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
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
This suggests that cellular IRESes do not share globally similar structure as do some viral IRESes.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
99
5,600
0
false
This suggests that cellular IRESes do not share globally similar structure as do some viral IRESes.
[]
This suggests that cellular IRESes do not share globally similar structure as do some viral IRESes.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
This conclusion is plausible when considering published evidence to date.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
73
5,601
0
false
This conclusion is plausible when considering published evidence to date.
[]
This conclusion is plausible when considering published evidence to date.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
First, no overall structural similarity has been found among the 11 known cellular IRES structures (23–32).
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
107
5,602
1
false
First, no overall structural similarity has been found among the 11 known cellular IRES structures.
[ "23–32" ]
First, no overall structural similarity has been found among the 11 known cellular IRES structures.
true
true
true
true
true
934
3
DISCUSSION
1
65
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Second, examination of the c-myc IRES has shown that its activity is not dependent on the overall structure but on distinct sequence modules (65).
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
146
5,603
1
false
Second, examination of the c-myc IRES has shown that its activity is not dependent on the overall structure but on distinct sequence modules.
[ "65" ]
Second, examination of the c-myc IRES has shown that its activity is not dependent on the overall structure but on distinct sequence modules.
true
true
true
true
true
934
3
DISCUSSION
1
29
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Third, mutations which opened up the Bag-1 IRES structure negated the need for the previously required ITAF, PCBP1, while still retaining full IRES activity (29).
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
162
5,604
1
false
Third, mutations which opened up the Bag-1 IRES structure negated the need for the previously required ITAF, PCBP1, while still retaining full IRES activity.
[ "29" ]
Third, mutations which opened up the Bag-1 IRES structure negated the need for the previously required ITAF, PCBP1, while still retaining full IRES activity.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Fourth, non-overlapping segments of IRES sequence that would not preserve the overall structure still retain partial IRES activity (28,66), suggesting different modules may synergistically act to provide full IRES activity in vivo.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
231
5,605
0
false
Fourth, non-overlapping segments of IRES sequence that would not preserve the overall structure still retain partial IRES activity, suggesting different modules may synergistically act to provide full IRES activity in vivo.
[ "28,66" ]
Fourth, non-overlapping segments of IRES sequence that would not preserve the overall structure still retain partial IRES activity, suggesting different modules may synergistically act to provide full IRES activity in vivo.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
In this light, it is not surprising that the XIAP IRES mutants we examined exhibited full IRES activity despite structural changes.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
131
5,606
0
false
In this light, it is not surprising that the XIAP IRES mutants we examined exhibited full IRES activity despite structural changes.
[]
In this light, it is not surprising that the XIAP IRES mutants we examined exhibited full IRES activity despite structural changes.
true
true
true
true
true
934
3
DISCUSSION
1
67
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Conversely, the point mutation of the IRES which attenuates the Sabin strain 3 of poliovirus does not change the structure (67) but it does effect the binding of PTB (68).
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
171
5,607
1
false
Conversely, the point mutation of the IRES which attenuates the Sabin strain 3 of poliovirus does not change the structure but it does effect the binding of PTB.
[ "67", "68" ]
Conversely, the point mutation of the IRES which attenuates the Sabin strain 3 of poliovirus does not change the structure but it does effect the binding of PTB.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
It would be wrong to over generalize and suggest that structure will never be required for the function of cellular IRESes.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
123
5,608
0
false
It would be wrong to over generalize and suggest that structure will never be required for the function of cellular IRESes.
[]
It would be wrong to over generalize and suggest that structure will never be required for the function of cellular IRESes.
true
true
true
true
true
934
3
DISCUSSION
1
31
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Such an exception is the CAT-1 IRES, which is induced during amino acid starvation, where a specific stem is required for functional activity regardless of its sequence makeup (31).
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
181
5,609
1
false
Such an exception is the CAT-1 IRES, which is induced during amino acid starvation, where a specific stem is required for functional activity regardless of its sequence makeup.
[ "31" ]
Such an exception is the CAT-1 IRES, which is induced during amino acid starvation, where a specific stem is required for functional activity regardless of its sequence makeup.
true
true
true
true
true
934
4
DISCUSSION
1
69
[ "B69", "B70", "B71" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
Whereas a virus needs to compete efficiently to get its proteins expressed within an infected cell, cellular transcripts with an IRES are more likely translationally regulated, with several trans-acting factors contributing differently depending upon the cellular context.
[ "69", "70", "71" ]
272
5,610
0
false
Whereas a virus needs to compete efficiently to get its proteins expressed within an infected cell, cellular transcripts with an IRES are more likely translationally regulated, with several trans-acting factors contributing differently depending upon the cellular context.
[]
Whereas a virus needs to compete efficiently to get its proteins expressed within an infected cell, cellular transcripts with an IRES are more likely translationally regulated, with several trans-acting factors contributing differently depending upon the cellular context.
true
true
true
true
true
935
4
DISCUSSION
1
69
[ "B69", "B70", "B71" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
Studies of the HCV IRES have shown it to directly interact with the ribosome and induce conformational change of the ribosome (69).
[ "69", "70", "71" ]
131
5,611
1
false
Studies of the HCV IRES have shown it to directly interact with the ribosome and induce conformational change of the ribosome.
[ "69" ]
Studies of the HCV IRES have shown it to directly interact with the ribosome and induce conformational change of the ribosome.
true
true
true
true
true
935
4
DISCUSSION
1
70
[ "B69", "B70", "B71" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
Cricket paralysis virus IRES has an RNA structure which allows it to interact with the ribosome and to initiate translation without an eIF2—initiator Met-tRNAi complex in the P-site (70).
[ "69", "70", "71" ]
187
5,612
1
false
Cricket paralysis virus IRES has an RNA structure which allows it to interact with the ribosome and to initiate translation without an eIF2—initiator Met-tRNAi complex in the P-site.
[ "70" ]
Cricket paralysis virus IRES has an RNA structure which allows it to interact with the ribosome and to initiate translation without an eIF2—initiator Met-tRNAi complex in the P-site.
true
true
true
true
true
935
4
DISCUSSION
1
71
[ "B69", "B70", "B71" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
This mechanism may have evolved to overcome the antiviral response of the cell to shut off protein synthesis though PKR phosphorylation of eIF2α (71).
[ "69", "70", "71" ]
150
5,613
1
false
This mechanism may have evolved to overcome the antiviral response of the cell to shut off protein synthesis though PKR phosphorylation of eIF2α.
[ "71" ]
This mechanism may have evolved to overcome the antiviral response of the cell to shut off protein synthesis though PKR phosphorylation of eIF2α.
true
true
true
true
true
935
4
DISCUSSION
1
69
[ "B69", "B70", "B71" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
The importance of structures seen in viruses has yet to be shown for any cellular IRES.
[ "69", "70", "71" ]
87
5,614
0
false
The importance of structures seen in viruses has yet to be shown for any cellular IRES.
