Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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INTRODUCTION
1
1–5
[ "B1 B2 B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,485,475
pmid-15993809|NA|pmid-11470599|pmid-15288245|pmid-11790605|NA|NA|NA|pmid-15667143|pmid-16845110|pmid-17170002
Very few free on-line tools are available to generate the 3D conformation of compounds.
[ "1–5", "6", "7", "8", "9", "10", "11" ]
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false
Very few free on-line tools are available to generate the 3D conformation of compounds.
[]
Very few free on-line tools are available to generate the 3D conformation of compounds.
true
true
true
true
true
328
0
INTRODUCTION
1
9
[ "B1 B2 B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,485,475
pmid-15993809|NA|pmid-11470599|pmid-15288245|pmid-11790605|NA|NA|NA|pmid-15667143|pmid-16845110|pmid-17170002
To overcome this limitation, sites such a Zinc (9), FAF-drugs (10) or very recently pubChem (11) take advantage of commercial software to propose the pre-calculated collections of compounds in 3D.
[ "1–5", "6", "7", "8", "9", "10", "11" ]
196
1,901
1
false
To overcome this limitation, sites such a Zinc, FAF-drugs or very recently pubChem take advantage of commercial software to propose the pre-calculated collections of compounds in 3D.
[ "9", "10", "11" ]
To overcome this limitation, sites such a Zinc, FAF-drugs or very recently pubChem take advantage of commercial software to propose the pre-calculated collections of compounds in 3D.
true
true
true
true
true
328
0
INTRODUCTION
1
1–5
[ "B1 B2 B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,485,475
pmid-15993809|NA|pmid-11470599|pmid-15288245|pmid-11790605|NA|NA|NA|pmid-15667143|pmid-16845110|pmid-17170002
Alternative services that provide direct 2D to 3D facilities come from demos of drug design package vendors, such as OpenEye’ Omega (http://www.eyesopen.com/products/applications/omega.html), Molsoft (http://www.molsoft.com/2dto3d.html), Corina (http://www.molecular-networks.com/software/corina/) and from academic site...
[ "1–5", "6", "7", "8", "9", "10", "11" ]
546
1,902
0
false
Alternative services that provide direct 2D to 3D facilities come from demos of drug design package vendors, such as OpenEye’ Omega (http://www.eyesopen.com/products/applications/omega.html), Molsoft (http://www.molsoft.com/2dto3d.html), Corina (http://www.molecular-networks.com/software/corina/) and from academic site...
[ "http://iris12.colby.edu/%7Ewww/jme/smiledg.html; http://davapc1.bioch.dundee.ac.uk/programs/prodrg/; http://bioserv.cbs.cnrs.fr/HTML_BIO/APPLET_ACD/create_molecule.html" ]
Alternative services that provide direct 2D to 3D facilities come from demos of drug design package vendors, such as OpenEye’ Omega (http://www.eyesopen.com/products/applications/omega.html), Molsoft (http://www.molsoft.com/2dto3d.html), Corina (http://www.molecular-networks.com/software/corina/) and from academic site...
true
true
true
true
true
328
0
INTRODUCTION
1
1–5
[ "B1 B2 B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,485,475
pmid-15993809|NA|pmid-11470599|pmid-15288245|pmid-11790605|NA|NA|NA|pmid-15667143|pmid-16845110|pmid-17170002
Such services are, however, usually limited to building one compound at a time and provide generally only one conformer (only the Omega's service is able to return an ensemble of conformations for the input compound).
[ "1–5", "6", "7", "8", "9", "10", "11" ]
217
1,903
0
false
Such services are, however, usually limited to building one compound at a time and provide generally only one conformer (only the Omega's service is able to return an ensemble of conformations for the input compound).
[]
Such services are, however, usually limited to building one compound at a time and provide generally only one conformer (only the Omega's service is able to return an ensemble of conformations for the input compound).
true
true
true
true
true
328
1
INTRODUCTION
1
12–13
[ "B12 B13" ]
17,485,475
NA|pmid-16796559
It is well known that generating an accurate 3D structure for a small chemical compound is not trivial and as such many different approaches have been developed over the years, starting from manual model building up to quantum mechanical calculations.
[ "12–13" ]
251
1,904
0
false
It is well known that generating an accurate 3D structure for a small chemical compound is not trivial and as such many different approaches have been developed over the years, starting from manual model building up to quantum mechanical calculations.
[]
It is well known that generating an accurate 3D structure for a small chemical compound is not trivial and as such many different approaches have been developed over the years, starting from manual model building up to quantum mechanical calculations.
true
true
true
true
true
329
1
INTRODUCTION
1
12–13
[ "B12 B13" ]
17,485,475
NA|pmid-16796559
Between these two extremes and because for quantum chemistry programs it is generally necessary to start from a reasonable initial 3D structure, other methods such as rule-based methods (approaches based essentially on structural data) or data-based methods are commonly used (12–13).
[ "12–13" ]
284
1,905
1
false
Between these two extremes and because for quantum chemistry programs it is generally necessary to start from a reasonable initial 3D structure, other methods such as rule-based methods (approaches based essentially on structural data) or data-based methods are commonly used.
[ "12–13" ]
Between these two extremes and because for quantum chemistry programs it is generally necessary to start from a reasonable initial 3D structure, other methods such as rule-based methods (approaches based essentially on structural data) or data-based methods are commonly used.
true
true
true
true
true
329
2
INTRODUCTION
0
null
null
17,485,475
null
Frog (a mixed rule-based data-based approach) aims at providing on-line generation of ensembles of 3D conformation for drug-like compounds (i.e.
null
144
1,906
0
false
null
null
Frog (a mixed rule-based data-based approach) aims at providing on-line generation of ensembles of 3D conformation for drug-like compounds (i.e.
true
true
true
true
true
330
2
INTRODUCTION
0
null
null
17,485,475
null
compounds that are ADME/tox compliant).
null
39
1,907
0
false
null
null
compounds that are ADME/tox compliant).
false
true
true
true
false
330
2
INTRODUCTION
0
null
null
17,485,475
null
It is based on Frowns (a chemoinformatics toolkit available at http://frowns.sourceforge.net/) to which several functionalities have been added to allow the generation of 3D structures starting from SMILES or SDF data input.
null
224
1,908
0
false
null
null
It is based on Frowns (a chemoinformatics toolkit available at http://frowns.sourceforge.net/) to which several functionalities have been added to allow the generation of 3D structures starting from SMILES or SDF data input.
true
true
true
true
true
330
2
INTRODUCTION
0
null
null
17,485,475
null
Frog is able to (i) fully or partially disambiguate compound stereochemistry including chiral sites, and to (ii) generate single or ensembles of low to medium energy 3D conformations for each isomer.
null
199
1,909
0
false
null
null
Frog is able to (i) fully or partially disambiguate compound stereochemistry including chiral sites, and to (ii) generate single or ensembles of low to medium energy 3D conformations for each isomer.
true
true
true
true
true
330
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,148,478
NA|NA|pmid-11210495|pmid-16237015
Pyrococcus furiosus is a hyperthermophilic anaerobic archaeon that grows optimally near 100°C using carbohydrates and peptides as carbon and energy sources (1).
