Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
Thus, both the nature of the substituents and the length of the alkyl chain seemed to be important determinants for the inhibitory activity towards TDT as well as the DNA pol λ Y505A mutant.
null
190
10,800
0
false
null
null
Thus, both the nature of the substituents and the length of the alkyl chain seemed to be important determinants for the inhibitory activity towards TDT as well as the DNA pol λ Y505A mutant.
true
true
true
true
true
1,717
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
When the activities of the same compounds were analysed in the case of the wild-type DNA polymerase λ, a decrease in inhibitory potency could be observed going from compound IIIa to compound IIIc, similarly to the Y505A mutant.
null
227
10,801
0
false
null
null
When the activities of the same compounds were analysed in the case of the wild-type DNA polymerase λ, a decrease in inhibitory potency could be observed going from compound IIIa to compound IIIc, similarly to the Y505A mutant.
true
true
true
true
true
1,717
1
DISCUSSION
0
null
null
17,148,482
pmid-7526780|pmid-9215631|pmid-9440683|pmid-10364165|pmid-11330999|pmid-14992725|NA
However, the other fluoro- or imidazolyl-substituted compounds (IIIb, IIId, IIIe and IIIf) were inactive against the wild-type enzyme, indicating that insertion of a substituent at the dinitrophenyl ring might cause steric hindrance with the side chain of tyrosine 505.
null
269
10,802
0
false
null
null
However, the other fluoro- or imidazolyl-substituted compounds (IIIb, IIId, IIIe and IIIf) were inactive against the wild-type enzyme, indicating that insertion of a substituent at the dinitrophenyl ring might cause steric hindrance with the side chain of tyrosine 505.
true
true
true
true
true
1,717
2
DISCUSSION
1
31
[ "b31", "b10" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
The compounds Ia, Ib, IIa and IIb constitute the second class, i.e.
[ "31", "10" ]
67
10,803
0
false
The compounds Ia, Ib, IIa and IIb constitute the second class, i.e.
[]
The compounds Ia, Ib, IIa and IIb constitute the second class, i.e.
true
true
true
true
true
1,718
2
DISCUSSION
1
31
[ "b31", "b10" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
the substrate inhibitors of DNA pol λ.
[ "31", "10" ]
38
10,804
0
false
the substrate inhibitors of DNA pol λ.
[]
the substrate inhibitors of DNA pol λ.
false
true
true
true
false
1,718
2
DISCUSSION
1
31
[ "b31", "b10" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
All of them were sensitive to steric factors, such as the presence/absence of a templating base and/or of the residue tyrosine 505 in the DNA pol λ active site.
[ "31", "10" ]
160
10,805
0
false
All of them were sensitive to steric factors, such as the presence/absence of a templating base and/or of the residue tyrosine 505 in the DNA pol λ active site.
[]
All of them were sensitive to steric factors, such as the presence/absence of a templating base and/or of the residue tyrosine 505 in the DNA pol λ active site.
true
true
true
true
true
1,718
2
DISCUSSION
1
31
[ "b31", "b10" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
The tyrosine 505 residue has been shown to modulate the ability of DNA pol λ to discriminate between purines and pyrimidines (31).
[ "31", "10" ]
130
10,806
1
false
The tyrosine 505 residue has been shown to modulate the ability of DNA pol λ to discriminate between purines and pyrimidines.
[ "31" ]
The tyrosine 505 residue has been shown to modulate the ability of DNA pol λ to discriminate between purines and pyrimidines.
true
true
true
true
true
1,718
2
DISCUSSION
1
10
[ "b31", "b10" ]
17,148,482
pmid-8171115|pmid-2290857|pmid-12045095|pmid-14627824|pmid-14992725
The crystal structure of the complex of DNA pol λ with its substrates, clearly showed that tyrosine 505 acted as a ‘gate’ to limit the access of the incoming nucleotide to its binding pocket (10).
[ "31", "10" ]
196
10,807
1
false
The crystal structure of the complex of DNA pol λ with its substrates, clearly showed that tyrosine 505 acted as a ‘gate’ to limit the access of the incoming nucleotide to its binding pocket.
[ "10" ]
The crystal structure of the complex of DNA pol λ with its substrates, clearly showed that tyrosine 505 acted as a ‘gate’ to limit the access of the incoming nucleotide to its binding pocket.
true
true
true
true
true
1,718
3
DISCUSSION
0
null
null
17,148,482
pmid-16918360|pmid-11945162
The presence of a natural base (Ia) or a base analog (Ib) in the place of a phenyl group did not improve the substrate properties of the compounds.
null
147
10,808
0
false
null
null
The presence of a natural base (Ia) or a base analog (Ib) in the place of a phenyl group did not improve the substrate properties of the compounds.
true
true
true
true
true
1,719
3
DISCUSSION
0
null
null
17,148,482
pmid-16918360|pmid-11945162
For example, incorporation of compound Ib by DNA pol λ wild type occurred only opposite an AP site, but with a lower efficiency than either compound IIb or dCTP (Table 2).
null
171
10,809
0
false
null
null
For example, incorporation of compound Ib by DNA pol λ wild type occurred only opposite an AP site, but with a lower efficiency than either compound IIb or dCTP (Table 2).
true
true
true
true
true
1,719
3
DISCUSSION
0
null
null
17,148,482
pmid-16918360|pmid-11945162
Only the DNA pol λ mutant Y505A was able to incorporate the compound Ib on a normal template opposite a G, with an efficiency close to normal dCTP, indicating that the main determinant of selectivity was a steric one.
null
217
10,810
0
false
null
null
Only the DNA pol λ mutant Y505A was able to incorporate the compound Ib on a normal template opposite a G, with an efficiency close to normal dCTP, indicating that the main determinant of selectivity was a steric one.
true
true
true
true
true
1,719
4
DISCUSSION
0
null
null
17,148,482
pmid-16043633
Small structural modifications in the hydrophobic moiety of the NNTPs can drastically change their substrate properties.
null
120
10,811
0
false
null
null
Small structural modifications in the hydrophobic moiety of the NNTPs can drastically change their substrate properties.
true
true
true
true
true
1,720
4
DISCUSSION
0
null
null
17,148,482
pmid-16043633
For example, incorporation of the benzyloxycarbonyl derivative IIa by DNA pol λ was restricted by steric mechanisms, requiring the absence of both the templating base and the ‘gating’ residue tyrosine 505.
null
205
10,812
0
false
null
null
For example, incorporation of the benzyloxycarbonyl derivative IIa by DNA pol λ was restricted by steric mechanisms, requiring the absence of both the templating base and the ‘gating’ residue tyrosine 505.