[]
The importance of structures seen in viruses has yet to be shown for any cellular IRES.
true
true
true
true
true
935
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
Importantly, we noted the presence of a polypyrimidine tract that was folded into a stem-loop structure in the both XIAP and AQP4 IRES.
[ "51", "32", "32" ]
135
5,615
0
false
Importantly, we noted the presence of a polypyrimidine tract that was folded into a stem-loop structure in the both XIAP and AQP4 IRES.
[]
Importantly, we noted the presence of a polypyrimidine tract that was folded into a stem-loop structure in the both XIAP and AQP4 IRES.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
As we have previously found that the polypyrimidine tract is absolutely necessary for XIAP IRES activity (51), we tested whether deletion of this sequence in the AQP4 5′UTR would also abrogate IRES function.
[ "51", "32", "32" ]
207
5,616
1
false
As we have previously found that the polypyrimidine tract is absolutely necessary for XIAP IRES activity, we tested whether deletion of this sequence in the AQP4 5′UTR would also abrogate IRES function.
[ "51" ]
As we have previously found that the polypyrimidine tract is absolutely necessary for XIAP IRES activity, we tested whether deletion of this sequence in the AQP4 5′UTR would also abrogate IRES function.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
Indeed, deletion of the AQP4 5′UTR polypyrimidine tract causes a loss of PTB binding and a complete loss of IRES activity.
[ "51", "32", "32" ]
122
5,617
0
false
Indeed, deletion of the AQP4 5′UTR polypyrimidine tract causes a loss of PTB binding and a complete loss of IRES activity.
[]
Indeed, deletion of the AQP4 5′UTR polypyrimidine tract causes a loss of PTB binding and a complete loss of IRES activity.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
Because this small region is required for IRES activity, we believe that short motifs may be critical determinants of IRES function.
[ "51", "32", "32" ]
132
5,618
0
false
Because this small region is required for IRES activity, we believe that short motifs may be critical determinants of IRES function.
[]
Because this small region is required for IRES activity, we believe that short motifs may be critical determinants of IRES function.
true
true
true
true
true
936
5
DISCUSSION
1
32
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
In agreement with this hypothesis, it has been found that a reiterated PTB-binding motif can induce internal ribosome entry (32).
[ "51", "32", "32" ]
129
5,619
1
false
In agreement with this hypothesis, it has been found that a reiterated PTB-binding motif can induce internal ribosome entry.
[ "32" ]
In agreement with this hypothesis, it has been found that a reiterated PTB-binding motif can induce internal ribosome entry.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
Moreover, a search by Mitchell et al.
[ "51", "32", "32" ]
37
5,620
0
false
Moreover, a search by Mitchell et al.
[]
Moreover, a search by Mitchell et al.
true
true
true
true
true
936
5
DISCUSSION
1
32
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
(32) for 5′UTRs that harbour this PTB-binding motif has resulted in the identification of novel IRES elements.
[ "51", "32", "32" ]
110
5,621
1
false
for 5′UTRs that harbour this PTB-binding motif has resulted in the identification of novel IRES elements.
[ "32" ]
for 5′UTRs that harbour this PTB-binding motif has resulted in the identification of novel IRES elements.
false
true
true
true
false
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
This search, however, would not have found XIAP or AQP4 because the (CCU)n motif pattern considered only a small subset of sequence sites that PTB can bind and is not found in XIAP or AQP4 IRES.
[ "51", "32", "32" ]
194
5,622
0
false
This search, however, would not have found XIAP or AQP4 because the (CCU)n motif pattern considered only a small subset of sequence sites that PTB can bind and is not found in XIAP or AQP4 IRES.
[]
This search, however, would not have found XIAP or AQP4 because the (CCU)n motif pattern considered only a small subset of sequence sites that PTB can bind and is not found in XIAP or AQP4 IRES.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
Even though the polypyrimidine tract region (UUCUCUUUU) is the same in XIAP and AQP4, PTB overexpression has an opposite effect on their IRES activity.
[ "51", "32", "32" ]
151
5,623
0
false
Even though the polypyrimidine tract region (UUCUCUUUU) is the same in XIAP and AQP4, PTB overexpression has an opposite effect on their IRES activity.
[]
Even though the polypyrimidine tract region (UUCUCUUUU) is the same in XIAP and AQP4, PTB overexpression has an opposite effect on their IRES activity.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
This may possibly be due to competing ITAFs for sequences in this region, which can have either a positive or negative effect on translation initiation.
[ "51", "32", "32" ]
152
5,624
0
false
This may possibly be due to competing ITAFs for sequences in this region, which can have either a positive or negative effect on translation initiation.
[]
This may possibly be due to competing ITAFs for sequences in this region, which can have either a positive or negative effect on translation initiation.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
Our observations, together with previously published findings, suggest that the recruitment of a particular cohort of trans-acting proteins is the critical factor in cellular IRES-mediated translation.
[ "51", "32", "32" ]
201
5,625
0
false
Our observations, together with previously published findings, suggest that the recruitment of a particular cohort of trans-acting proteins is the critical factor in cellular IRES-mediated translation.
[]
Our observations, together with previously published findings, suggest that the recruitment of a particular cohort of trans-acting proteins is the critical factor in cellular IRES-mediated translation.
true
true
true
true
true
936
5
DISCUSSION
1
51
[ "B51", "B32", "B32" ]
17,591,613
pmid-10848591|pmid-15998809|pmid-15998809
Therefore, a cataloguing of the trans-acting factors required by each IRES may allow functional grouping of these elements and aid in the identification of common features required for cellular IRES-dependent translation.
[ "51", "32", "32" ]
221
5,626
0
false
Therefore, a cataloguing of the trans-acting factors required by each IRES may allow functional grouping of these elements and aid in the identification of common features required for cellular IRES-dependent translation.
[]
Therefore, a cataloguing of the trans-acting factors required by each IRES may allow functional grouping of these elements and aid in the identification of common features required for cellular IRES-dependent translation.
true
true
true
true
true
936
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b7", "b8", "b9", "b10", "b11", "b12", "b15", "b16" ]
17,012,279
pmid-16151404|pmid-16151408|pmid-2658060|pmid-8507399|pmid-1644788|pmid-11223067|pmid-1507232|pmid-10984501|pmid-9144168|pmid-14754898|pmid-15653626
Selection technologies, to obtain monoclonal antibodies with high affinity and specificity against defined antigens, are required for the development of diagnostic and therapeutic antibodies [reviewed in (1–4)], both to improve the detection limit for diagnostics and to decrease the required dose for therapeutics.
[ "1", "4", "5", "7", "8", "9", "10", "11", "12", "15", "16" ]
315
5,627
0
false
Selection technologies, to obtain monoclonal antibodies with high affinity and specificity against defined antigens, are required for the development of diagnostic and therapeutic antibodies, both to improve the detection limit for diagnostics and to decrease the required dose for therapeutics.
