA molecules have a variety of important biological functions in cells, including protein synthesis, RNA processing and modification, mRNA translation, gene regulation, chromosome replication and so on.
true
true
true
true
true
6,961