true
true
true
true
true
1,720
4
DISCUSSION
0
null
null
17,148,482
pmid-16043633
However, the structurally related biphenylcarbonyl derivative IIb, required the presence of tyrosine 505, suggesting that the pendant hydrophobic group might take stabilizing π–π stacking interactions with the side chain of tyrosine 505.
null
237
10,813
0
false
null
null
However, the structurally related biphenylcarbonyl derivative IIb, required the presence of tyrosine 505, suggesting that the pendant hydrophobic group might take stabilizing π–π stacking interactions with the side chain of tyrosine 505.
true
true
true
true
true
1,720
5
DISCUSSION
0
null
null
17,148,482
null
Whereas several NNTPs were efficiently incorporated by the strictly template-independent DNA pol TDT, paradoxically, none of them was incorporated by the related template-independent activity of DNA pol λ.
null
205
10,814
0
false
null
null
Whereas several NNTPs were efficiently incorporated by the strictly template-independent DNA pol TDT, paradoxically, none of them was incorporated by the related template-independent activity of DNA pol λ.
true
true
true
true
true
1,721
5
DISCUSSION
0
null
null
17,148,482
null
This observation demonstrates that the presence of a template strand is essential for NNTPs incorporation by DNA pol λ, even if, in some cases, they further require the absence of a templating base (i.e.
null
203
10,815
0
false
null
null
This observation demonstrates that the presence of a template strand is essential for NNTPs incorporation by DNA pol λ, even if, in some cases, they further require the absence of a templating base (i.e.
true
true
true
true
true
1,721
5
DISCUSSION
0
null
null
17,148,482
null
an abasic site), suggesting that additional interactions with an intact sugar-phosphate backbone on the template strand might be important.
null
139
10,816
0
false
null
null
an abasic site), suggesting that additional interactions with an intact sugar-phosphate backbone on the template strand might be important.
false
true
true
true
false
1,721
6
DISCUSSION
1
33
[ "b33", "b34" ]
17,148,482
pmid-12459443|pmid-16522650
Perhaps, the most surprising finding was the discovery of the non-nucleoside compound IIb, which is incorporated by DNA pol β in a strictly Mg2+-dependent and template-dependent manner.
[ "33", "34" ]
185
10,817
0
false
Perhaps, the most surprising finding was the discovery of the non-nucleoside compound IIb, which is incorporated by DNA pol β in a strictly Mg2+-dependent and template-dependent manner.
[]
Perhaps, the most surprising finding was the discovery of the non-nucleoside compound IIb, which is incorporated by DNA pol β in a strictly Mg2+-dependent and template-dependent manner.
true
true
true
true
true
1,722
6
DISCUSSION
1
33
[ "b33", "b34" ]
17,148,482
pmid-12459443|pmid-16522650
Strikingly, DNA pol β showed a clear preference for incorporation of compound IIb opposite an A.
[ "33", "34" ]
96
10,818
0
false
Strikingly, DNA pol β showed a clear preference for incorporation of compound IIb opposite an A.
[]
Strikingly, DNA pol β showed a clear preference for incorporation of compound IIb opposite an A.
true
true
true
true
true
1,722
6
DISCUSSION
1
33
[ "b33", "b34" ]
17,148,482
pmid-12459443|pmid-16522650
The so-called ‘A-rule’ predicts that when a DNA pol encounters a lesion on the template strand, it often incorporates an A opposite the lesion (33).
[ "33", "34" ]
148
10,819
1
false
The so-called ‘A-rule’ predicts that when a DNA pol encounters a lesion on the template strand, it often incorporates an A opposite the lesion.
[ "33" ]
The so-called ‘A-rule’ predicts that when a DNA pol encounters a lesion on the template strand, it often incorporates an A opposite the lesion.
true
true
true
true
true
1,722
6
DISCUSSION
1
33
[ "b33", "b34" ]
17,148,482
pmid-12459443|pmid-16522650
This rule, albeit not absolute, is followed by many DNA pols, and the reason lies in the favourable base-pairing properties of A, which can then be accommodated in front of a variety of modified bases.
[ "33", "34" ]
201
10,820
0
false
This rule, albeit not absolute, is followed by many DNA pols, and the reason lies in the favourable base-pairing properties of A, which can then be accommodated in front of a variety of modified bases.
[]
This rule, albeit not absolute, is followed by many DNA pols, and the reason lies in the favourable base-pairing properties of A, which can then be accommodated in front of a variety of modified bases.
true
true
true
true
true
1,722
6
DISCUSSION
1
33
[ "b33", "b34" ]
17,148,482
pmid-12459443|pmid-16522650
The results presented here suggest that, in the case of compound IIb, pol β exploits the favourable base-pairing properties of a templating A to accommodate the incoming NNTP in the active site.
[ "33", "34" ]
194
10,821
0
false
The results presented here suggest that, in the case of compound IIb, pol β exploits the favourable base-pairing properties of a templating A to accommodate the incoming NNTP in the active site.
[]
The results presented here suggest that, in the case of compound IIb, pol β exploits the favourable base-pairing properties of a templating A to accommodate the incoming NNTP in the active site.
true
true
true
true
true
1,722
6
DISCUSSION
1
34
[ "b33", "b34" ]
17,148,482
pmid-12459443|pmid-16522650
This observation is in agreement with the hypothesis that A-rich sequences might be more prone to misincorporations by exonuclease-deficient DNA pols, as it has been suggested recently for DNA pol λ (34).
[ "33", "34" ]
204
10,822
1
false
This observation is in agreement with the hypothesis that A-rich sequences might be more prone to misincorporations by exonuclease-deficient DNA pols, as it has been suggested recently for DNA pol λ.
[ "34" ]
This observation is in agreement with the hypothesis that A-rich sequences might be more prone to misincorporations by exonuclease-deficient DNA pols, as it has been suggested recently for DNA pol λ.
true
true
true
true
true
1,722
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
The biphenyl moiety of compound IIb has a length of 6.9 Å and it is 2.7 Å wide.
[ "21", "35", "36" ]
79
10,823
0
false
The biphenyl moiety of compound IIb has a length of 6.9 Å and it is 2.7 Å wide.
[]
The biphenyl moiety of compound IIb has a length of 6.9 Å and it is 2.7 Å wide.
true
true
true
true
true
1,723
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
As a comparison, the length of an adenosine nucleoside is 7.4 Å and its wideness is 2.5 Å.
[ "21", "35", "36" ]
90
10,824
0
false
As a comparison, the length of an adenosine nucleoside is 7.4 Å and its wideness is 2.5 Å.
[]
As a comparison, the length of an adenosine nucleoside is 7.4 Å and its wideness is 2.5 Å.
true
true
true
true
true
1,723
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
Also, the distance between the two phenyl rings in the biphenyl moiety is 1.4 Å, which is almost identical to the length of the glycosidic bond connecting the ribose to the base in a nucleoside, which is 1.5 Å.