[ "reviewed in (1–4)" ]
Selection technologies, to obtain monoclonal antibodies with high affinity and specificity against defined antigens, are required for the development of diagnostic and therapeutic antibodies, both to improve the detection limit for diagnostics and to decrease the required dose for therapeutics.
true
true
true
true
true
937
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b7", "b8", "b9", "b10", "b11", "b12", "b15", "b16" ]
17,012,279
pmid-16151404|pmid-16151408|pmid-2658060|pmid-8507399|pmid-1644788|pmid-11223067|pmid-1507232|pmid-10984501|pmid-9144168|pmid-14754898|pmid-15653626
In immunized animals, affinity maturation of antibodies occurs via repeated stimulation of antigen-specific proliferation of B cells and accumulation of point mutations introduced into the DNA (5–7).
[ "1", "4", "5", "7", "8", "9", "10", "11", "12", "15", "16" ]
199
5,628
0
false
In immunized animals, affinity maturation of antibodies occurs via repeated stimulation of antigen-specific proliferation of B cells and accumulation of point mutations introduced into the DNA.
[ "5–7" ]
In immunized animals, affinity maturation of antibodies occurs via repeated stimulation of antigen-specific proliferation of B cells and accumulation of point mutations introduced into the DNA.
true
true
true
true
true
937
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b7", "b8", "b9", "b10", "b11", "b12", "b15", "b16" ]
17,012,279
pmid-16151404|pmid-16151408|pmid-2658060|pmid-8507399|pmid-1644788|pmid-11223067|pmid-1507232|pmid-10984501|pmid-9144168|pmid-14754898|pmid-15653626
Therefore, it has been suggested that the affinity of antibodies can be improved by mimicking affinity maturation in the laboratory (8,9).
[ "1", "4", "5", "7", "8", "9", "10", "11", "12", "15", "16" ]
138
5,629
0
false
Therefore, it has been suggested that the affinity of antibodies can be improved by mimicking affinity maturation in the laboratory.
[ "8,9" ]
Therefore, it has been suggested that the affinity of antibodies can be improved by mimicking affinity maturation in the laboratory.
true
true
true
true
true
937
0
INTRODUCTION
1
10
[ "b1", "b4", "b5", "b7", "b8", "b9", "b10", "b11", "b12", "b15", "b16" ]
17,012,279
pmid-16151404|pmid-16151408|pmid-2658060|pmid-8507399|pmid-1644788|pmid-11223067|pmid-1507232|pmid-10984501|pmid-9144168|pmid-14754898|pmid-15653626
For the in vitro evolution of recombinant antibodies such as single-chain Fv (scFv) and Fab antibodies, several display technologies such as phage display (10), yeast surface display (11), ribosome display (12–15) and DNA display (16) have been used to link an antibody (phenotype) and its encoding nucleic acid (genotyp...
[ "1", "4", "5", "7", "8", "9", "10", "11", "12", "15", "16" ]
323
5,630
1
false
For the in vitro evolution of recombinant antibodies such as single-chain Fv (scFv) and Fab antibodies, several display technologies such as phage display, yeast surface display, ribosome display and DNA display have been used to link an antibody (phenotype) and its encoding nucleic acid (genotype).
[ "10", "11", "12–15", "16" ]
For the in vitro evolution of recombinant antibodies such as single-chain Fv (scFv) and Fab antibodies, several display technologies such as phage display, yeast surface display, ribosome display and DNA display have been used to link an antibody (phenotype) and its encoding nucleic acid (genotype).
true
true
true
true
true
937
1
INTRODUCTION
1
17
[ "b17", "b19", "b20", "b21", "b17", "b19", "b22", "b23", "b24", "b11", "b14" ]
17,012,279
pmid-9315729|pmid-12888530|pmid-12204693|pmid-16087651|pmid-9315729|pmid-12888530|pmid-9356443|pmid-8637844|pmid-10963664|pmid-10984501|pmid-11134506
In this study, we have applied our in vitro virus (IVV) mRNA display system (17–19) for directed evolution of a single-chain antibody for the first time, although evolution of antibody mimics (fibronectin type III domains) using mRNA display has been reported previously (20,21).
[ "17", "19", "20", "21", "17", "19", "22", "23", "24", "11", "14" ]
279
5,631
0
false
In this study, we have applied our in vitro virus (IVV) mRNA display system for directed evolution of a single-chain antibody for the first time, although evolution of antibody mimics (fibronectin type III domains) using mRNA display has been reported previously.
[ "17–19", "20,21" ]
In this study, we have applied our in vitro virus (IVV) mRNA display system for directed evolution of a single-chain antibody for the first time, although evolution of antibody mimics (fibronectin type III domains) using mRNA display has been reported previously.
true
true
true
true
true
938
1
INTRODUCTION
1
17
[ "b17", "b19", "b20", "b21", "b17", "b19", "b22", "b23", "b24", "b11", "b14" ]
17,012,279
pmid-9315729|pmid-12888530|pmid-12204693|pmid-16087651|pmid-9315729|pmid-12888530|pmid-9356443|pmid-8637844|pmid-10963664|pmid-10984501|pmid-11134506
In mRNA display, an in vitro-synthesized polypeptide is covalently attached to its encoding mRNA through puromycin (17,19,22).
[ "17", "19", "20", "21", "17", "19", "22", "23", "24", "11", "14" ]
126
5,632
0
false
In mRNA display, an in vitro-synthesized polypeptide is covalently attached to its encoding mRNA through puromycin.
[ "17,19,22" ]
In mRNA display, an in vitro-synthesized polypeptide is covalently attached to its encoding mRNA through puromycin.
true
true
true
true
true
938
1
INTRODUCTION
1
17
[ "b17", "b19", "b20", "b21", "b17", "b19", "b22", "b23", "b24", "b11", "b14" ]
17,012,279
pmid-9315729|pmid-12888530|pmid-12204693|pmid-16087651|pmid-9315729|pmid-12888530|pmid-9356443|pmid-8637844|pmid-10963664|pmid-10984501|pmid-11134506
Unlike phage display and yeast surface display, mRNA display (as well as ribosome display) is a totally in vitro system that does not require the transformation of living cells; thus, very large protein libraries (>1010 unique members) can easily be constructed and used for the selection of antibodies directed against ...
[ "17", "19", "20", "21", "17", "19", "22", "23", "24", "11", "14" ]
341
5,633
0
false
Unlike phage display and yeast surface display, mRNA display (as well as ribosome display) is a totally in vitro system that does not require the transformation of living cells; thus, very large protein libraries (>1010 unique members) can easily be constructed and used for the selection of antibodies directed against ...
[]
Unlike phage display and yeast surface display, mRNA display (as well as ribosome display) is a totally in vitro system that does not require the transformation of living cells; thus, very large protein libraries can easily be constructed and used for the selection of antibodies directed against antigens of interest.
true
true
true
true
true
938
1
INTRODUCTION
1
17
[ "b17", "b19", "b20", "b21", "b17", "b19", "b22", "b23", "b24", "b11", "b14" ]
17,012,279
pmid-9315729|pmid-12888530|pmid-12204693|pmid-16087651|pmid-9315729|pmid-12888530|pmid-9356443|pmid-8637844|pmid-10963664|pmid-10984501|pmid-11134506
The covalent bond of the mRNA–protein complex in mRNA display should be more stable than the protein–ribosome–mRNA complex used in ribosome display with respect to thermal or physicochemical stress as a selection pressure.
