SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction
Identifieur interne : 002612 ( Main/Exploration ); précédent : 002611; suivant : 002613SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction
Auteurs : Lawrence Jk Wee ; Diane Simarmata ; Yiu-Wing Kam ; Lisa Fp Ng [Singapour] ; Joo Chuan Tong [Singapour]Source :
- BMC Genomics [ 1471-2164 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Antigens, Peptides.
- chemical , immunology : Antigens, Epitopes, B-Lymphocyte, Peptides.
- Algorithms, Bayes Theorem, Benchmarking, Computer Simulation, Internet, Predictive Value of Tests.
Abstract
The identification of B-cell epitopes on antigens has been a subject of intense research as the knowledge of these markers has great implications for the development of peptide-based diagnostics, therapeutics and vaccines. As experimental approaches are often laborious and time consuming,
We analyzed two benchmark datasets and found that linear B-cell epitopes possess distinctive residue conservation and position-specific residue propensities which could be exploited for epitope discrimination
We developed a SVM prediction model utilizing Bayes Feature Extraction and showed that it was effective in discriminating epitopes from non-epitopes in benchmark datasets and annotated antigenic proteins. A web server for predicting linear B-cell epitopes was developed and is available, together with supplementary materials, at
Url:
DOI: 10.1186/1471-2164-11-S4-S21
PubMed: 21143805
PubMed Central: 3005920
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000A95
- to stream Pmc, to step Curation: 000A95
- to stream Pmc, to step Checkpoint: 001351
- to stream PubMed, to step Corpus: 001F19
- to stream PubMed, to step Curation: 001F19
- to stream PubMed, to step Checkpoint: 001E21
- to stream Ncbi, to step Merge: 000792
- to stream Ncbi, to step Curation: 000792
- to stream Ncbi, to step Checkpoint: 000792
- to stream Main, to step Merge: 002637
- to stream Main, to step Curation: 002612
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction</title><author><name sortKey="Wee, Lawrence Jk" sort="Wee, Lawrence Jk" uniqKey="Wee L" first="Lawrence Jk" last="Wee">Lawrence Jk Wee</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation><affiliation><nlm:aff id="I2">Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis South Tower, Singapore 138632</nlm:aff><wicri:noCountry code="subfield">Singapore 138632</wicri:noCountry></affiliation></author><author><name sortKey="Simarmata, Diane" sort="Simarmata, Diane" uniqKey="Simarmata D" first="Diane" last="Simarmata">Diane Simarmata</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation></author><author><name sortKey="Kam, Yiu Wing" sort="Kam, Yiu Wing" uniqKey="Kam Y" first="Yiu-Wing" last="Kam">Yiu-Wing Kam</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation></author><author><name sortKey="Ng, Lisa Fp" sort="Ng, Lisa Fp" uniqKey="Ng L" first="Lisa Fp" last="Ng">Lisa Fp Ng</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation><affiliation wicri:level="4"><nlm:aff id="I3">Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597</nlm:aff><orgName type="university">Université nationale de Singapour</orgName><country>Singapour</country></affiliation></author><author><name sortKey="Tong, Joo Chuan" sort="Tong, Joo Chuan" uniqKey="Tong J" first="Joo Chuan" last="Tong">Joo Chuan Tong</name><affiliation><nlm:aff id="I2">Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis South Tower, Singapore 138632</nlm:aff><wicri:noCountry code="subfield">Singapore 138632</wicri:noCountry></affiliation><affiliation wicri:level="4"><nlm:aff id="I3">Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597</nlm:aff><orgName type="university">Université nationale de Singapour</orgName><country>Singapour</country></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21143805</idno><idno type="pmc">3005920</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005920</idno><idno type="RBID">PMC:3005920</idno><idno type="doi">10.1186/1471-2164-11-S4-S21</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000A95</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A95</idno><idno type="wicri:Area/Pmc/Curation">000A95</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000A95</idno><idno type="wicri:Area/Pmc/Checkpoint">001351</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001351</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:21143805</idno><idno type="wicri:Area/PubMed/Corpus">001F19</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F19</idno><idno type="wicri:Area/PubMed/Curation">001F19</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F19</idno><idno type="wicri:Area/PubMed/Checkpoint">001E21</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001E21</idno><idno type="wicri:Area/Ncbi/Merge">000792</idno><idno type="wicri:Area/Ncbi/Curation">000792</idno><idno type="wicri:Area/Ncbi/Checkpoint">000792</idno><idno type="wicri:Area/Main/Merge">002637</idno><idno type="wicri:Area/Main/Curation">002612</idno><idno type="wicri:Area/Main/Exploration">002612</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction</title><author><name sortKey="Wee, Lawrence Jk" sort="Wee, Lawrence Jk" uniqKey="Wee L" first="Lawrence Jk" last="Wee">Lawrence Jk Wee</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation><affiliation><nlm:aff id="I2">Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis South Tower, Singapore 