[ "1", "2", "3", "4" ]
160
1,910
1
false
Pyrococcus furiosus is a hyperthermophilic anaerobic archaeon that grows optimally near 100°C using carbohydrates and peptides as carbon and energy sources.
[ "1" ]
Pyrococcus furiosus is a hyperthermophilic anaerobic archaeon that grows optimally near 100°C using carbohydrates and peptides as carbon and energy sources.
true
true
true
true
true
331
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,148,478
NA|NA|pmid-11210495|pmid-16237015
This organism is commonly found in hydrothermal vents on the seafloor near volcanos.
[ "1", "2", "3", "4" ]
84
1,911
0
false
This organism is commonly found in hydrothermal vents on the seafloor near volcanos.
[]
This organism is commonly found in hydrothermal vents on the seafloor near volcanos.
true
true
true
true
true
331
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b4" ]
17,148,478
NA|NA|pmid-11210495|pmid-16237015
Its ability to grow to high cell densities under laboratory conditions without the need of elemental sulfur, and thus production of toxic hydrogen sulfide, has made it a useful model organism with which to study thermostable enzymes and adaptations to high-temperature environments (2).
[ "1", "2", "3", "4" ]
286
1,912
1
false
Its ability to grow to high cell densities under laboratory conditions without the need of elemental sulfur, and thus production of toxic hydrogen sulfide, has made it a useful model organism with which to study thermostable enzymes and adaptations to high-temperature environments.
[ "2" ]
Its ability to grow to high cell densities under laboratory conditions without the need of elemental sulfur, and thus production of toxic hydrogen sulfide, has made it a useful model organism with which to study thermostable enzymes and adaptations to high-temperature environments.
true
true
true
true
true
331
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,148,478
NA|NA|pmid-11210495|pmid-16237015
The genome sequence of P.furiosus has been determined (3,4) and is available at .
[ "1", "2", "3", "4" ]
81
1,913
0
false
The genome sequence of P.furiosus has been determined and is available at.
[ "3,4" ]
The genome sequence of P.furiosus has been determined and is available at.
true
true
true
true
true
331
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,148,478
NA|NA|pmid-11210495|pmid-16237015
The latest annotation contains 2125 genes, which is used for the study herein.
[ "1", "2", "3", "4" ]
78
1,914
0
false
The latest annotation contains 2125 genes, which is used for the study herein.
[]
The latest annotation contains 2125 genes, which is used for the study herein.
true
true
true
true
true
331
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,148,478
NA|NA|pmid-11210495|pmid-16237015
Similar to most genome annotations that of P.furiosus provides a unique source of information for molecular and biochemical studies, but it is mostly gene-centric and does not provide much structural and functional information about higher-level organizations.
[ "1", "2", "3", "4" ]
260
1,915
0
false
Similar to most genome annotations that of P.furiosus provides a unique source of information for molecular and biochemical studies, but it is mostly gene-centric and does not provide much structural and functional information about higher-level organizations.
[]
Similar to most genome annotations that of P.furiosus provides a unique source of information for molecular and biochemical studies, but it is mostly gene-centric and does not provide much structural and functional information about higher-level organizations.
true
true
true
true
true
331
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4" ]
17,148,478
NA|NA|pmid-11210495|pmid-16237015
In this paper, we present our recent work on the identification of operons in P.furiosus.
[ "1", "2", "3", "4" ]
89
1,916
0
false
In this paper, we present our recent work on the identification of operons in P.furiosus.
[]
In this paper, we present our recent work on the identification of operons in P.furiosus.
true
true
true
true
true
331
1
INTRODUCTION
1
5
[ "b5", "b10" ]
17,148,478
pmid-15096577|NA
An operon is defined as a basic transcriptional unit in prokaryotes.
[ "5", "10" ]
68
1,917
0
false
An operon is defined as a basic transcriptional unit in prokaryotes.
[]
An operon is defined as a basic transcriptional unit in prokaryotes.
true
true
true
true
true
332
1
INTRODUCTION
1
5
[ "b5", "b10" ]
17,148,478
pmid-15096577|NA
Characterization of operons represents an important step in understanding many cellular processes and deciphering transcriptional regulatory networks.
[ "5", "10" ]
150
1,918
0
false
Characterization of operons represents an important step in understanding many cellular processes and deciphering transcriptional regulatory networks.
[]
Characterization of operons represents an important step in understanding many cellular processes and deciphering transcriptional regulatory networks.
true
true
true
true
true
332
1
INTRODUCTION
1
5
[ "b5", "b10" ]
17,148,478
pmid-15096577|NA
Insights into the function and regulation of genes in the context of pathways and networks can be gained if we can annotate operons accurately.
[ "5", "10" ]
143
1,919
0
false
Insights into the function and regulation of genes in the context of pathways and networks can be gained if we can annotate operons accurately.
[]
Insights into the function and regulation of genes in the context of pathways and networks can be gained if we can annotate operons accurately.
true
true
true
true
true
332
1
INTRODUCTION
1
5
[ "b5", "b10" ]
17,148,478
pmid-15096577|NA
Due to the arduous nature of experimentally determining operons on an individual basis, several computational approaches have been proposed for predicting them (5–10).
[ "5", "10" ]
167
1,920
0
false
Due to the arduous nature of experimentally determining operons on an individual basis, several computational approaches have been proposed for predicting them.
[ "5–10" ]
Due to the arduous nature of experimentally determining operons on an individual basis, several computational approaches have been proposed for predicting them.
true
true
true
true
true
332
1
INTRODUCTION
1
5
[ "b5", "b10" ]
17,148,478
pmid-15096577|NA
Generally, these approaches use information derived from comparative genomics, transcriptional signals upstream and downstream of operons, features such as intergenic distances, functional annotation of genes and experimentally derived DNA microarray data.
[ "5", "10" ]
256
1,921
0
false
Generally, these approaches use information derived from comparative genomics, transcriptional signals upstream and downstream of operons, features such as intergenic distances, functional annotation of genes and experimentally derived DNA microarray data.
[]
Generally, these approaches use information derived from comparative genomics, transcriptional signals upstream and downstream of operons, features such as intergenic distances, functional annotation of genes and experimentally derived DNA microarray data.
true
true
true
true
true
332
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
We have recently developed a novel method for operon prediction by integrating three existing operon prediction methods and have applied it to the bacteria Escherichia coli and Bacillus subtilis and P.furiosus.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
210
1,922
0
false
We have recently developed a novel method for operon prediction by integrating three existing operon prediction methods and have applied it to the bacteria Escherichia coli and Bacillus subtilis and P.furiosus.
[]
We have recently developed a novel method for operon prediction by integrating three existing operon prediction methods and have applied it to the bacteria Escherichia coli and Bacillus subtilis and P.furiosus.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
The three methods were chosen because they are considered as better prediction methods among all publicly available operon prediction programs.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
143
1,923
0
false
The three methods were chosen because they are considered as better prediction methods among all publicly available operon prediction programs.