[ "17", "19", "20", "21", "17", "19", "22", "23", "24", "11", "14" ]
222
5,634
0
false
The covalent bond of the mRNA–protein complex in mRNA display should be more stable than the protein–ribosome–mRNA complex used in ribosome display with respect to thermal or physicochemical stress as a selection pressure.
[]
The covalent bond of the mRNA–protein complex in mRNA display should be more stable than the protein–ribosome–mRNA complex used in ribosome display with respect to thermal or physicochemical stress as a selection pressure.
true
true
true
true
true
938
1
INTRODUCTION
1
17
[ "b17", "b19", "b20", "b21", "b17", "b19", "b22", "b23", "b24", "b11", "b14" ]
17,012,279
pmid-9315729|pmid-12888530|pmid-12204693|pmid-16087651|pmid-9315729|pmid-12888530|pmid-9356443|pmid-8637844|pmid-10963664|pmid-10984501|pmid-11134506
For the present study, we used an anti-fluorescein antibody as a model, because it has been well-characterized both structurally and kinetically (23,24).
[ "17", "19", "20", "21", "17", "19", "22", "23", "24", "11", "14" ]
153
5,635
0
false
For the present study, we used an anti-fluorescein antibody as a model, because it has been well-characterized both structurally and kinetically.
[ "23,24" ]
For the present study, we used an anti-fluorescein antibody as a model, because it has been well-characterized both structurally and kinetically.
true
true
true
true
true
938
1
INTRODUCTION
1
11
[ "b17", "b19", "b20", "b21", "b17", "b19", "b22", "b23", "b24", "b11", "b14" ]
17,012,279
pmid-9315729|pmid-12888530|pmid-12204693|pmid-16087651|pmid-9315729|pmid-12888530|pmid-9356443|pmid-8637844|pmid-10963664|pmid-10984501|pmid-11134506
Further, laboratory evolution of the anti-fluorescein antibody was previously performed by yeast surface display (11) and ribosome display (14); hence, the antibody is a suitable model for evaluating our new method in comparison with the previous methods.
[ "17", "19", "20", "21", "17", "19", "22", "23", "24", "11", "14" ]
255
5,636
1
false
Further, laboratory evolution of the anti-fluorescein antibody was previously performed by yeast surface display and ribosome display ; hence, the antibody is a suitable model for evaluating our new method in comparison with the previous methods.
[ "11", "14" ]
Further, laboratory evolution of the anti-fluorescein antibody was previously performed by yeast surface display and ribosome display ; hence, the antibody is a suitable model for evaluating our new method in comparison with the previous methods.
true
true
true
true
true
938
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,478,503
pmid-15226172|pmid-15709178
Tumor markers are widely used to detect cancer and to monitor cancer progression.
[ "1", "2" ]
81
5,637
0
false
Tumor markers are widely used to detect cancer and to monitor cancer progression.
[]
Tumor markers are widely used to detect cancer and to monitor cancer progression.
true
true
true
true
true
939
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,478,503
pmid-15226172|pmid-15709178
They can be grouped into markers that are identified in cancer cells and markers that are secreted into body fluids.
[ "1", "2" ]
116
5,638
0
false
They can be grouped into markers that are identified in cancer cells and markers that are secreted into body fluids.
[]
They can be grouped into markers that are identified in cancer cells and markers that are secreted into body fluids.
true
true
true
true
true
939
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,478,503
pmid-15226172|pmid-15709178
To perform early stage cancer diagnosis, the second group of markers is more appropriate.
[ "1", "2" ]
89
5,639
0
false
To perform early stage cancer diagnosis, the second group of markers is more appropriate.
[]
To perform early stage cancer diagnosis, the second group of markers is more appropriate.
true
true
true
true
true
939
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,478,503
pmid-15226172|pmid-15709178
A promising method that allows minimal invasive tumor diagnosis based on markers is mass spectroscopy.
[ "1", "2" ]
102
5,640
0
false
A promising method that allows minimal invasive tumor diagnosis based on markers is mass spectroscopy.
[]
A promising method that allows minimal invasive tumor diagnosis based on markers is mass spectroscopy.
true
true
true
true
true
939
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,478,503
pmid-15226172|pmid-15709178
Matrix-Assisted Laser Desorption and Ionization (MALDI) mass spectroscopy evaluated by ‘peak probability contrasts’ revealed an accuracy of around 70% for ovarian cancer (1).
[ "1", "2" ]
174
5,641
1
false
Matrix-Assisted Laser Desorption and Ionization (MALDI) mass spectroscopy evaluated by ‘peak probability contrasts’ revealed an accuracy of around 70% for ovarian cancer.
[ "1" ]
Matrix-Assisted Laser Desorption and Ionization (MALDI) mass spectroscopy evaluated by ‘peak probability contrasts’ revealed an accuracy of around 70% for ovarian cancer.
true
true
true
true
true
939
0
INTRODUCTION
1
2
[ "B1", "B2" ]
17,478,503
pmid-15226172|pmid-15709178
Similar approaches for pancreatic cancer performed slightly better with 88% sensitivity and 75% specificity (2).
[ "1", "2" ]
112
5,642
1
false
Similar approaches for pancreatic cancer performed slightly better with 88% sensitivity and 75% specificity.
[ "2" ]
Similar approaches for pancreatic cancer performed slightly better with 88% sensitivity and 75% specificity.
true
true
true
true
true
939
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
Tumor antigens in blood sera represent an alternative approach for minimally invasive cancer diagnosis.
[ "3", "4", "5–7", "8" ]
103
5,643
0
false
Tumor antigens in blood sera represent an alternative approach for minimally invasive cancer diagnosis.
[]
Tumor antigens in blood sera represent an alternative approach for minimally invasive cancer diagnosis.
true
true
true
true
true
940
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
A popular example is the prostate specific antigen (PSA) that is widely used in the diagnosis of prostate cancer (3).
[ "3", "4", "5–7", "8" ]
117
5,644
1
false
A popular example is the prostate specific antigen (PSA) that is widely used in the diagnosis of prostate cancer.
[ "3" ]
A popular example is the prostate specific antigen (PSA) that is widely used in the diagnosis of prostate cancer.
true
true
true
true
true
940
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
Since PSA is also present in the blood sera of 33% of unaffected people, PSA as a single tumor marker shows a lack of specificity.
[ "3", "4", "5–7", "8" ]
130
5,645
0
false
Since PSA is also present in the blood sera of 33% of unaffected people, PSA as a single tumor marker shows a lack of specificity.
[]
Since PSA is also present in the blood sera of 33% of unaffected people, PSA as a single tumor marker shows a lack of specificity.
true
true
true
true
true
940
1
INTRODUCTION
1
4
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
Likewise, other single antigen markers including CA-19.9 (pancreatic cancer) and CA-15.3 (breast cancer) show severe limitations (4).