[ "21", "35", "36" ]
210
10,825
0
false
Also, the distance between the two phenyl rings in the biphenyl moiety is 1.4 Å, which is almost identical to the length of the glycosidic bond connecting the ribose to the base in a nucleoside, which is 1.5 Å.
[]
Also, the distance between the two phenyl rings in the biphenyl moiety is 1.4 Å, which is almost identical to the length of the glycosidic bond connecting the ribose to the base in a nucleoside, which is 1.5 Å.
true
true
true
true
true
1,723
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
No structure is available for compound IIb; however, its biphenyl moiety lacks hydrogen (H-) bonding groups and for this reason might be compared to non-polar nucleoside analogs.
[ "21", "35", "36" ]
178
10,826
0
false
No structure is available for compound IIb; however, its biphenyl moiety lacks hydrogen (H-) bonding groups and for this reason might be compared to non-polar nucleoside analogs.
[]
No structure is available for compound IIb; however, its biphenyl moiety lacks hydrogen (H-) bonding groups and for this reason might be compared to non-polar nucleoside analogs.
true
true
true
true
true
1,723
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
Toluene, phenyl, styril, pyrene and benzimidazole moieties have been exploited as non-polar isosteres of natural bases (21).
[ "21", "35", "36" ]
124
10,827
1
false
Toluene, phenyl, styril, pyrene and benzimidazole moieties have been exploited as non-polar isosteres of natural bases.
[ "21" ]
Toluene, phenyl, styril, pyrene and benzimidazole moieties have been exploited as non-polar isosteres of natural bases.
true
true
true
true
true
1,723
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
When coupled to a 5′-triphosphate ribose, the resulting nucleoside analogs are incorporated with variable efficiencies by DNA pols.
[ "21", "35", "36" ]
131
10,828
0
false
When coupled to a 5′-triphosphate ribose, the resulting nucleoside analogs are incorporated with variable efficiencies by DNA pols.
[]
When coupled to a 5′-triphosphate ribose, the resulting nucleoside analogs are incorporated with variable efficiencies by DNA pols.
true
true
true
true
true
1,723
7
DISCUSSION
1
35
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
In particular, the non-polar shape analog of thymidine difluorotoluene, could be efficiently processed by bacterial and viral DNA pols, but not by DNA pol β, suggesting that this enzyme is not able to recognize non-H-bonding analogs (35).
[ "21", "35", "36" ]
238
10,829
1
false
In particular, the non-polar shape analog of thymidine difluorotoluene, could be efficiently processed by bacterial and viral DNA pols, but not by DNA pol β, suggesting that this enzyme is not able to recognize non-H-bonding analogs.
[ "35" ]
In particular, the non-polar shape analog of thymidine difluorotoluene, could be efficiently processed by bacterial and viral DNA pols, but not by DNA pol β, suggesting that this enzyme is not able to recognize non-H-bonding analogs.
true
true
true
true
true
1,723
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
The results presented here with compound IIb seem to indicate that H-bonding is not an absolute requirement for nucleotide recognition and incorporation by DNA pol β.
[ "21", "35", "36" ]
166
10,830
0
false
The results presented here with compound IIb seem to indicate that H-bonding is not an absolute requirement for nucleotide recognition and incorporation by DNA pol β.
[]
The results presented here with compound IIb seem to indicate that H-bonding is not an absolute requirement for nucleotide recognition and incorporation by DNA pol β.
true
true
true
true
true
1,723
7
DISCUSSION
1
21
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
However, the strong reduction in catalytic efficiency for IIb incorporation opposite normal bases (95- to 1428-fold) might be, at least in part, due to lack of H-bonding capability.
[ "21", "35", "36" ]
181
10,831
0
false
However, the strong reduction in catalytic efficiency for IIb incorporation opposite normal bases (95- to 1428-fold) might be, at least in part, due to lack of H-bonding capability.
[]
However, the strong reduction in catalytic efficiency for IIb incorporation opposite normal bases might be, at least in part, due to lack of H-bonding capability.
true
true
true
true
true
1,723
7
DISCUSSION
1
36
[ "b21", "b35", "b36" ]
17,148,482
pmid-12045095|pmid-16285726|pmid-16411765
Indeed, recent pre-seady-state kinetic analysis have shown that non-polar nucleotide analogs in the nascent base pair caused a reduction of the incorporation efficiency by E.coli DNA pol I (36).
[ "21", "35", "36" ]
194
10,832
1
false
Indeed, recent pre-seady-state kinetic analysis have shown that non-polar nucleotide analogs in the nascent base pair caused a reduction of the incorporation efficiency by E.coli DNA pol I.
[ "36" ]
Indeed, recent pre-seady-state kinetic analysis have shown that non-polar nucleotide analogs in the nascent base pair caused a reduction of the incorporation efficiency by E.coli DNA pol I.
true
true
true
true
true
1,723
8
DISCUSSION
0
null
null
17,148,482
null
The possibility of directing incorporation of non-nucleoside molecules by DNA pols, not only opposite to DNA lesions, as in the case of DNA pol λ, but also in a template-dependent manner, as for compound IIb and DNA pol β, can be exploited for the development of a novel class of molecular probes that can be used either...
null
417
10,833
0
false
null
null
The possibility of directing incorporation of non-nucleoside molecules by DNA pols, not only opposite to DNA lesions, as in the case of DNA pol λ, but also in a template-dependent manner, as for compound IIb and DNA pol β, can be exploited for the development of a novel class of molecular probes that can be used either...
true
true
true
true
true
1,724
8
DISCUSSION
0
null
null
17,148,482
null
For example, non-nucleoside chain-terminating triphosphates bearing markers groups (such as fluorescent groups) can be successfully applied for DNA labelling during post-PCR target preparation for microarray analysis.
null
217
10,834
0
false
null
null
For example, non-nucleoside chain-terminating triphosphates bearing markers groups (such as fluorescent groups) can be successfully applied for DNA labelling during post-PCR target preparation for microarray analysis.
true
true
true
true
true
1,724
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Identification of gene regulatory networks is one promise of the post-genomic era.
[ "1–3", "4", "5" ]
82
10,835
0
false
Identification of gene regulatory networks is one promise of the post-genomic era.
[]
Identification of gene regulatory networks is one promise of the post-genomic era.
true
true
true
true
true
1,725
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Identification of cis-regulatory elements and the patterns of gene expression they control become increasingly possible as large-scale expression studies and high-throughput genome sequencing are carried out.
[ "1–3", "4", "5" ]
208
10,836
0
false
Identification of cis-regulatory elements and the patterns of gene expression they control become increasingly possible as large-scale expression studies and high-throughput genome sequencing are carried out.