[]
The three methods were chosen because they are considered as better prediction methods among all publicly available operon prediction programs.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
All three prediction programs assume that genes within an operon are in the same directon, which is defined as consecutive open reading frames (ORFs) transcribed in the same direction with no intervening ORF on the opposite strand (6,8,10).
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
240
1,924
0
false
All three prediction programs assume that genes within an operon are in the same directon, which is defined as consecutive open reading frames (ORFs) transcribed in the same direction with no intervening ORF on the opposite strand.
[ "6,8,10" ]
All three prediction programs assume that genes within an operon are in the same directon, which is defined as consecutive open reading frames (ORFs) transcribed in the same direction with no intervening ORF on the opposite strand.
true
true
true
true
true
333
2
INTRODUCTION
1
10
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
The first program is the JPOP (Joint Prediction of Operons) program (10), which classifies each pair of consecutive genes as an ‘operonic’ or an ‘non-operonic’ boundary based on their intergenic distance, similarity between their phylogenetic profiles, and relatedness of their annotated functions from COGs (11).
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
313
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1
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The first program is the JPOP (Joint Prediction of Operons) program, which classifies each pair of consecutive genes as an ‘operonic’ or an ‘non-operonic’ boundary based on their intergenic distance, similarity between their phylogenetic profiles, and relatedness of their annotated functions from COGs.
[ "10", "11" ]
The first program is the JPOP (Joint Prediction of Operons) program, which classifies each pair of consecutive genes as an ‘operonic’ or an ‘non-operonic’ boundary based on their intergenic distance, similarity between their phylogenetic profiles, and relatedness of their annotated functions from COGs.
true
true
true
true
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333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
Each of these sets of supporting data is integrated using a neural network (NN) to generate operon predictions.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
111
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0
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Each of these sets of supporting data is integrated using a neural network (NN) to generate operon predictions.
[]
Each of these sets of supporting data is integrated using a neural network (NN) to generate operon predictions.
true
true
true
true
true
333
2
INTRODUCTION
1
8
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
The second program, Operon Finding Software (OFS) (8), combines conserved gene-order information across multiple genomes with intergenic distance and similarity information of annotated gene functions to make operon predictions.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
228
1,927
1
false
The second program, Operon Finding Software (OFS), combines conserved gene-order information across multiple genomes with intergenic distance and similarity information of annotated gene functions to make operon predictions.
[ "8" ]
The second program, Operon Finding Software (OFS), combines conserved gene-order information across multiple genomes with intergenic distance and similarity information of annotated gene functions to make operon predictions.
true
true
true
true
true
333
2
INTRODUCTION
1
7
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
This work generalized the gene-order conservation approach used in (7) by relaxing the adjacency and orthology criteria.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
120
1,928
1
false
This work generalized the gene-order conservation approach used in by relaxing the adjacency and orthology criteria.
[ "7" ]
This work generalized the gene-order conservation approach used in by relaxing the adjacency and orthology criteria.
true
true
true
true
true
333
2
INTRODUCTION
1
8
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
The authors of OFS (8) claimed to be able to predict operons without extensive training.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
88
1,929
1
false
The authors of OFS claimed to be able to predict operons without extensive training.
[ "8" ]
The authors of OFS claimed to be able to predict operons without extensive training.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
The third program, developed by the Virtual Institute for Microbial Stress and Survival (VIMSS) (6), is similar to the first two programs because it uses intergenic distance and COG information.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
194
1,930
1
false
The third program, developed by the Virtual Institute for Microbial Stress and Survival (VIMSS), is similar to the first two programs because it uses intergenic distance and COG information.
[ "6" ]
The third program, developed by the Virtual Institute for Microbial Stress and Survival (VIMSS), is similar to the first two programs because it uses intergenic distance and COG information.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
VIMSS differs, however, in also employing the codon adaptation index (CAI) and applying a different approach for comparative genome analysis to make operon predictions.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
168
1,931
0
false
VIMSS differs, however, in also employing the codon adaptation index (CAI) and applying a different approach for comparative genome analysis to make operon predictions.
[]
VIMSS differs, however, in also employing the codon adaptation index (CAI) and applying a different approach for comparative genome analysis to make operon predictions.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
The comparative genome analysis examines how often orthologous genes are close to each other within 5 kb across multiple genomes, while the CAI measures synonymous codon usage.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
176
1,932
0
false
The comparative genome analysis examines how often orthologous genes are close to each other within 5 kb across multiple genomes, while the CAI measures synonymous codon usage.
[]
The comparative genome analysis examines how often orthologous genes are close to each other within 5 kb across multiple genomes, while the CAI measures synonymous codon usage.
true
true
true
true
true
333
2
INTRODUCTION
1
7
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
Another operon prediction method developed by The Institute for Genomic Research (TIGR) (7) was considered but not integrated into our method due to the high number of missing confidence values between adjacent gene pairs in the same directon.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
243
1,933
1
false
Another operon prediction method developed by The Institute for Genomic Research (TIGR) was considered but not integrated into our method due to the high number of missing confidence values between adjacent gene pairs in the same directon.
[ "7" ]
Another operon prediction method developed by The Institute for Genomic Research (TIGR) was considered but not integrated into our method due to the high number of missing confidence values between adjacent gene pairs in the same directon.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
A summary of the default operon prediction results for the three programs for E.coli and B.subtilis are shown in Supplementary Figure S1.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
137
1,934
0
false
A summary of the default operon prediction results for the three programs for E.coli and B.subtilis are shown in Supplementary Figure S1.
[]
A summary of the default operon prediction results for the three programs for E.coli and B.subtilis are shown in Supplementary Figure S1.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
The Venn diagram displays the number of gene pairs predicted to be within operons by each program and the overlap in gene pairs predicted among the three programs.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
163
1,935
0
false
The Venn diagram displays the number of gene pairs predicted to be within operons by each program and the overlap in gene pairs predicted among the three programs.
[]
The Venn diagram displays the number of gene pairs predicted to be within operons by each program and the overlap in gene pairs predicted among the three programs.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
Out of a total of 2985 adjacent gene pairs in the same directon in E.coli, 1885 gene pairs are predicted to be in operons by at least one program and only 55% (=1037/1885) of gene pairs are predicted to be in operons by all three programs.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
239
1,936
0
false
Out of a total of 2985 adjacent gene pairs in the same directon in E.coli, 1885 gene pairs are predicted to be in operons by at least one program and only 55% of gene pairs are predicted to be in operons by all three programs.
[ "=1037/1885" ]
Out of a total of 2985 adjacent gene pairs in the same directon in E.coli, 1885 gene pairs are predicted to be in operons by at least one program and only 55% of gene pairs are predicted to be in operons by all three programs.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
Likewise in B.subtilis with a total of 3005 gene pairs, 2122 gene pairs are predicted to be in operons, but only 28% (=599/2122) of gene pairs are predicted by all three programs.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
179
1,937
0
false
Likewise in B.subtilis with a total of 3005 gene pairs, 2122 gene pairs are predicted to be in operons, but only 28% (=599/2122) of gene pairs are predicted by all three programs.