[ "3", "4", "5–7", "8" ]
133
5,646
1
false
Likewise, other single antigen markers including CA-19.9 (pancreatic cancer) and CA-15.3 (breast cancer) show severe limitations.
[ "4" ]
Likewise, other single antigen markers including CA-19.9 (pancreatic cancer) and CA-15.3 (breast cancer) show severe limitations.
true
true
true
true
true
940
1
INTRODUCTION
1
5–7
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
Recent studies strongly indicate that antigen marker sets significantly improve the specificity and sensitivity of cancer diagnosis compared to single antigen markers (5–7).
[ "3", "4", "5–7", "8" ]
173
5,647
1
false
Recent studies strongly indicate that antigen marker sets significantly improve the specificity and sensitivity of cancer diagnosis compared to single antigen markers.
[ "5–7" ]
Recent studies strongly indicate that antigen marker sets significantly improve the specificity and sensitivity of cancer diagnosis compared to single antigen markers.
true
true
true
true
true
940
1
INTRODUCTION
1
8
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
Our Minimally Invasive Multiple Marker (MIMM) approach for meningioma (8) e.g.
[ "3", "4", "5–7", "8" ]
78
5,648
1
false
Our Minimally Invasive Multiple Marker (MIMM) approach for meningioma e.g.
[ "8" ]
Our Minimally Invasive Multiple Marker (MIMM) approach for meningioma e.g.
true
true
true
true
true
940
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
is based on 57 meningioma-associated antigens.
[ "3", "4", "5–7", "8" ]
46
5,649
0
false
is based on 57 meningioma-associated antigens.
[]
is based on 57 meningioma-associated antigens.
false
true
true
true
false
940
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
Meningiomas are frequently occurring, generally benign intracranial tumors that are grouped by the World Health Organization (WHO) in three grades, grade I (common type), grade II (atypical) and grade III (anaplastic) meningioma.
[ "3", "4", "5–7", "8" ]
229
5,650
0
false
Meningiomas are frequently occurring, generally benign intracranial tumors that are grouped by the World Health Organization (WHO) in three grades, grade I (common type), grade II (atypical) and grade III (anaplastic) meningioma.
[]
Meningiomas are frequently occurring, generally benign intracranial tumors that are grouped by the World Health Organization (WHO) in three grades, grade I (common type), grade II (atypical) and grade III (anaplastic) meningioma.
true
true
true
true
true
940
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
On a data set of 183 seroreactivity profiles from 83 meningioma and 90 normal sera, MIMM reached a specificity of 96.2% [95% confidence interval (CI) = (96.0–96.5%)], sensitivity of 84.5% (95% CI = 84.3–84.8%), and accuracy of 90.3% (95% CI = 90.1–90.4%).
[ "3", "4", "5–7", "8" ]
255
5,651
0
false
On a data set of 183 seroreactivity profiles from 83 meningioma and 90 normal sera, MIMM reached a specificity of 96.2% [95% confidence interval (CI) = (96.0–96.5%)], sensitivity of 84.5%, and accuracy of 90.3%.
[ "95% CI = 84.3–84.8%", "95% CI = 90.1–90.4%" ]
On a data set of 183 seroreactivity profiles from 83 meningioma and 90 normal sera, MIMM reached a specificity of 96.2% [95% confidence interval (CI) = (96.0–96.5%)], sensitivity of 84.5%, and accuracy of 90.3%.
true
true
true
true
true
940
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
The area under the receiver operator curve (AUC-value) was 0.957
[ "3", "4", "5–7", "8" ]
64
5,652
0
false
The area under the receiver operator curve (AUC-value) was 0.957
[]
The area under the receiver operator curve (AUC-value) was 0.957
true
true
false
true
false
940
1
INTRODUCTION
1
3
[ "B3", "B4", "B5 B6 B7", "B8" ]
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
(95% CI = 0.956–0.957%).
[ "3", "4", "5–7", "8" ]
24
5,653
0
false
(95% CI = 0.956–0.957%).
[]
(95% CI = 0.956–0.957%).
false
false
true
true
false
940
2
INTRODUCTION
0
null
null
17,478,503
null
We developed a web-based application, called ‘Seroreactivity Profile Classification Service’ (SePaCS) that gives experimental groups easy access to several supervised statistical learning approaches for classifying seroreactivity profiles.
null
239
5,654
0
false
null
null
We developed a web-based application, called ‘Seroreactivity Profile Classification Service’ (SePaCS) that gives experimental groups easy access to several supervised statistical learning approaches for classifying seroreactivity profiles.
true
true
true
true
true
941
2
INTRODUCTION
0
null
null
17,478,503
null
The results of SePaCS are summarized in an easy interpretable table that contains for each seroreactivity profile and each classification method the predicted class label.
null
171
5,655
0
false
null
null
The results of SePaCS are summarized in an easy interpretable table that contains for each seroreactivity profile and each classification method the predicted class label.
true
true
true
true
true
941
2
INTRODUCTION
0
null
null
17,478,503
null
Our tool also provides a detailed result file containing for example, graphical representation of computed results.
null
115
5,656
0
false
null
null
Our tool also provides a detailed result file containing for example, graphical representation of computed results.
true
true
true
true
true
941
2
INTRODUCTION
0
null
null
17,478,503
null
We demonstrate the capabilities and the ease-of-use of our web-based application on the example of meningioma.
null
110
5,657
0
false
null
null
We demonstrate the capabilities and the ease-of-use of our web-based application on the example of meningioma.
true
true
true
true
true
941
0
DISCUSSION
0
null
null
17,478,503
pmid-15226172|pmid-15709178
SePaCS grants non-experts in the field of statistical learning easy access to a comprehensive analysis framework for classifying seroreactivity profiles.
null
153
5,658
0
false
null
null
SePaCS grants non-experts in the field of statistical learning easy access to a comprehensive analysis framework for classifying seroreactivity profiles.
true
true
true
true
true
942
0
DISCUSSION
0
null
null
17,478,503
pmid-15226172|pmid-15709178
Our tool offers the possibility to analyze seroreactivity profiles not only from different tumor entities, but from a wide variety of other human diseases that trigger a complex immune response, e.g.
null
199
5,659
0
false
null
null
Our tool offers the possibility to analyze seroreactivity profiles not only from different tumor entities, but from a wide variety of other human diseases that trigger a complex immune response, e.g.
true
true
true
true
true
942
0
DISCUSSION
0
null
null
17,478,503
pmid-15226172|pmid-15709178
autoimmune diseases.
null
20
5,660
0
false
null
null
autoimmune diseases.
false
true
true
true
false
942
0
DISCUSSION
0
null
null
17,478,503
pmid-15226172|pmid-15709178
Although, SePaCS was designed to analyze autoantibody profiles, it can be used for any kind of binary data.
null
107
5,661
0
false
null
null
Although, SePaCS was designed to analyze autoantibody profiles, it can be used for any kind of binary data.
true
true
true
true
true
942
1
DISCUSSION
0
null
null
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
The easy usage of our statistical framework and its diagnostic value have been demonstrated with a meningioma data set.
null
119
5,662
0
false
null
null
The easy usage of our statistical framework and its diagnostic value have been demonstrated with a meningioma data set.
true
true
true
true
true
943
1
DISCUSSION
0
null
null
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
A second test with glioma seroreactivity profiles showed a similar performance.
null
79
5,663
0
false
null
null
A second test with glioma seroreactivity profiles showed a similar performance.
true
true
true
true
true
943
1
DISCUSSION
0
null
null
17,478,503
pmid-15821460|pmid-11990857|pmid-16177248|pmid-15983380|pmid-16452240|pmid-17184519
Currently, we are preparing analyzes of seroreactivity profiles for other tumor types.
null
86
5,664
0
false
null
null
Currently, we are preparing analyzes of seroreactivity profiles for other tumor types.
true
true
true
true
true
943
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
Homeobox-containing genes encode a large family of transcription factors involved in body plan organization during embryogenesis and in tissue homeostasis in many adult organs (1,2).