[]
Identification of cis-regulatory elements and the patterns of gene expression they control become increasingly possible as large-scale expression studies and high-throughput genome sequencing are carried out.
true
true
true
true
true
1,725
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
A number of approaches can be used to identify cis-regulatory elements that control expression of large numbers of genes.
[ "1–3", "4", "5" ]
121
10,837
0
false
A number of approaches can be used to identify cis-regulatory elements that control expression of large numbers of genes.
[]
A number of approaches can be used to identify cis-regulatory elements that control expression of large numbers of genes.
true
true
true
true
true
1,725
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Bioinformatic techniques can identify putative regulatory elements that are conserved in the promoters of co-expressed genes, conserved in promoters in evolutionarily distant species, or both in concert (1–3).
[ "1–3", "4", "5" ]
209
10,838
1
false
Bioinformatic techniques can identify putative regulatory elements that are conserved in the promoters of co-expressed genes, conserved in promoters in evolutionarily distant species, or both in concert.
[ "1–3" ]
Bioinformatic techniques can identify putative regulatory elements that are conserved in the promoters of co-expressed genes, conserved in promoters in evolutionarily distant species, or both in concert.
true
true
true
true
true
1,725
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Computational identification of motifs can be coupled with Bayesian statistics to allow the identification of potential interactions between transcription factors.
[ "1–3", "4", "5" ]
163
10,839
0
false
Computational identification of motifs can be coupled with Bayesian statistics to allow the identification of potential interactions between transcription factors.
[]
Computational identification of motifs can be coupled with Bayesian statistics to allow the identification of potential interactions between transcription factors.
true
true
true
true
true
1,725
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
In Saccharomyces cerevisiae and Caenorhabditis elegans, computational approaches and extremely large expression data sets, comprising upwards of 255 experiments, were used to identify regulatory modules controlling gene expression during many conditions, including progression through the cell cycle, sporulation and osm...
[ "1–3", "4", "5" ]
355
10,840
0
false
In Saccharomyces cerevisiae and Caenorhabditis elegans, computational approaches and extremely large expression data sets, comprising upwards of 255 experiments, were used to identify regulatory modules controlling gene expression during many conditions, including progression through the cell cycle, sporulation and osm...
[ "4,5" ]
In Saccharomyces cerevisiae and Caenorhabditis elegans, computational approaches and extremely large expression data sets, comprising upwards of 255 experiments, were used to identify regulatory modules controlling gene expression during many conditions, including progression through the cell cycle, sporulation and osm...
true
true
true
true
true
1,725
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Additionally these studies accurately predicted gene expression based on promoter content.
[ "1–3", "4", "5" ]
90
10,841
0
false
Additionally these studies accurately predicted gene expression based on promoter content.
[]
Additionally these studies accurately predicted gene expression based on promoter content.
true
true
true
true
true
1,725
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Unfortunately, however, in most systems such detailed microarray data are not currently available.
[ "1–3", "4", "5" ]
98
10,842
0
false
Unfortunately, however, in most systems such detailed microarray data are not currently available.
[]
Unfortunately, however, in most systems such detailed microarray data are not currently available.
true
true
true
true
true
1,725
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9 B10", "B8", "B11", "B12", "B13" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
Entamoeba histolytica is a protozoan parasite and the etiologic agent of amebic colitis and amebic liver abscess causing invasive disease in 50 million people annually (6).
[ "6", "7–10", "8", "11", "12", "13" ]
172
10,843
1
false
Entamoeba histolytica is a protozoan parasite and the etiologic agent of amebic colitis and amebic liver abscess causing invasive disease in 50 million people annually.
[ "6" ]
Entamoeba histolytica is a protozoan parasite and the etiologic agent of amebic colitis and amebic liver abscess causing invasive disease in 50 million people annually.
true
true
true
true
true
1,726
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9 B10", "B8", "B11", "B12", "B13" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
The amebic life cycle has two stages, a trophozoite form that causes invasive disease, and an encysted form that is the transmissible agent.
[ "6", "7–10", "8", "11", "12", "13" ]
140
10,844
0
false
The amebic life cycle has two stages, a trophozoite form that causes invasive disease, and an encysted form that is the transmissible agent.
[]
The amebic life cycle has two stages, a trophozoite form that causes invasive disease, and an encysted form that is the transmissible agent.
true
true
true
true
true
1,726
1
INTRODUCTION
1
7–10
[ "B6", "B7 B8 B9 B10", "B8", "B11", "B12", "B13" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
Changes in amebic transcription underlie developmental pathways, parasite response to host stresses, drug resistance and tissue invasion (7–10).
[ "6", "7–10", "8", "11", "12", "13" ]
144
10,845
1
false
Changes in amebic transcription underlie developmental pathways, parasite response to host stresses, drug resistance and tissue invasion.
[ "7–10" ]
Changes in amebic transcription underlie developmental pathways, parasite response to host stresses, drug resistance and tissue invasion.
true
true
true
true
true
1,726
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9 B10", "B8", "B11", "B12", "B13" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
A number of recent studies have utilized microarray technology to characterize the amebic transcriptional profile associated with adhesion to collagen, parasite virulence, stage conversion and tissue invasion (8,11,12,13).
[ "6", "7–10", "8", "11", "12", "13" ]
222
10,846
0
false
A number of recent studies have utilized microarray technology to characterize the amebic transcriptional profile associated with adhesion to collagen, parasite virulence, stage conversion and tissue invasion.
[ "8,11,12,13" ]
A number of recent studies have utilized microarray technology to characterize the amebic transcriptional profile associated with adhesion to collagen, parasite virulence, stage conversion and tissue invasion.
true
true
true
true
true
1,726
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9 B10", "B8", "B11", "B12", "B13" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
Although global changes in gene expression were observed, the promoter elements controlling these transcriptional changes were not identified.
[ "6", "7–10", "8", "11", "12", "13" ]
142
10,847
0
false
Although global changes in gene expression were observed, the promoter elements controlling these transcriptional changes were not identified.
[]
Although global changes in gene expression were observed, the promoter elements controlling these transcriptional changes were not identified.
true
true
true
true
true
1,726
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9 B10", "B8", "B11", "B12", "B13" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
Identifying regulatory pathways controlling transcriptional responses is key to understanding how and why amebae cause disease.
[ "6", "7–10", "8", "11", "12", "13" ]
127
10,848
0
false
Identifying regulatory pathways controlling transcriptional responses is key to understanding how and why amebae cause disease.
[]
Identifying regulatory pathways controlling transcriptional responses is key to understanding how and why amebae cause disease.
true
true
true
true
true
1,726
2
INTRODUCTION
1
14
[ "B14", "B15", "B16", "B15", "B18 B19 B20", "B21" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
The basal transcriptional machinery in E. histolytica has been well characterized, including identification of a TATA box (TATTTAAAG/C) and an Initiator (Inr) element (AAAAATTCA) (14,15).