[]
Likewise in B.subtilis with a total of 3005 gene pairs, 2122 gene pairs are predicted to be in operons, but only 28% (=599/2122) of gene pairs are predicted by all three programs.
true
true
true
true
true
333
2
INTRODUCTION
1
6
[ "b6", "b8", "b10", "b10", "b11", "b8", "b7", "b8", "b6", "b7" ]
17,148,478
pmid-15701760|pmid-15539453|NA|NA|pmid-9381173|pmid-15539453|pmid-11222772|pmid-15539453|pmid-15701760|pmid-11222772
With low consensus among individual operon prediction programs, there is a need to incorporate the additional information provided by each program into a general operon predictor.
[ "6", "8", "10", "10", "11", "8", "7", "8", "6", "7" ]
179
1,938
0
false
With low consensus among individual operon prediction programs, there is a need to incorporate the additional information provided by each program into a general operon predictor.
[]
With low consensus among individual operon prediction programs, there is a need to incorporate the additional information provided by each program into a general operon predictor.
true
true
true
true
true
333
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
Our initial prediction stems from training a NN-based classifier (to classify a pair of adjacent genes as either operonic boundary or not), based on the outputs of the three aforementioned programs.
[ "10", "12", "13" ]
198
1,939
0
false
Our initial prediction stems from training a NN-based classifier (to classify a pair of adjacent genes as either operonic boundary or not), based on the outputs of the three aforementioned programs.
[]
Our initial prediction stems from training a NN-based classifier (to classify a pair of adjacent genes as either operonic boundary or not), based on the outputs of the three aforementioned programs.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
Furthermore, we use additional computational data from (i) Gene Ontology (GO) information, (ii) known pathway information and (iii) log-likelihood intergenic distance to improve the operon prediction accuracy.
[ "10", "12", "13" ]
209
1,940
0
false
Furthermore, we use additional computational data from (i) Gene Ontology (GO) information, (ii) known pathway information and (iii) log-likelihood intergenic distance to improve the operon prediction accuracy.
[]
Furthermore, we use additional computational data from (i) Gene Ontology (GO) information, (ii) known pathway information and (iii) log-likelihood intergenic distance to improve the operon prediction accuracy.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
The GO classification is used to compute a functional similarity score between pairs of adjacent genes in the same directon.
[ "10", "12", "13" ]
124
1,941
0
false
The GO classification is used to compute a functional similarity score between pairs of adjacent genes in the same directon.
[]
The GO classification is used to compute a functional similarity score between pairs of adjacent genes in the same directon.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
Additionally, we have computed KEGG pathway scores based on whether or not gene pairs belong to common KEGG pathways.
[ "10", "12", "13" ]
117
1,942
0
false
Additionally, we have computed KEGG pathway scores based on whether or not gene pairs belong to common KEGG pathways.
[]
Additionally, we have computed KEGG pathway scores based on whether or not gene pairs belong to common KEGG pathways.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
The intergenic distance feature as used in previous studies is also inputted directly into the NN to aid prediction since it has been found to be a strong discriminatory feature (10,12,13).
[ "10", "12", "13" ]
189
1,943
0
false
The intergenic distance feature as used in previous studies is also inputted directly into the NN to aid prediction since it has been found to be a strong discriminatory feature.
[ "10,12,13" ]
The intergenic distance feature as used in previous studies is also inputted directly into the NN to aid prediction since it has been found to be a strong discriminatory feature.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
Three-fold cross-validation and train/test set validation was analyzed for E.coli and B.subtilis to examine the performance of these features within and across species, respectively.
[ "10", "12", "13" ]
182
1,944
0
false
Three-fold cross-validation and train/test set validation was analyzed for E.coli and B.subtilis to examine the performance of these features within and across species, respectively.
[]
Three-fold cross-validation and train/test set validation was analyzed for E.coli and B.subtilis to examine the performance of these features within and across species, respectively.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
Using the optimal training set, our method is applied to make operon predictions in P.furiosus.
[ "10", "12", "13" ]
95
1,945
0
false
Using the optimal training set, our method is applied to make operon predictions in P.furiosus.
[]
Using the optimal training set, our method is applied to make operon predictions in P.furiosus.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
We have used experimental data obtained from time-course microarray gene expression data to verify these operon predictions.
[ "10", "12", "13" ]
124
1,946
0
false
We have used experimental data obtained from time-course microarray gene expression data to verify these operon predictions.
[]
We have used experimental data obtained from time-course microarray gene expression data to verify these operon predictions.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
The idea is that genes in the same operon should in general exhibit similar expression patterns under any experimental conditions.
[ "10", "12", "13" ]
130
1,947
0
false
The idea is that genes in the same operon should in general exhibit similar expression patterns under any experimental conditions.
[]
The idea is that genes in the same operon should in general exhibit similar expression patterns under any experimental conditions.
true
true
true
true
true
334
3
INTRODUCTION
1
10
[ "b10", "b12", "b13" ]
17,148,478
NA|pmid-12169563|pmid-10823905
All predicted operons are available at along with the prediction program.
[ "10", "12", "13" ]
74
1,948
0
false
All predicted operons are available at along with the prediction program.
[]
All predicted operons are available at along with the prediction program.
true
true
true
true
true
334
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5" ]
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
The partitioning of eukaryotic cells into distinct compartments by lipid membranes necessitates the existence of an elaborate transport system capable of transferring membrane components and cargos between different membrane-bounded organelles and between these organelles and the plasma membrane (PM).
[ "1", "3", "4", "5" ]
302
1,949
0
false
The partitioning of eukaryotic cells into distinct compartments by lipid membranes necessitates the existence of an elaborate transport system capable of transferring membrane components and cargos between different membrane-bounded organelles and between these organelles and the plasma membrane (PM).
[]
The partitioning of eukaryotic cells into distinct compartments by lipid membranes necessitates the existence of an elaborate transport system capable of transferring membrane components and cargos between different membrane-bounded organelles and between these organelles and the plasma membrane (PM).
true
true
true
true
true
335
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5" ]
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
The various intracellular trafficking routes are served by specialized lipid vesicles that travel to their destination along cytoskeleton filaments and fuse with their target membranes by tightly regulated mechanisms.
[ "1", "3", "4", "5" ]
217
1,950
0
false
The various intracellular trafficking routes are served by specialized lipid vesicles that travel to their destination along cytoskeleton filaments and fuse with their target membranes by tightly regulated mechanisms.
[]
The various intracellular trafficking routes are served by specialized lipid vesicles that travel to their destination along cytoskeleton filaments and fuse with their target membranes by tightly regulated mechanisms.
true
true
true
true
true
335
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5" ]
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
Proteins belonging to the Rab family of small Ras-related GTPases play pivotal roles in the regulation of intracellular vesicular traffic (1–3).