[ "1", "2", "3", "4" ]
182
5,665
0
false
Homeobox-containing genes encode a large family of transcription factors involved in body plan organization during embryogenesis and in tissue homeostasis in many adult organs.
[ "1,2" ]
Homeobox-containing genes encode a large family of transcription factors involved in body plan organization during embryogenesis and in tissue homeostasis in many adult organs.
true
true
true
true
true
944
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
Mutations within these genes cause malformations and metabolic diseases.
[ "1", "2", "3", "4" ]
72
5,666
0
false
Mutations within these genes cause malformations and metabolic diseases.
[]
Mutations within these genes cause malformations and metabolic diseases.
true
true
true
true
true
944
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
In addition, several lines of evidence indicate that changes in homeobox gene expression are involved in malignant tumor progression (3,4).
[ "1", "2", "3", "4" ]
139
5,667
0
false
In addition, several lines of evidence indicate that changes in homeobox gene expression are involved in malignant tumor progression.
[ "3,4" ]
In addition, several lines of evidence indicate that changes in homeobox gene expression are involved in malignant tumor progression.
true
true
true
true
true
944
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
Although homeobox genes are thought to control large genetic programs, their molecular mechanisms of action are not fully elucidated.
[ "1", "2", "3", "4" ]
133
5,668
0
false
Although homeobox genes are thought to control large genetic programs, their molecular mechanisms of action are not fully elucidated.
[]
Although homeobox genes are thought to control large genetic programs, their molecular mechanisms of action are not fully elucidated.
true
true
true
true
true
944
1
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
The three mammalian homeobox genes of the CDX family, related to the Drosophila gene caudal, are major components of the network that defines the antero-posterior axis in embryos.
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
179
5,669
0
false
The three mammalian homeobox genes of the CDX family, related to the Drosophila gene caudal, are major components of the network that defines the antero-posterior axis in embryos.
[]
The three mammalian homeobox genes of the CDX family, related to the Drosophila gene caudal, are major components of the network that defines the antero-posterior axis in embryos.
true
true
true
true
true
945
1
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
At the adult stage, CDX1 and CDX2 remain selectively active in the continuously renewing intestinal epithelium (5,6).
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
117
5,670
0
false
At the adult stage, CDX1 and CDX2 remain selectively active in the continuously renewing intestinal epithelium.
[ "5,6" ]
At the adult stage, CDX1 and CDX2 remain selectively active in the continuously renewing intestinal epithelium.
true
true
true
true
true
945
1
INTRODUCTION
1
7
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
Although CDX2 is expressed in most gut epithelial cells, CDX1 expression is limited to crypts cells, which belong to the proliferating cell compartment (7).
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
156
5,671
1
false
Although CDX2 is expressed in most gut epithelial cells, CDX1 expression is limited to crypts cells, which belong to the proliferating cell compartment.
[ "7" ]
Although CDX2 is expressed in most gut epithelial cells, CDX1 expression is limited to crypts cells, which belong to the proliferating cell compartment.
true
true
true
true
true
945
1
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
The two genes have both common and specific cellular effects.
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
61
5,672
0
false
The two genes have both common and specific cellular effects.
[]
The two genes have both common and specific cellular effects.
true
true
true
true
true
945
1
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
Indeed, whereas they both trigger cell differentiation, CDX1 stimulates while CDX2 decreases proliferation in cell cultures (8–10).
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
131
5,673
0
false
Indeed, whereas they both trigger cell differentiation, CDX1 stimulates while CDX2 decreases proliferation in cell cultures.
[ "8–10" ]
Indeed, whereas they both trigger cell differentiation, CDX1 stimulates while CDX2 decreases proliferation in cell cultures.
true
true
true
true
true
945
1
INTRODUCTION
1
11
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
They are also differently targeted by regulatory pathways as for example, CDX1 is directly upregulated by Wnt/β-catenin signaling (11), which is mostly active in the crypt compartment, whereas CDX2 is indirectly downregulated by this pathway (12).
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
247
5,674
1
false
They are also differently targeted by regulatory pathways as for example, CDX1 is directly upregulated by Wnt/β-catenin signaling, which is mostly active in the crypt compartment, whereas CDX2 is indirectly downregulated by this pathway.
[ "11", "12" ]
They are also differently targeted by regulatory pathways as for example, CDX1 is directly upregulated by Wnt/β-catenin signaling, which is mostly active in the crypt compartment, whereas CDX2 is indirectly downregulated by this pathway.
true
true
true
true
true
945
1
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
Transgenic models have provided further evidence that the CDX1 and CDX2 genes exert both common and specific effects in relation to pathological conditions.
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
156
5,675
0
false
Transgenic models have provided further evidence that the CDX1 and CDX2 genes exert both common and specific effects in relation to pathological conditions.
[]
Transgenic models have provided further evidence that the CDX1 and CDX2 genes exert both common and specific effects in relation to pathological conditions.
true
true
true
true
true
945
1
INTRODUCTION
1
13
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
Indeed, on the one hand the ectopic expression of either CDX1 or CDX2 causes intestinal-type metaplasia of the gastric epithelium (13).
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
135
5,676
1
false
Indeed, on the one hand the ectopic expression of either CDX1 or CDX2 causes intestinal-type metaplasia of the gastric epithelium.
[ "13" ]
Indeed, on the one hand the ectopic expression of either CDX1 or CDX2 causes intestinal-type metaplasia of the gastric epithelium.
true
true
true
true
true
945
1
INTRODUCTION
1
16
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
On the other hand, CDX2 has been shown to play a tumor suppressor role in murine models of sporadic and genetic colorectal cancers (14,15), whereas CDX1 was reported to mediate the hyperproliferative condition linked to Rb and p130 deficiency in the gut (16).
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
259
5,677
1
false
On the other hand, CDX2 has been shown to play a tumor suppressor role in murine models of sporadic and genetic colorectal cancers, whereas CDX1 was reported to mediate the hyperproliferative condition linked to Rb and p130 deficiency in the gut.