[ "14", "15", "16", "17", "18–20", "21" ]
187
10,849
0
false
The basal transcriptional machinery in E. histolytica has been well characterized, including identification of a TATA box (TATTTAAAG/C) and an Initiator (Inr) element (AAAAATTCA).
[ "14,15" ]
The basal transcriptional machinery in E. histolytica has been well characterized, including identification of a TATA box (TATTTAAAG/C) and an Initiator (Inr) element (AAAAATTCA).
true
true
true
true
true
1,727
2
INTRODUCTION
1
14
[ "B14", "B15", "B16", "B15", "B18 B19 B20", "B21" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
In addition to the TATA box and Inr element, a third-core promoter element, the GAAC box (AA/TGAACT), is independently able to control the rate and site of transcription initiation (16,17).
[ "14", "15", "16", "17", "18–20", "21" ]
189
10,850
0
false
In addition to the TATA box and Inr element, a third-core promoter element, the GAAC box (AA/TGAACT), is independently able to control the rate and site of transcription initiation.
[ "16,17" ]
In addition to the TATA box and Inr element, a third-core promoter element, the GAAC box (AA/TGAACT), is independently able to control the rate and site of transcription initiation.
true
true
true
true
true
1,727
2
INTRODUCTION
1
14
[ "B14", "B15", "B16", "B15", "B18 B19 B20", "B21" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
The presence of a third conserved core promoter element contributes to the unusual core promoter architecture in E. histolytica compared to other metazoan systems.
[ "14", "15", "16", "17", "18–20", "21" ]
163
10,851
0
false
The presence of a third conserved core promoter element contributes to the unusual core promoter architecture in E. histolytica compared to other metazoan systems.
[]
The presence of a third conserved core promoter element contributes to the unusual core promoter architecture in E. histolytica compared to other metazoan systems.
true
true
true
true
true
1,727
2
INTRODUCTION
1
14
[ "B14", "B15", "B16", "B15", "B18 B19 B20", "B21" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
A number of other regulatory elements and transcription factors have also been identified in E. histolytica.
[ "14", "15", "16", "17", "18–20", "21" ]
108
10,852
0
false
A number of other regulatory elements and transcription factors have also been identified in E. histolytica.
[]
A number of other regulatory elements and transcription factors have also been identified in E. histolytica.
true
true
true
true
true
1,727
2
INTRODUCTION
1
18–20
[ "B14", "B15", "B16", "B15", "B18 B19 B20", "B21" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
The most well characterized are the transcription factors upstream regulatory element 3-binding protein (URE3-BP), a calcium-sensitive EF hand protein and the E. histolytica enhancer binding proteins 1 and 2 (EhEBP1 and EhEBP2) (18–20).
[ "14", "15", "16", "17", "18–20", "21" ]
236
10,853
1
false
The most well characterized are the transcription factors upstream regulatory element 3-binding protein (URE3-BP), a calcium-sensitive EF hand protein and the E. histolytica enhancer binding proteins 1 and 2 (EhEBP1 and EhEBP2).
[ "18–20" ]
The most well characterized are the transcription factors upstream regulatory element 3-binding protein (URE3-BP), a calcium-sensitive EF hand protein and the E. histolytica enhancer binding proteins 1 and 2.
true
true
true
true
true
1,727
2
INTRODUCTION
1
21
[ "B14", "B15", "B16", "B15", "B18 B19 B20", "B21" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Additionally, the recent completion of the E. histolytica genome sequence indicates that canonical transcription factors are encoded in the genome (21).
[ "14", "15", "16", "17", "18–20", "21" ]
152
10,854
1
false
Additionally, the recent completion of the E. histolytica genome sequence indicates that canonical transcription factors are encoded in the genome.
[ "21" ]
Additionally, the recent completion of the E. histolytica genome sequence indicates that canonical transcription factors are encoded in the genome.
true
true
true
true
true
1,727
2
INTRODUCTION
1
14
[ "B14", "B15", "B16", "B15", "B18 B19 B20", "B21" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Thus, it appears that sequence-specific DNA-binding proteins control multiple aspects of basal and activated transcription in E. histolytica.
[ "14", "15", "16", "17", "18–20", "21" ]
141
10,855
0
false
Thus, it appears that sequence-specific DNA-binding proteins control multiple aspects of basal and activated transcription in E. histolytica.
[]
Thus, it appears that sequence-specific DNA-binding proteins control multiple aspects of basal and activated transcription in E. histolytica.
true
true
true
true
true
1,727
3
INTRODUCTION
0
null
null
17,355,990
pmid-12874327
Although much work has been done in E. histolytica to characterize the regulation of a handful of genes, global transcriptional networks have not been identified.
null
162
10,856
0
false
null
null
Although much work has been done in E. histolytica to characterize the regulation of a handful of genes, global transcriptional networks have not been identified.
true
true
true
true
true
1,728
3
INTRODUCTION
0
null
null
17,355,990
pmid-12874327
We have applied a gene regulatory network approach towards understanding coordinate control and regulation of gene expression in this parasite.
null
143
10,857
0
false
null
null
We have applied a gene regulatory network approach towards understanding coordinate control and regulation of gene expression in this parasite.
true
true
true
true
true
1,728
3
INTRODUCTION
0
null
null
17,355,990
pmid-12874327
Utilizing expression data from two microarray experiments, we identified cis-promoter motifs that correlated with the level of gene expression.
null
143
10,858
0
false
null
null
Utilizing expression data from two microarray experiments, we identified cis-promoter motifs that correlated with the level of gene expression.
true
true
true
true
true
1,728
3
INTRODUCTION
0
null
null
17,355,990
pmid-12874327
In addition, we identified a set of three promoter motifs that when present in combination of ⩾2 motifs were associated with increased gene expression in response to heat shock.
null
177
10,859
0
false
null
null
In addition, we identified a set of three promoter motifs that when present in combination of ⩾2 motifs were associated with increased gene expression in response to heat shock.
true
true
true
true
true
1,728
3
INTRODUCTION
0
null
null
17,355,990
pmid-12874327
Furthermore, by using electrophoretic mobility shift assays (EMSAs) we confirmed that a number of the motifs predicted by bioinformatic analyses specifically bind amebic nuclear protein(s).
null
189
10,860
0
false
null
null
Furthermore, by using electrophoretic mobility shift assays (EMSAs) we confirmed that a number of the motifs predicted by bioinformatic analyses specifically bind amebic nuclear protein(s).
true
true
true
true
true
1,728
0
DISCUSSION
0
null
null
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
We have identified patterns of promoter motifs in genes with similar expression levels in the protozoan parasite E. histolytica using Bayesian algorithms.