[ "1", "3", "4", "5" ]
144
1,951
0
false
Proteins belonging to the Rab family of small Ras-related GTPases play pivotal roles in the regulation of intracellular vesicular traffic.
[ "1–3" ]
Proteins belonging to the Rab family of small Ras-related GTPases play pivotal roles in the regulation of intracellular vesicular traffic.
true
true
true
true
true
335
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5" ]
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
Rab proteins associate with specific vesicles and regulate multiple steps in their trafficking, including their formation and transport, cargo selection, as well as docking to and fusion with their target membranes.
[ "1", "3", "4", "5" ]
215
1,952
0
false
Rab proteins associate with specific vesicles and regulate multiple steps in their trafficking, including their formation and transport, cargo selection, as well as docking to and fusion with their target membranes.
[]
Rab proteins associate with specific vesicles and regulate multiple steps in their trafficking, including their formation and transport, cargo selection, as well as docking to and fusion with their target membranes.
true
true
true
true
true
335
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5" ]
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
To fulfill these functions, Rab proteins are tightly regulated at the level of their localization, membrane association, activation and expression.
[ "1", "3", "4", "5" ]
147
1,953
0
false
To fulfill these functions, Rab proteins are tightly regulated at the level of their localization, membrane association, activation and expression.
[]
To fulfill these functions, Rab proteins are tightly regulated at the level of their localization, membrane association, activation and expression.
true
true
true
true
true
335
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5" ]
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
The importance of the latter is underscored by the fact that deregulated Rab expression is tightly correlated with several pathologies, including vascular, lung and thyroid disorders as well as a number of cancers (4,5).
[ "1", "3", "4", "5" ]
220
1,954
0
false
The importance of the latter is underscored by the fact that deregulated Rab expression is tightly correlated with several pathologies, including vascular, lung and thyroid disorders as well as a number of cancers.
[ "4,5" ]
The importance of the latter is underscored by the fact that deregulated Rab expression is tightly correlated with several pathologies, including vascular, lung and thyroid disorders as well as a number of cancers.
true
true
true
true
true
335
1
INTRODUCTION
0
null
null
17,175,541
pmid-15528357
Vesicular traffic is of central importance for the presentation of peptides by Major Histocompatibility Complex (MHC) molecules to the antigen receptors (TCRs) of T lymphocytes.
null
177
1,955
0
false
null
null
Vesicular traffic is of central importance for the presentation of peptides by Major Histocompatibility Complex (MHC) molecules to the antigen receptors (TCRs) of T lymphocytes.
true
true
true
true
true
336
1
INTRODUCTION
0
null
null
17,175,541
pmid-15528357
MHC-mediated peptide presentation is essential for the adaptive immune system because it governs the development and activation of T cells.
null
139
1,956
0
false
null
null
MHC-mediated peptide presentation is essential for the adaptive immune system because it governs the development and activation of T cells.
true
true
true
true
true
336
1
INTRODUCTION
0
null
null
17,175,541
pmid-15528357
The engagement of MHC-peptide complexes by the TCR of thymocytes during their development in the thymus directs the positive and negative selection processes that shape the mature T cell repertoire.
null
198
1,957
0
false
null
null
The engagement of MHC-peptide complexes by the TCR of thymocytes during their development in the thymus directs the positive and negative selection processes that shape the mature T cell repertoire.
true
true
true
true
true
336
1
INTRODUCTION
0
null
null
17,175,541
pmid-15528357
In the periphery, the recognition of peptides presented by MHC molecules controls the initiation and development of T cell-mediated immune responses directed against pathogens and tumors.
null
187
1,958
0
false
null
null
In the periphery, the recognition of peptides presented by MHC molecules controls the initiation and development of T cell-mediated immune responses directed against pathogens and tumors.
true
true
true
true
true
336
1
INTRODUCTION
0
null
null
17,175,541
pmid-15528357
MHC-mediated peptide presentation is also critical for the maintenance of tolerance to self-antigens and is implicated in the breakdown of this self-tolerance during autoimmune diseases.
null
186
1,959
0
false
null
null
MHC-mediated peptide presentation is also critical for the maintenance of tolerance to self-antigens and is implicated in the breakdown of this self-tolerance during autoimmune diseases.
true
true
true
true
true
336
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
There are two classes of MHC molecules—MHC class I (MHC-I) and MHC class II (MHC-II)—which differ with respect to their pattern of expression, the nature of the peptides they present, the T cell subsets that recognize them and their functions in the immune system.
[ "6", "7", "7", "8" ]
264
1,960
0
false
There are two classes of MHC molecules—MHC class I (MHC-I) and MHC class II (MHC-II)—which differ with respect to their pattern of expression, the nature of the peptides they present, the T cell subsets that recognize them and their functions in the immune system.
[]
There are two classes of MHC molecules—MHC class I (MHC-I) and MHC class II (MHC-II)—which differ with respect to their pattern of expression, the nature of the peptides they present, the T cell subsets that recognize them and their functions in the immune system.
true
true
true
true
true
337
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
MHC-I molecules are expressed by all nucleated cells, and are specialized for the presentation of peptides derived from the degradation of intracellular proteins to the TCR of CD8+ T cells (6,7).
[ "6", "7", "7", "8" ]
195
1,961
0
false
MHC-I molecules are expressed by all nucleated cells, and are specialized for the presentation of peptides derived from the degradation of intracellular proteins to the TCR of CD8+ T cells.
[ "6,7" ]
MHC-I molecules are expressed by all nucleated cells, and are specialized for the presentation of peptides derived from the degradation of intracellular proteins to the TCR of CD8+ T cells.
true
true
true
true
true
337
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
Peptides presented by MHC-I molecules are generated in the cytoplasm by the proteasome and transported by a peptide transporter (TAP) into the endoplasmic reticulum (ER), where they are loaded onto newly synthesized MHC-I molecules.
[ "6", "7", "7", "8" ]
232
1,962
0
false
Peptides presented by MHC-I molecules are generated in the cytoplasm by the proteasome and transported by a peptide transporter (TAP) into the endoplasmic reticulum (ER), where they are loaded onto newly synthesized MHC-I molecules.
[]
Peptides presented by MHC-I molecules are generated in the cytoplasm by the proteasome and transported by a peptide transporter (TAP) into the endoplasmic reticulum (ER), where they are loaded onto newly synthesized MHC-I molecules.
true
true
true
true
true
337
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
The MHC-I-peptide complexes are then transported via the golgi apparatus to the PM.
[ "6", "7", "7", "8" ]
83
1,963
0
false
The MHC-I-peptide complexes are then transported via the golgi apparatus to the PM.
[]
The MHC-I-peptide complexes are then transported via the golgi apparatus to the PM.
true
true
true
true
true
337
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
MHC-II molecules are expressed mainly by thymic epithelial cells and specialized antigen presenting cells (APC; dendritic cells (DC), macrophages, B cells) and present peptides derived from extracellular proteins to the TCR of CD4+ T cells (7,8).