[ "14,15", "16" ]
On the other hand, CDX2 has been shown to play a tumor suppressor role in murine models of sporadic and genetic colorectal cancers, whereas CDX1 was reported to mediate the hyperproliferative condition linked to Rb and p130 deficiency in the gut.
true
true
true
true
true
945
1
INTRODUCTION
1
17
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
Outside the gut, recent studies have reported that the CDX2 and CDX1 proteins have different effects on the promoters of genes involved in early embryonic development (17).
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
172
5,678
1
false
Outside the gut, recent studies have reported that the CDX2 and CDX1 proteins have different effects on the promoters of genes involved in early embryonic development.
[ "17" ]
Outside the gut, recent studies have reported that the CDX2 and CDX1 proteins have different effects on the promoters of genes involved in early embryonic development.
true
true
true
true
true
945
1
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17" ]
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
On this basis, it is therefore important to delineate the specific molecular functions of the CDX1 and CDX2 proteins.
[ "5", "6", "7", "8", "10", "11", "12", "13", "14", "15", "16", "17" ]
117
5,679
0
false
On this basis, it is therefore important to delineate the specific molecular functions of the CDX1 and CDX2 proteins.
[]
On this basis, it is therefore important to delineate the specific molecular functions of the CDX1 and CDX2 proteins.
true
true
true
true
true
945
2
INTRODUCTION
1
18
[ "b18" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
One mechanism to account for the different effects exerted by the CDX1 and CDX2 proteins postulates that they could interact with different functional partners.
[ "18" ]
160
5,680
0
false
One mechanism to account for the different effects exerted by the CDX1 and CDX2 proteins postulates that they could interact with different functional partners.
[]
One mechanism to account for the different effects exerted by the CDX1 and CDX2 proteins postulates that they could interact with different functional partners.
true
true
true
true
true
946
2
INTRODUCTION
1
18
[ "b18" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
The CDX1 and CDX2 proteins exhibit extensive sequence similarity in their homeodomains responsible for DNA-binding (96.6%), whereas the percentage of identity is lower in the N-terminal (35.5%) and C-terminal domains (36.5%) flanking the homeodomain.
[ "18" ]
250
5,681
0
false
The CDX1 and CDX2 proteins exhibit extensive sequence similarity in their homeodomains responsible for DNA-binding (96.6%), whereas the percentage of identity is lower in the N-terminal (35.5%) and C-terminal domains (36.5%) flanking the homeodomain.
[]
The CDX1 and CDX2 proteins exhibit extensive sequence similarity in their homeodomains responsible for DNA-binding (96.6%), whereas the percentage of identity is lower in the N-terminal (35.5%) and C-terminal domains (36.5%) flanking the homeodomain.
true
true
true
true
true
946
2
INTRODUCTION
1
18
[ "b18" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
We have recently shown that the promoter of the glucose-6-phosphatase (G6Pase) gene is selectively activated by CDX1, whereas CDX2 counteracts this stimulatory effect (18).
[ "18" ]
172
5,682
1
false
We have recently shown that the promoter of the glucose-6-phosphatase (G6Pase) gene is selectively activated by CDX1, whereas CDX2 counteracts this stimulatory effect.
[ "18" ]
We have recently shown that the promoter of the glucose-6-phosphatase (G6Pase) gene is selectively activated by CDX1, whereas CDX2 counteracts this stimulatory effect.
true
true
true
true
true
946
2
INTRODUCTION
1
18
[ "b18" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
Both homeoproteins bind to the G6Pase promoter at the level of the TATA-box, but only CDX1 was found to interact with the TATA-box binding protein (TBP) by means of co-immunoprecipitation.
[ "18" ]
188
5,683
0
false
Both homeoproteins bind to the G6Pase promoter at the level of the TATA-box, but only CDX1 was found to interact with the TATA-box binding protein (TBP) by means of co-immunoprecipitation.
[]
Both homeoproteins bind to the G6Pase promoter at the level of the TATA-box, but only CDX1 was found to interact with the TATA-box binding protein (TBP) by means of co-immunoprecipitation.
true
true
true
true
true
946
2
INTRODUCTION
1
18
[ "b18" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
In the present study, we have analyzed the functionality of the interaction between TBP and CDX1, and we have used hybrid molecules between CDX1 and CDX2 to investigate the differential effects of these homeoproteins on the G6Pase promoter.
[ "18" ]
240
5,684
0
false
In the present study, we have analyzed the functionality of the interaction between TBP and CDX1, and we have used hybrid molecules between CDX1 and CDX2 to investigate the differential effects of these homeoproteins on the G6Pase promoter.
[]
In the present study, we have analyzed the functionality of the interaction between TBP and CDX1, and we have used hybrid molecules between CDX1 and CDX2 to investigate the differential effects of these homeoproteins on the G6Pase promoter.
true
true
true
true
true
946
0
DISCUSSION
0
null
null
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
The TBP binds to TAFs within TFIID and also to Mediator, two major complexes of the general transcription machinery, whereas homeodomain proteins are transcription activators acting in a stage- and/or tissue-specific manner.
null
224
5,685
0
false
null
null
The TBP binds to TAFs within TFIID and also to Mediator, two major complexes of the general transcription machinery, whereas homeodomain proteins are transcription activators acting in a stage- and/or tissue-specific manner.
true
true
true
true
true
947
0
DISCUSSION
0
null
null
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
Here we show by means of co-immunoprecipitation and GST-pulldown that CDX1 interacts with TBP in connection to several components of TFIID, TAF7, TAF12 and TAF15, and to Med7, a common component of the Mediator complexes.
null
221
5,686
0
false
null
null
Here we show by means of co-immunoprecipitation and GST-pulldown that CDX1 interacts with TBP in connection to several components of TFIID, TAF7, TAF12 and TAF15, and to Med7, a common component of the Mediator complexes.
true
true
true
true
true
947
0
DISCUSSION
0
null
null
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
Unlike CDX1, CDX2 does not interact with TBP.
null
45
5,687
0
false
null
null
Unlike CDX1, CDX2 does not interact with TBP.
true
true
true
true
true
947
0
DISCUSSION
0
null
null
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
Truncated forms of CDX1 and swapped mutants between CDX1 and CDX2 (Table 1) provide evidence that separate domains of these homeoproteins, namely the N-terminal domain, the central homeodomain and the C-terminal domain, are involved in transcriptional activity, TBP interaction and regulation, and that the combination o...
null
413
5,688
0
false
null
null
Truncated forms of CDX1 and swapped mutants between CDX1 and CDX2 (Table 1) provide evidence that separate domains of these homeoproteins, namely the N-terminal domain, the central homeodomain and the C-terminal domain, are involved in transcriptional activity, TBP interaction and regulation, and that the combination o...
true
true
true
true
true
947
0
DISCUSSION
0
null
null
17,158,164
pmid-9631657|pmid-14641327|pmid-11424082|pmid-16199152
Finally, using an altered-specificity mutant of TBP, we demonstrate that the TBP–CDX1 interaction is functional and that co-operativity is selective for G6Pase promoter activation.
null
180
5,689
0
false
null
null
Finally, using an altered-specificity mutant of TBP, we demonstrate that the TBP–CDX1 interaction is functional and that co-operativity is selective for G6Pase promoter activation.
true
true
true
true
true
947
1
DISCUSSION
0
null
null
17,158,164
pmid-15361482|pmid-10392709|pmid-11040183|pmid-9396760|pmid-8552090|pmid-10934025|pmid-15240568|pmid-15361487|pmid-14625550|pmid-12970140|pmid-16258171|pmid-16325584
Functional organization of the CDX1 and CDX2 homeoproteins
null
58
5,690
0
false
null
null
Functional organization of the CDX1 and CDX2 homeoproteins
true
true
false
true
false
948
2
DISCUSSION
1
1
[ "b1", "b2" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
The organization of the N-terminal domain (ND), the homeodomain (HD) and the C-terminal domain (CD) of CDX homeoproteins is schematized.