null
154
10,861
0
false
null
null
We have identified patterns of promoter motifs in genes with similar expression levels in the protozoan parasite E. histolytica using Bayesian algorithms.
true
true
true
true
true
1,729
0
DISCUSSION
0
null
null
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Despite the small size of our microarray data set, we identified a number of interesting motifs that were predictive of gene expression in E. histolytica trophozoites.
null
167
10,862
0
false
null
null
Despite the small size of our microarray data set, we identified a number of interesting motifs that were predictive of gene expression in E. histolytica trophozoites.
true
true
true
true
true
1,729
0
DISCUSSION
0
null
null
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Additionally, we identified a set of three motifs, which in combination of ⩾2 motifs predicted low baseline gene expression and transcriptional up-regulation under heat shock.
null
175
10,863
0
false
null
null
Additionally, we identified a set of three motifs, which in combination of ⩾2 motifs predicted low baseline gene expression and transcriptional up-regulation under heat shock.
true
true
true
true
true
1,729
0
DISCUSSION
0
null
null
17,355,990
pmid-10391217|pmid-16380193|pmid-14747145|pmid-15084257|pmid-12740579
Finally, we have validated by EMSA analysis that a number of motifs we identified represent specific binding sites for amebic nuclear protein(s).
null
145
10,864
0
false
null
null
Finally, we have validated by EMSA analysis that a number of motifs we identified represent specific binding sites for amebic nuclear protein(s).
true
true
true
true
true
1,729
1
DISCUSSION
1
4
[ "B4", "B5" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
Microarray expression analysis is a powerful method to characterize transcriptional changes that regulate multiple aspects of pathogenesis.
[ "4", "5" ]
139
10,865
0
false
Microarray expression analysis is a powerful method to characterize transcriptional changes that regulate multiple aspects of pathogenesis.
[]
Microarray expression analysis is a powerful method to characterize transcriptional changes that regulate multiple aspects of pathogenesis.
true
true
true
true
true
1,730
1
DISCUSSION
1
4
[ "B4", "B5" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
The large data sets produced by such experiments create the opportunity to find global regulatory patterns.
[ "4", "5" ]
107
10,866
0
false
The large data sets produced by such experiments create the opportunity to find global regulatory patterns.
[]
The large data sets produced by such experiments create the opportunity to find global regulatory patterns.
true
true
true
true
true
1,730
1
DISCUSSION
1
4
[ "B4", "B5" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
Previous studies in S. cerevisiae and C. elegans generated statistical models of gene expression, predicted gene expression levels based on promoter motifs and identified regulatory modules controlling gene expression during the cell cycle, sporulation and osmotic stress, and developmental changes (4,5).
[ "4", "5" ]
305
10,867
0
false
Previous studies in S. cerevisiae and C. elegans generated statistical models of gene expression, predicted gene expression levels based on promoter motifs and identified regulatory modules controlling gene expression during the cell cycle, sporulation and osmotic stress, and developmental changes.
[ "4,5" ]
Previous studies in S. cerevisiae and C. elegans generated statistical models of gene expression, predicted gene expression levels based on promoter motifs and identified regulatory modules controlling gene expression during the cell cycle, sporulation and osmotic stress, and developmental changes.
true
true
true
true
true
1,730
1
DISCUSSION
1
4
[ "B4", "B5" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
These studies relied on exquisitely detailed expression data from multiple conditions and time points of interest with data from up to 255 microarrays in S. cerevisiae.
[ "4", "5" ]
168
10,868
0
false
These studies relied on exquisitely detailed expression data from multiple conditions and time points of interest with data from up to 255 microarrays in S. cerevisiae.
[]
These studies relied on exquisitely detailed expression data from multiple conditions and time points of interest with data from up to 255 microarrays in S. cerevisiae.
true
true
true
true
true
1,730
1
DISCUSSION
1
4
[ "B4", "B5" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
In these situations, the vast amount of transcriptional profiling proved invaluable.
[ "4", "5" ]
84
10,869
0
false
In these situations, the vast amount of transcriptional profiling proved invaluable.
[]
In these situations, the vast amount of transcriptional profiling proved invaluable.
true
true
true
true
true
1,730
1
DISCUSSION
1
4
[ "B4", "B5" ]
17,355,990
pmid-9100475|pmid-7838173|pmid-16569449|pmid-14698431|pmid-12427095|pmid-16569449|pmid-15243916|pmid-16368989|NA|pmid-15084257|pmid-12740579
However, such detailed information is unlikely to be available for most other systems of interest.
[ "4", "5" ]
98
10,870
0
false
However, such detailed information is unlikely to be available for most other systems of interest.
[]
However, such detailed information is unlikely to be available for most other systems of interest.
true
true
true
true
true
1,730
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
We have shown that substantially less expression data can still be successfully applied to the identification of global transcriptional networks.
[ "36", "37", "30" ]
145
10,871
0
false
We have shown that substantially less expression data can still be successfully applied to the identification of global transcriptional networks.
[]
We have shown that substantially less expression data can still be successfully applied to the identification of global transcriptional networks.
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Using data from two microarrays hybridized with RNA from log-phase E. histolytica trophozoites we were able to identify promoter motifs that correlate with gene expression level.
[ "36", "37", "30" ]
178
10,872
0
false
Using data from two microarrays hybridized with RNA from log-phase E. histolytica trophozoites we were able to identify promoter motifs that correlate with gene expression level.
[]
Using data from two microarrays hybridized with RNA from log-phase E. histolytica trophozoites we were able to identify promoter motifs that correlate with gene expression level.
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Although none of these motifs were restricted to promoters of genes within a given expression profile, several motifs were enriched in the promoters of genes with similar functions or gene family members, likely indicating biologically significant enrichment.
[ "36", "37", "30" ]
259
10,873
0
false
Although none of these motifs were restricted to promoters of genes within a given expression profile, several motifs were enriched in the promoters of genes with similar functions or gene family members, likely indicating biologically significant enrichment.
[]
Although none of these motifs were restricted to promoters of genes within a given expression profile, several motifs were enriched in the promoters of genes with similar functions or gene family members, likely indicating biologically significant enrichment.
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Three of these motifs bound to specific protein(s) in nuclear extracts from E. histolytica trophozoites.
[ "36", "37", "30" ]
104
10,874
0
false
Three of these motifs bound to specific protein(s) in nuclear extracts from E. histolytica trophozoites.
[]
Three of these motifs bound to specific protein(s) in nuclear extracts from E. histolytica trophozoites.
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
The promoter motifs identified by this method should not be core promoter elements as these would be found in all genes, and several of the motifs identified are enriched in groups of co-regulated genes (the ribosomal protein genes, tRNA synthetases and the Ehssp gene family).