[ "6", "7", "7", "8" ]
246
1,964
0
false
MHC-II molecules are expressed mainly by thymic epithelial cells and specialized antigen presenting cells (APC; dendritic cells (DC), macrophages, B cells) and present peptides derived from extracellular proteins to the TCR of CD4+ T cells.
[ "7,8" ]
MHC-II molecules are expressed mainly by thymic epithelial cells and specialized antigen presenting cells (APC; dendritic cells (DC), macrophages, B cells) and present peptides derived from extracellular proteins to the TCR of CD4+ T cells.
true
true
true
true
true
337
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
These peptides are generated in endocytic compartments by the proteolysis of internalized proteins and are loaded onto MHC-II molecules that have been transported into the endocytic compartments thanks to their association with an accessory protein called the invariant chain (Ii).
[ "6", "7", "7", "8" ]
281
1,965
0
false
These peptides are generated in endocytic compartments by the proteolysis of internalized proteins and are loaded onto MHC-II molecules that have been transported into the endocytic compartments thanks to their association with an accessory protein called the invariant chain (Ii).
[]
These peptides are generated in endocytic compartments by the proteolysis of internalized proteins and are loaded onto MHC-II molecules that have been transported into the endocytic compartments thanks to their association with an accessory protein called the invariant chain (Ii).
true
true
true
true
true
337
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
Peptide-loaded MHC-II complexes are then transported to the cell surface.
[ "6", "7", "7", "8" ]
73
1,966
0
false
Peptide-loaded MHC-II complexes are then transported to the cell surface.
[]
Peptide-loaded MHC-II complexes are then transported to the cell surface.
true
true
true
true
true
337
2
INTRODUCTION
1
6
[ "b6", "b7", "b7", "b8" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
The classical MHC-I and MHC-II antigen presentation pathways depend on vesicular transport routes that are regulated by well known members of the Rab family.
[ "6", "7", "7", "8" ]
157
1,967
0
false
The classical MHC-I and MHC-II antigen presentation pathways depend on vesicular transport routes that are regulated by well known members of the Rab family.
[]
The classical MHC-I and MHC-II antigen presentation pathways depend on vesicular transport routes that are regulated by well known members of the Rab family.
true
true
true
true
true
337
3
INTRODUCTION
1
9
[ "b9", "b10", "b12", "b13", "b7", "b14", "b15", "b16" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
In addition to the classical antigen presentation pathways, there is growing evidence that endocytic recycling processes play important roles in antigen presentation (9).
[ "9", "10", "12", "13", "7", "14", "15", "16" ]
170
1,968
1
false
In addition to the classical antigen presentation pathways, there is growing evidence that endocytic recycling processes play important roles in antigen presentation.
[ "9" ]
In addition to the classical antigen presentation pathways, there is growing evidence that endocytic recycling processes play important roles in antigen presentation.
true
true
true
true
true
338
3
INTRODUCTION
1
9
[ "b9", "b10", "b12", "b13", "b7", "b14", "b15", "b16" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
The presentation of certain antigens requires the loading of peptides onto MHC-II molecules that have been internalized by endocytosis, followed by recycling of these peptide-MHC-II complexes back to the cell surface (10–12).
[ "9", "10", "12", "13", "7", "14", "15", "16" ]
225
1,969
0
false
The presentation of certain antigens requires the loading of peptides onto MHC-II molecules that have been internalized by endocytosis, followed by recycling of these peptide-MHC-II complexes back to the cell surface.
[ "10–12" ]
The presentation of certain antigens requires the loading of peptides onto MHC-II molecules that have been internalized by endocytosis, followed by recycling of these peptide-MHC-II complexes back to the cell surface.
true
true
true
true
true
338
3
INTRODUCTION
1
13
[ "b9", "b10", "b12", "b13", "b7", "b14", "b15", "b16" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Such a recycling pathway has notably been documented to be required for certain antigens taken up by receptor-mediated endocytosis in B cells (13).
[ "9", "10", "12", "13", "7", "14", "15", "16" ]
147
1,970
1
false
Such a recycling pathway has notably been documented to be required for certain antigens taken up by receptor-mediated endocytosis in B cells.
[ "13" ]
Such a recycling pathway has notably been documented to be required for certain antigens taken up by receptor-mediated endocytosis in B cells.
true
true
true
true
true
338
3
INTRODUCTION
1
9
[ "b9", "b10", "b12", "b13", "b7", "b14", "b15", "b16" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Recycling of internalized cell surface MHC-I molecules is also one of the mechanisms that allows peptides derived from endocytosed proteins to be presented by MHC-I molecules.
[ "9", "10", "12", "13", "7", "14", "15", "16" ]
175
1,971
0
false
Recycling of internalized cell surface MHC-I molecules is also one of the mechanisms that allows peptides derived from endocytosed proteins to be presented by MHC-I molecules.
[]
Recycling of internalized cell surface MHC-I molecules is also one of the mechanisms that allows peptides derived from endocytosed proteins to be presented by MHC-I molecules.
true
true
true
true
true
338
3
INTRODUCTION
1
9
[ "b9", "b10", "b12", "b13", "b7", "b14", "b15", "b16" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
This cross-presentation process is most efficient in DC (7,14,15).
[ "9", "10", "12", "13", "7", "14", "15", "16" ]
66
1,972
0
false
This cross-presentation process is most efficient in DC.
[ "7,14,15" ]
This cross-presentation process is most efficient in DC.
true
true
true
true
true
338
3
INTRODUCTION
1
16
[ "b9", "b10", "b12", "b13", "b7", "b14", "b15", "b16" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Finally, recent results have demonstrated that a recycling pathway is involved in the presentation of intact proteins by DC to the antigen receptors of B cells (16).
[ "9", "10", "12", "13", "7", "14", "15", "16" ]
165
1,973
1
false
Finally, recent results have demonstrated that a recycling pathway is involved in the presentation of intact proteins by DC to the antigen receptors of B cells.
[ "16" ]
Finally, recent results have demonstrated that a recycling pathway is involved in the presentation of intact proteins by DC to the antigen receptors of B cells.
true
true
true
true
true
338
4
INTRODUCTION
1
1
[ "b1", "b17", "b18", "b19", "b13" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
RAB4 is a key player in endocytic recycling.
[ "1", "17", "18", "19", "13" ]
44
1,974
0
false
RAB4 is a key player in endocytic recycling.
[]
RAB4 is a key player in endocytic recycling.
true
true
true
true
true
339
4
INTRODUCTION
1
1
[ "b1", "b17", "b18", "b19", "b13" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
It is associated with early endosomes (EE) and recycling endosomes (RE), and regulates the recycling of membranes and proteins from these compartments back to the PM (1,17).
[ "1", "17", "18", "19", "13" ]
173
1,975
0
false
It is associated with early endosomes (EE) and recycling endosomes (RE), and regulates the recycling of membranes and proteins from these compartments back to the PM.