[ "1", "2" ]
136
5,691
0
false
The organization of the N-terminal domain (ND), the homeodomain (HD) and the C-terminal domain (CD) of CDX homeoproteins is schematized.
[]
The organization of the N-terminal domain (ND), the homeodomain (HD) and the C-terminal domain (CD) of CDX homeoproteins is schematized.
true
true
true
true
true
949
2
DISCUSSION
1
1
[ "b1", "b2" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
(1) and (2), respectively, designate the CDX1 or CDX2 origin of each domain.
[ "1", "2" ]
76
5,692
1
false
and, respectively, designate the CDX1 or CDX2 origin of each domain.
[ "1", "2" ]
and, respectively, designate the CDX1 or CDX2 origin of each domain.
false
true
true
true
false
949
2
DISCUSSION
1
1
[ "b1", "b2" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
Thus, the wild-type CDX1 and CDX2 proteins appear here as ND1-HD1-CD1 and ND2-HD2-CD2, respectively.
[ "1", "2" ]
100
5,693
0
false
Thus, the wild-type CDX1 and CDX2 proteins appear here as ND1-HD1-CD1 and ND2-HD2-CD2, respectively.
[]
Thus, the wild-type CDX1 and CDX2 proteins appear here as ND1-HD1-CD1 and ND2-HD2-CD2, respectively.
true
true
true
true
true
949
2
DISCUSSION
1
1
[ "b1", "b2" ]
17,158,164
pmid-12954759|pmid-9631657|pmid-14641327
Interaction with TBP is defined by means of co-immunoprecipitation or GST-pulldown experiments.
[ "1", "2" ]
95
5,694
0
false
Interaction with TBP is defined by means of co-immunoprecipitation or GST-pulldown experiments.
[]
Interaction with TBP is defined by means of co-immunoprecipitation or GST-pulldown experiments.
true
true
true
true
true
949
3
DISCUSSION
1
28
[ "b28" ]
17,158,164
pmid-15044625
Co-immunoprecipitation and GST-pulldown indicate that CDX1 and TBP belong to a common complex with TAFs, although the direct physical interaction between CDX1 and TBP could not be established.
[ "28" ]
192
5,695
0
false
Co-immunoprecipitation and GST-pulldown indicate that CDX1 and TBP belong to a common complex with TAFs, although the direct physical interaction between CDX1 and TBP could not be established.
[]
Co-immunoprecipitation and GST-pulldown indicate that CDX1 and TBP belong to a common complex with TAFs, although the direct physical interaction between CDX1 and TBP could not be established.
true
true
true
true
true
950
3
DISCUSSION
1
28
[ "b28" ]
17,158,164
pmid-15044625
Indeed, while GST-TBP interacts with CDX1 produced in intestinal cells, it does not with in vitro translated CDX1 nor with the in vitro translated homeodomain, which indicates either that the TBP–CDX1 interaction is indirect and needs cofactors, or that it is direct but that the conformation of in vitro-synthesized CDX...
[ "28" ]
353
5,696
0
false
Indeed, while GST-TBP interacts with CDX1 produced in intestinal cells, it does not with in vitro translated CDX1 nor with the in vitro translated homeodomain, which indicates either that the TBP–CDX1 interaction is indirect and needs cofactors, or that it is direct but that the conformation of in vitro-synthesized CDX...
[]
Indeed, while GST-TBP interacts with CDX1 produced in intestinal cells, it does not with in vitro translated CDX1 nor with the in vitro translated homeodomain, which indicates either that the TBP–CDX1 interaction is indirect and needs cofactors, or that it is direct but that the conformation of in vitro-synthesized CDX...
true
true
true
true
true
950
3
DISCUSSION
1
28
[ "b28" ]
17,158,164
pmid-15044625
However, evidence is provided here for the functionality of the TBP–CDX1 interaction, using the specificity mutant of TBP, spm3 and the TGTA variant of the G6Pase TATA-box.
[ "28" ]
172
5,697
0
false
However, evidence is provided here for the functionality of the TBP–CDX1 interaction, using the specificity mutant of TBP, spm3 and the TGTA variant of the G6Pase TATA-box.
[]
However, evidence is provided here for the functionality of the TBP–CDX1 interaction, using the specificity mutant of TBP, spm3 and the TGTA variant of the G6Pase TATA-box.
true
true
true
true
true
950
3
DISCUSSION
1
28
[ "b28" ]
17,158,164
pmid-15044625
The use of TBP-spm3 together with the TGTA variant of the G6Pase promoter allowed us to bypass the effects of endogenous TBP in cotransfections studies.
[ "28" ]
152
5,698
0
false
The use of TBP-spm3 together with the TGTA variant of the G6Pase promoter allowed us to bypass the effects of endogenous TBP in cotransfections studies.
[]
The use of TBP-spm3 together with the TGTA variant of the G6Pase promoter allowed us to bypass the effects of endogenous TBP in cotransfections studies.
true
true
true
true
true
950
3
DISCUSSION
1
28
[ "b28" ]
17,158,164
pmid-15044625
Interestingly, we found that CDX1 and TBP-spm3 cooperatively activate the pTGTA-G6Pase-Luc reporter, but not the standard pTGTA-Luc vector based on the RARAβ2 proximal promoter, suggesting that CDX1 functions in a context-dependent manner and that sequences outside the TATA-box are also important for controlling CDX1 D...
[ "28" ]
347
5,699
0
false
Interestingly, we found that CDX1 and TBP-spm3 cooperatively activate the pTGTA-G6Pase-Luc reporter, but not the standard pTGTA-Luc vector based on the RARAβ2 proximal promoter, suggesting that CDX1 functions in a context-dependent manner and that sequences outside the TATA-box are also important for controlling CDX1 D...
[]
Interestingly, we found that CDX1 and TBP-spm3 cooperatively activate the pTGTA-G6Pase-Luc reporter, but not the standard pTGTA-Luc vector based on the RARAβ2 proximal promoter, suggesting that CDX1 functions in a context-dependent manner and that sequences outside the TATA-box are also important for controlling CDX1 D...
true
true
true
true
true
950