[ "36", "37", "30" ]
277
10,875
0
false
The promoter motifs identified by this method should not be core promoter elements as these would be found in all genes, and several of the motifs identified are enriched in groups of co-regulated genes (the ribosomal protein genes, tRNA synthetases and the Ehssp gene family).
[]
The promoter motifs identified by this method should not be core promoter elements as these would be found in all genes, and several of the motifs identified are enriched in groups of co-regulated genes (the ribosomal protein genes, tRNA synthetases and the Ehssp gene family).
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Thus we would expect transcriptional regulators identified by this approach to be either general transcription factors, or transcriptional enhancers or repressors.
[ "36", "37", "30" ]
163
10,876
0
false
Thus we would expect transcriptional regulators identified by this approach to be either general transcription factors, or transcriptional enhancers or repressors.
[]
Thus we would expect transcriptional regulators identified by this approach to be either general transcription factors, or transcriptional enhancers or repressors.
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
One interesting motif identified in this analysis (A/TAAACCCT) strongly correlated with high gene expression under trophozoite conditions.
[ "36", "37", "30" ]
138
10,877
0
false
One interesting motif identified in this analysis (A/TAAACCCT) strongly correlated with high gene expression under trophozoite conditions.
[]
One interesting motif identified in this analysis (A/TAAACCCT) strongly correlated with high gene expression under trophozoite conditions.
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
In E. histolytica this motif is highly enriched in the promoters of several groups of genes, including ribosomal proteins and tRNA synthetases.
[ "36", "37", "30" ]
143
10,878
0
false
In E. histolytica this motif is highly enriched in the promoters of several groups of genes, including ribosomal proteins and tRNA synthetases.
[]
In E. histolytica this motif is highly enriched in the promoters of several groups of genes, including ribosomal proteins and tRNA synthetases.
true
true
true
true
true
1,731
2
DISCUSSION
1
36
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Ribosomal protein genes often show co-regulated expression, as has been extensively detailed in S. cerevisiae (36).
[ "36", "37", "30" ]
115
10,879
1
false
Ribosomal protein genes often show co-regulated expression, as has been extensively detailed in S. cerevisiae.
[ "36" ]
Ribosomal protein genes often show co-regulated expression, as has been extensively detailed in S. cerevisiae.
true
true
true
true
true
1,731
2
DISCUSSION
1
37
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
Additionally, two promoter motifs were identified in 95% of ribosomal protein genes in Toxoplasma gondii, though neither of these motifs is similar to the A/TAAACCCT motif identified in E. histolytica (37).
[ "36", "37", "30" ]
206
10,880
1
false
Additionally, two promoter motifs were identified in 95% of ribosomal protein genes in Toxoplasma gondii, though neither of these motifs is similar to the A/TAAACCCT motif identified in E. histolytica.
[ "37" ]
Additionally, two promoter motifs were identified in 95% of ribosomal protein genes in Toxoplasma gondii, though neither of these motifs is similar to the A/TAAACCCT motif identified in E. histolytica.
true
true
true
true
true
1,731
2
DISCUSSION
1
30
[ "B36", "B37", "B30" ]
17,355,990
pmid-9238060|pmid-8813680|pmid-11849710|pmid-8813680|pmid-11038357|pmid-11278344|pmid-12466263|pmid-15729342|pmid-16782874|pmid-16674839|pmid-4092687
An analogous promoter motif (AAACCCT) has been described in S. pombe, where it is present in tandem repeats and is found in the promoter of all histone genes (30).
[ "36", "37", "30" ]
163
10,881
1
false
An analogous promoter motif (AAACCCT) has been described in S. pombe, where it is present in tandem repeats and is found in the promoter of all histone genes.
[ "30" ]
An analogous promoter motif (AAACCCT) has been described in S. pombe, where it is present in tandem repeats and is found in the promoter of all histone genes.
true
true
true
true
true
1,731
3
DISCUSSION
1
32
[ "B32" ]
17,355,990
pmid-12874327
We identified three promoter motifs (M24, GAATGAGT; M23, AACTATTTAAACATC/TC; and M9, TGAACTTATAAACATC) that in any combination of ⩾2 motifs were highly predictive of low baseline gene expression in E. histolytica trophozoites.
[ "32" ]
226
10,882
0
false
We identified three promoter motifs (M24, GAATGAGT; M23, AACTATTTAAACATC/TC; and M9, TGAACTTATAAACATC) that in any combination of ⩾2 motifs were highly predictive of low baseline gene expression in E. histolytica trophozoites.
[]
We identified three promoter motifs that in any combination of ⩾2 motifs were highly predictive of low baseline gene expression in E. histolytica trophozoites.
true
true
true
true
true
1,732
3
DISCUSSION
1
32
[ "B32" ]
17,355,990
pmid-12874327
The M9, M23 and M24 motifs are overrepresented in the promoters of a large gene family homologous to Ehssp1, a stress-sensitive antigen (32).
[ "32" ]
141
10,883
1
false
The M9, M23 and M24 motifs are overrepresented in the promoters of a large gene family homologous to Ehssp1, a stress-sensitive antigen.
[ "32" ]
The M9, M23 and M24 motifs are overrepresented in the promoters of a large gene family homologous to Ehssp1, a stress-sensitive antigen.
true
true
true
true
true
1,732
3
DISCUSSION
1
32
[ "B32" ]
17,355,990
pmid-12874327
A majority (55%) of the 253 predicted genes in this family contain ⩾2 of these promoter motifs.
[ "32" ]
95
10,884
0
false
A majority (55%) of the 253 predicted genes in this family contain ⩾2 of these promoter motifs.
[]
A majority (55%) of the 253 predicted genes in this family contain ⩾2 of these promoter motifs.
true
true
true
true
true
1,732
3
DISCUSSION
1
32
[ "B32" ]
17,355,990
pmid-12874327
In promoters of the Ehssp gene family that contain ⩾2 motifs, the position and spacing of these motifs is conserved.
[ "32" ]
116
10,885
0
false
In promoters of the Ehssp gene family that contain ⩾2 motifs, the position and spacing of these motifs is conserved.
[]
In promoters of the Ehssp gene family that contain ⩾2 motifs, the position and spacing of these motifs is conserved.
true
true
true
true
true
1,732
3
DISCUSSION
1
32
[ "B32" ]
17,355,990
pmid-12874327
Interestingly, it appears that the Ehssp genes with ⩾2 motifs appear to be more similar to each other than Ehssp genes with ⩽1 motif, suggesting that they either have a more recent evolutionary origin, or that the Ehssp genes with ⩽1 motif may no longer be subjected to the same degree of evolutionary pressure as the Eh...
[ "32" ]
345
10,886
0
false
Interestingly, it appears that the Ehssp genes with ⩾2 motifs appear to be more similar to each other than Ehssp genes with ⩽1 motif, suggesting that they either have a more recent evolutionary origin, or that the Ehssp genes with ⩽1 motif may no longer be subjected to the same degree of evolutionary pressure as the Eh...