[ "1,17" ]
It is associated with early endosomes (EE) and recycling endosomes (RE), and regulates the recycling of membranes and proteins from these compartments back to the PM.
true
true
true
true
true
339
4
INTRODUCTION
1
1
[ "b1", "b17", "b18", "b19", "b13" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
There are two highly homologous RAB4 isoforms—RAB4A and RAB4B—encoded by two separate genes (RAB4A and RAB4B).
[ "1", "17", "18", "19", "13" ]
110
1,976
0
false
There are two highly homologous RAB4 isoforms—RAB4A and RAB4B—encoded by two separate genes (RAB4A and RAB4B).
[]
There are two highly homologous RAB4 isoforms—RAB4A and RAB4B—encoded by two separate genes (RAB4A and RAB4B).
true
true
true
true
true
339
4
INTRODUCTION
1
1
[ "b1", "b17", "b18", "b19", "b13" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
RAB4A and RAB4B are localized in the same cellular compartments and are believed to have similar or identical functions in recycling (18,19).
[ "1", "17", "18", "19", "13" ]
141
1,977
0
false
RAB4A and RAB4B are localized in the same cellular compartments and are believed to have similar or identical functions in recycling.
[ "18,19" ]
RAB4A and RAB4B are localized in the same cellular compartments and are believed to have similar or identical functions in recycling.
true
true
true
true
true
339
4
INTRODUCTION
1
13
[ "b1", "b17", "b18", "b19", "b13" ]
17,175,541
pmid-11252952|pmid-1516131|pmid-9261061|pmid-14500507|pmid-9815254|pmid-1425574|pmid-10888662
Importantly, RAB4 has been implicated directly in MHC-II-restricted antigen presentation; a dominant negative mutant of RAB4 was shown to block the presentation of antigens internalized by receptor-mediated uptake in B cells (13).
[ "1", "17", "18", "19", "13" ]
230
1,978
1
false
Importantly, RAB4 has been implicated directly in MHC-II-restricted antigen presentation; a dominant negative mutant of RAB4 was shown to block the presentation of antigens internalized by receptor-mediated uptake in B cells.
[ "13" ]
Importantly, RAB4 has been implicated directly in MHC-II-restricted antigen presentation; a dominant negative mutant of RAB4 was shown to block the presentation of antigens internalized by receptor-mediated uptake in B cells.
true
true
true
true
true
339
5
INTRODUCTION
0
null
null
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
We show here that transcription of the RAB4B gene is controlled by the same regulatory machinery that is critical for the expression of MHC-II genes and enhances the expression of MHC-I genes.
null
192
1,979
0
false
null
null
We show here that transcription of the RAB4B gene is controlled by the same regulatory machinery that is critical for the expression of MHC-II genes and enhances the expression of MHC-I genes.
true
true
true
true
true
340
5
INTRODUCTION
0
null
null
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
The promoter of RAB4B contains a strongly conserved enhancer known as the S-Y module, which was until now believed to be highly specific for MHC-II and related genes.
null
166
1,980
0
false
null
null
The promoter of RAB4B contains a strongly conserved enhancer known as the S-Y module, which was until now believed to be highly specific for MHC-II and related genes.
true
true
true
true
true
340
5
INTRODUCTION
0
null
null
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
This RAB4B S-Y module is regulated by the same transcription factors that are dedicated for the activation of MHC-II expression.
null
128
1,981
0
false
null
null
This RAB4B S-Y module is regulated by the same transcription factors that are dedicated for the activation of MHC-II expression.
true
true
true
true
true
340
5
INTRODUCTION
0
null
null
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
These notably include the transcription factor called Regulatory Factor X (RFX) and a transcriptional co-activator known as the MHC class II transactivator (CIITA).
null
164
1,982
0
false
null
null
These notably include the transcription factor called Regulatory Factor X (RFX) and a transcriptional co-activator known as the MHC class II transactivator (CIITA).
true
true
true
true
true
340
5
INTRODUCTION
0
null
null
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254
This molecular link between the transcriptional activation of RAB4B and genes involved in antigen presentation implies that APC boost their antigen presentation capacity by increasing the efficiency of endocytic recycling.
null
222
1,983
0
false
null
null
This molecular link between the transcriptional activation of RAB4B and genes involved in antigen presentation implies that APC boost their antigen presentation capacity by increasing the efficiency of endocytic recycling.
true
true
true
true
true
340
0
DISCUSSION
0
null
null
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
We have used two strategies to identify genes that are co-regulated with MHC-II genes.
null
86
1,984
0
false
null
null
We have used two strategies to identify genes that are co-regulated with MHC-II genes.
true
true
true
true
true
341
0
DISCUSSION
0
null
null
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
First, we used a computer scan to search for genes that contain MHC-II-like S-Y enhancers in their upstream regions.
null
116
1,985
0
false
null
null
First, we used a computer scan to search for genes that contain MHC-II-like S-Y enhancers in their upstream regions.
true
true
true
true
true
341
0
DISCUSSION
0
null
null
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
Second, we performed ChIP-on-chip screens to identify genes that are direct targets of CIITA, the master regulator of MHC-II genes.
null
131
1,986
0
false
null
null
Second, we performed ChIP-on-chip screens to identify genes that are direct targets of CIITA, the master regulator of MHC-II genes.
true
true
true
true
true
341
0
DISCUSSION
0
null
null
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
These two approaches have converged on RAB4B, a gene encoding a protein implicated in endosome recycling.
null
105
1,987
0
false
null
null
These two approaches have converged on RAB4B, a gene encoding a protein implicated in endosome recycling.
true
true
true
true
true
341
0
DISCUSSION
0
null
null
17,175,541
pmid-11252952|pmid-16262719|pmid-15805241|pmid-14597139
A combination of ChIP, ChIP-on-chip, expression analysis and functional studies in wild-type and mutant cells lacking CIITA or RFX have confirmed that RAB4B expression is indeed driven by a typical S-Y enhancer that is regulated by both CIITA and the MHC-II enhanceosome complex composed of RFX, CREB and NF-Y.
null
310
1,988
0
false
null
null
A combination of ChIP, ChIP-on-chip, expression analysis and functional studies in wild-type and mutant cells lacking CIITA or RFX have confirmed that RAB4B expression is indeed driven by a typical S-Y enhancer that is regulated by both CIITA and the MHC-II enhanceosome complex composed of RFX, CREB and NF-Y.
true
true
true
true
true
341
1
DISCUSSION
1
20
[ "b20" ]
17,175,541
pmid-15528357
Searching for potential binding sites in genomic DNA sequences is generally of limited usefulness for identifying target genes regulated by specific transcription factors.
[ "20" ]
171
1,989
0
false
Searching for potential binding sites in genomic DNA sequences is generally of limited usefulness for identifying target genes regulated by specific transcription factors.
[]
Searching for potential binding sites in genomic DNA sequences is generally of limited usefulness for identifying target genes regulated by specific transcription factors.
true
true
true
true
true
342
1
DISCUSSION
1
20
[ "b20" ]
17,175,541
pmid-15528357
A major problem with such approaches is that transcription factor binding sites are often short and degenerate with respect to their consensus sequence, such that computer searches for potential binding sites tend to yield overwhelmingly large numbers of irrelevant hits.
[ "20" ]
271
1,990
0
false
A major problem with such approaches is that transcription factor binding sites are often short and degenerate with respect to their consensus sequence, such that computer searches for potential binding sites tend to yield overwhelmingly large numbers of irrelevant hits.
[]
A major problem with such approaches is that transcription factor binding sites are often short and degenerate with respect to their consensus sequence, such that computer searches for potential binding sites tend to yield overwhelmingly large numbers of irrelevant hits.
true
true
true
true
true
342
1
DISCUSSION
1
20
[ "b20" ]
17,175,541
pmid-15528357
Our searches with the MHC-II S-Y profile constitute an exception to this rule because they have proved to be remarkably reliable—in this report and in a previous study (20)—for the identification of novel enhancers regulated by the MHC-II enhanceosome complex and CIITA.
[ "20" ]
270
1,991
1
false
Our searches with the MHC-II S-Y profile constitute an exception to this rule because they have proved to be remarkably reliable—in this report and in a previous study —for the identification of novel enhancers regulated by the MHC-II enhanceosome complex and CIITA.
[ "20" ]
Our searches with the MHC-II S-Y profile constitute an exception to this rule because they have proved to be remarkably reliable—in this report and in a previous study —for the identification of novel enhancers regulated by the MHC-II enhanceosome complex and CIITA.
true
true
true
true
true
342
1
DISCUSSION
1
20
[ "b20" ]
17,175,541
pmid-15528357
The success of our approach implies that similar strategies could be valuable for identifying genes regulated by higher order transcription factor complexes, particularly in systems where gene expression is controlled by well-defined composite regulatory modules.
[ "20" ]
263
1,992
0
false
The success of our approach implies that similar strategies could be valuable for identifying genes regulated by higher order transcription factor complexes, particularly in systems where gene expression is controlled by well-defined composite regulatory modules.
[]
The success of our approach implies that similar strategies could be valuable for identifying genes regulated by higher order transcription factor complexes, particularly in systems where gene expression is controlled by well-defined composite regulatory modules.
true
true
true
true
true
342
2
DISCUSSION
1
48
[ "b48", "b52" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
The use of genome-scale ChIP-on-chip-based binding studies to identify target genes of specific transcription factors in eukaryotic organisms has become feasible only recently thanks to the availability of microarrays covering entire genomes, large genomic regions or the promoter regions of comprehensive sets of genes.
[ "48", "52" ]
320
1,993
0
false
The use of genome-scale ChIP-on-chip-based binding studies to identify target genes of specific transcription factors in eukaryotic organisms has become feasible only recently thanks to the availability of microarrays covering entire genomes, large genomic regions or the promoter regions of comprehensive sets of genes.
[]
The use of genome-scale ChIP-on-chip-based binding studies to identify target genes of specific transcription factors in eukaryotic organisms has become feasible only recently thanks to the availability of microarrays covering entire genomes, large genomic regions or the promoter regions of comprehensive sets of genes.
true
true
true
true
true
343
2
DISCUSSION
1
48
[ "b48", "b52" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
To date, ChIP-on-chip studies have investigated the target gene specificity of DNA-binding transcription factors (48–52).
[ "48", "52" ]
121
1,994
0
false
To date, ChIP-on-chip studies have investigated the target gene specificity of DNA-binding transcription factors.
[ "48–52" ]
To date, ChIP-on-chip studies have investigated the target gene specificity of DNA-binding transcription factors.
true
true
true
true
true
343
2
DISCUSSION
1
48
[ "b48", "b52" ]
17,175,541
pmid-8729447|pmid-15771591|pmid-15771591|pmid-8011283|pmid-16606705|pmid-14980218
We demonstrate here that such ChIP-on-chip experiments can also be very powerful for studying the target genes of non-DNA-binding transcriptional co-activators such as CIITA.
[ "48", "52" ]
174
1,995
0
false
We demonstrate here that such ChIP-on-chip experiments can also be very powerful for studying the target genes of non-DNA-binding transcriptional co-activators such as CIITA.
[]
We demonstrate here that such ChIP-on-chip experiments can also be very powerful for studying the target genes of non-DNA-binding transcriptional co-activators such as CIITA.
true
true
true
true
true
343
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Past efforts to identify new genes regulated by CIITA have led to a certain amount of controversy concerning the target gene specificity of CIITA (53).
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
151
1,996
1
false
Past efforts to identify new genes regulated by CIITA have led to a certain amount of controversy concerning the target gene specificity of CIITA.
[ "53" ]
Past efforts to identify new genes regulated by CIITA have led to a certain amount of controversy concerning the target gene specificity of CIITA.
true
true
true
true
true
344
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
CIITA was initially believed to be dedicated for the expression of classical MHC-II genes and related genes implicated in antigen presentation, including the Ii, HLA–DO, HLA–DM and MHC-I genes.
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
193
1,997
0
false
CIITA was initially believed to be dedicated for the expression of classical MHC-II genes and related genes implicated in antigen presentation, including the Ii, HLA–DO, HLA–DM and MHC-I genes.
[]
CIITA was initially believed to be dedicated for the expression of classical MHC-II genes and related genes implicated in antigen presentation, including the Ii, HLA–DO, HLA–DM and MHC-I genes.
true
true
true
true
true
344
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Subsequent reports suggested that CIITA might be more pleiotropic in its function.
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
82
1,998
0
false
Subsequent reports suggested that CIITA might be more pleiotropic in its function.
[]
Subsequent reports suggested that CIITA might be more pleiotropic in its function.
true
true
true
true
true
344
3
DISCUSSION
1
53
[ "b53", "b54", "b57", "b58", "b58", "b59", "b54", "b57", "b60" ]
17,175,541
pmid-11918686|pmid-7540726|pmid-11208144|pmid-9815254|pmid-15771591|pmid-16287713|pmid-15224093|pmid-16286018|pmid-15162420|pmid-11564890|pmid-11970984|pmid-12391224|pmid-12391224|pmid-12910265|pmid-11564890|pmid-11970984|pmid-16703565
Several genes were suggested to be repressed by CIITA in various cell types, including those encoding IL4 and FasL in T cells, cathepsin E and IL-10 in B cells and DC, and collagen type I α2, thymidine kinase and cyclin D1 in IFN-γ induced cells (54–57).
[ "53", "54", "57", "58", "58", "59", "54", "57", "60" ]
254
1,999
0
false
Several genes were suggested to be repressed by CIITA in various cell types, including those encoding IL4 and FasL in T cells, cathepsin E and IL-10 in B cells and DC, and collagen type I α2, thymidine kinase and cyclin D1 in IFN-γ induced cells.
[ "54–57" ]
Several genes were suggested to be repressed by CIITA in various cell types, including those encoding IL4 and FasL in T cells, cathepsin E and IL-10 in B cells and DC, and collagen type I α2, thymidine kinase and cyclin D1 in IFN-γ induced cells.
true
true
true
true
true
344