[]
Interestingly, it appears that the Ehssp genes with ⩾2 motifs appear to be more similar to each other than Ehssp genes with ⩽1 motif, suggesting that they either have a more recent evolutionary origin, or that the Ehssp genes with ⩽1 motif may no longer be subjected to the same degree of evolutionary pressure as the Eh...
true
true
true
true
true
1,732
4
DISCUSSION
0
null
null
17,355,990
null
Ehssp family genes with ⩾2 motifs were highly up-regulated by heat shock.
null
73
10,887
0
false
null
null
Ehssp family genes with ⩾2 motifs were highly up-regulated by heat shock.
true
true
true
true
true
1,733
4
DISCUSSION
0
null
null
17,355,990
null
In contrast, the Ehssp family genes with ⩽1 motif and the non-Ehssp family members with ⩾ 2 motifs showed more modest up-regulation of gene expression after heat shock.
null
168
10,888
0
false
null
null
In contrast, the Ehssp family genes with ⩽1 motif and the non-Ehssp family members with ⩾ 2 motifs showed more modest up-regulation of gene expression after heat shock.
true
true
true
true
true
1,733
4
DISCUSSION
0
null
null
17,355,990
null
We have demonstrated that the M9 motif binds amebic nuclear protein(s) in a specific manner in nuclear extracts prepared from heat-shocked trophozoites, whereas no substantial specific interaction was identified with nuclear extracts prepared from untreated trophozoites.
null
271
10,889
0
false
null
null
We have demonstrated that the M9 motif binds amebic nuclear protein(s) in a specific manner in nuclear extracts prepared from heat-shocked trophozoites, whereas no substantial specific interaction was identified with nuclear extracts prepared from untreated trophozoites.
true
true
true
true
true
1,733
4
DISCUSSION
0
null
null
17,355,990
null
Our model is that transcriptional activator(s) bind to the M9 motif under heat shock conditions, up-regulating transcription of the Ehssp genes.
null
144
10,890
0
false
null
null
Our model is that transcriptional activator(s) bind to the M9 motif under heat shock conditions, up-regulating transcription of the Ehssp genes.
true
true
true
true
true
1,733
4
DISCUSSION
0
null
null
17,355,990
null
How binding of the potential activator(s) relates to the presence of other motif(s), and to the spacing between motif M9 and the transcription start site are yet to be determined.
null
179
10,891
0
false
null
null
How binding of the potential activator(s) relates to the presence of other motif(s), and to the spacing between motif M9 and the transcription start site are yet to be determined.
true
true
true
true
true
1,733
5
DISCUSSION
1
2
[ "B2", "B3" ]
17,355,990
pmid-16380193|pmid-14747145
Few complex transcriptional regulatory networks have been identified to date in other parasitic systems.
[ "2", "3" ]
104
10,892
0
false
Few complex transcriptional regulatory networks have been identified to date in other parasitic systems.
[]
Few complex transcriptional regulatory networks have been identified to date in other parasitic systems.
true
true
true
true
true
1,734
5
DISCUSSION
1
2
[ "B2", "B3" ]
17,355,990
pmid-16380193|pmid-14747145
Recent bioinformatic analysis of P. falciparum promoters relied on large-scale expression data combined with evolutionary conservation to identify 12 putative regulatory elements, two of which had been previously described (2).
[ "2", "3" ]
227
10,893
1
false
Recent bioinformatic analysis of P. falciparum promoters relied on large-scale expression data combined with evolutionary conservation to identify 12 putative regulatory elements, two of which had been previously described.
[ "2" ]
Recent bioinformatic analysis of P. falciparum promoters relied on large-scale expression data combined with evolutionary conservation to identify 12 putative regulatory elements, two of which had been previously described.
true
true
true
true
true
1,734
5
DISCUSSION
1
2
[ "B2", "B3" ]
17,355,990
pmid-16380193|pmid-14747145
This work also identified an overrepresented group of promoter motifs, many of which had potentially opposing activities.
[ "2", "3" ]
121
10,894
0
false
This work also identified an overrepresented group of promoter motifs, many of which had potentially opposing activities.
[]
This work also identified an overrepresented group of promoter motifs, many of which had potentially opposing activities.
true
true
true
true
true
1,734
5
DISCUSSION
1
3
[ "B2", "B3" ]
17,355,990
pmid-16380193|pmid-14747145
The most complex transcriptional network characterized in a protozoan parasite to date was found in analysis of promoters from heat shock protein (hsp) genes in P. falciparum (3).
[ "2", "3" ]
179
10,895
1
false
The most complex transcriptional network characterized in a protozoan parasite to date was found in analysis of promoters from heat shock protein (hsp) genes in P. falciparum.
[ "3" ]
The most complex transcriptional network characterized in a protozoan parasite to date was found in analysis of promoters from heat shock protein (hsp) genes in P. falciparum.
true
true
true
true
true
1,734
5
DISCUSSION
1
2
[ "B2", "B3" ]
17,355,990
pmid-16380193|pmid-14747145
This work identified a novel G-box motif that was conserved in the promoters of the related Plasmodium species, P. yoelii, P. berghei and P. vivax.
[ "2", "3" ]
147
10,896
0
false
This work identified a novel G-box motif that was conserved in the promoters of the related Plasmodium species, P. yoelii, P. berghei and P. vivax.
[]
This work identified a novel G-box motif that was conserved in the promoters of the related Plasmodium species, P. yoelii, P. berghei and P. vivax.
true
true
true
true
true
1,734
5
DISCUSSION
1
2
[ "B2", "B3" ]
17,355,990
pmid-16380193|pmid-14747145
Further in vitro analysis identified a second control element within the hsp86 promoter.
[ "2", "3" ]
88
10,897
0
false
Further in vitro analysis identified a second control element within the hsp86 promoter.
[]
Further in vitro analysis identified a second control element within the hsp86 promoter.
true
true
true
true
true
1,734
6
DISCUSSION
0
null
null
17,355,990
null
We have demonstrated a method for identification of promoter motifs in E. histolytica promoters relying upon small expression data sets.
null
136
10,898
0
false
null
null
We have demonstrated a method for identification of promoter motifs in E. histolytica promoters relying upon small expression data sets.
true
true
true
true
true
1,735
6
DISCUSSION
0
null
null
17,355,990
null
As more amebic expression profiles are determined, this analysis can be extended to identify novel genetic regulatory pathways involved in pathogenesis and developmental control.
null
178
10,899
0
false
null
null
As more amebic expression profiles are determined, this analysis can be extended to identify novel genetic regulatory pathways involved in pathogenesis and developmental control.
true
true
true
true
true
1,735