138632</nlm:aff><wicri:noCountry code="subfield">Singapore 138632</wicri:noCountry></affiliation></author><author><name sortKey="Simarmata, Diane" sort="Simarmata, Diane" uniqKey="Simarmata D" first="Diane" last="Simarmata">Diane Simarmata</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation></author><author><name sortKey="Kam, Yiu Wing" sort="Kam, Yiu Wing" uniqKey="Kam Y" first="Yiu-Wing" last="Kam">Yiu-Wing Kam</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation></author><author><name sortKey="Ng, Lisa Fp" sort="Ng, Lisa Fp" uniqKey="Ng L" first="Lisa Fp" last="Ng">Lisa Fp Ng</name><affiliation><nlm:aff id="I1">Singapore Immunology Network, 8A Biomedical Grove, #04-06 Immunos, Biopolis, Singapore 138648</nlm:aff><wicri:noCountry code="subfield">Singapore 138648</wicri:noCountry></affiliation><affiliation wicri:level="4"><nlm:aff id="I3">Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597</nlm:aff><orgName type="university">Université nationale de Singapour</orgName><country>Singapour</country></affiliation></author><author><name sortKey="Tong, Joo Chuan" sort="Tong, Joo Chuan" uniqKey="Tong J" first="Joo Chuan" last="Tong">Joo Chuan Tong</name><affiliation><nlm:aff id="I2">Data Mining Department, Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis South Tower, Singapore 138632</nlm:aff><wicri:noCountry code="subfield">Singapore 138632</wicri:noCountry></affiliation><affiliation wicri:level="4"><nlm:aff id="I3">Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597</nlm:aff><orgName type="university">Université nationale de Singapour</orgName><country>Singapour</country></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Antigens (chemistry)</term><term>Antigens (immunology)</term><term>Bayes Theorem</term><term>Benchmarking</term><term>Computer Simulation</term><term>Epitopes, B-Lymphocyte (immunology)</term><term>Internet</term><term>Peptides (chemistry)</term><term>Peptides (immunology)</term><term>Predictive Value of Tests</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Antigènes ()</term><term>Antigènes (immunologie)</term><term>Déterminants antigéniques des lymphocytes B (immunologie)</term><term>Internet</term><term>Peptides ()</term><term>Peptides (immunologie)</term><term>Référenciation</term><term>Simulation numérique</term><term>Théorème de Bayes</term><term>Valeur prédictive des tests</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Antigens</term><term>Peptides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="immunology" xml:lang="en"><term>Antigens</term><term>Epitopes, B-Lymphocyte</term><term>Peptides</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Antigènes</term><term>Déterminants antigéniques des lymphocytes B</term><term>Peptides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Bayes Theorem</term><term>Benchmarking</term><term>Computer Simulation</term><term>Internet</term><term>Predictive Value of Tests</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Antigènes</term><term>Internet</term><term>Peptides</term><term>Référenciation</term><term>Simulation numérique</term><term>Théorème de Bayes</term><term>Valeur prédictive des tests</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Backgound</title><p>The identification of B-cell epitopes on antigens has been a subject of intense research as the knowledge of these markers has great implications for the development of peptide-based diagnostics, therapeutics and vaccines. As experimental approaches are often laborious and time consuming, <italic>in silico</italic> methods for prediction of these immunogenic regions are critical. Such efforts, however, have been significantly hindered by high variability in the length and composition of the epitope sequences, making naïve modeling methods difficult to apply.</p></sec><sec><title>Results</title><p>We analyzed two benchmark datasets and found that linear B-cell epitopes possess distinctive residue conservation and position-specific residue propensities which could be exploited for epitope discrimination <italic>in silico</italic>. We developed a support vector machines (SVM) prediction model employing Bayes Feature Extraction to predict linear B-cell epitopes of diverse lengths (12- to 20-mers). The best SVM classifier achieved an accuracy of 74.50% and A<sub>ROC</sub> of 0.84 on an independent test set and was shown to outperform existing linear B-cell epitope prediction algorithms. In addition, we applied our model to a dataset of antigenic proteins with experimentally-verified epitopes and found it to be generally effective for discriminating the epitopes from non-epitopes.</p></sec><sec><title>Conclusion</title><p>We developed a SVM prediction model utilizing Bayes Feature Extraction and showed that it was effective in discriminating epitopes from non-epitopes in benchmark datasets and annotated antigenic proteins. A web server for predicting linear B-cell epitopes was developed and is available, together with supplementary materials, at <ext-link ext-link-type="uri" xlink:href="http://www.immunopred.org/bayesb/index.html">http://www.immunopred.org/bayesb/index.html</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Korber, B" uniqKey="Korber B">B Korber</name></author><author><name sortKey="Labute, M" uniqKey="Labute M">M LaBute</name></author><author><name sortKey="Yusim, K" uniqKey="Yusim K">K Yusim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pellequer, Jl" uniqKey="Pellequer J">JL Pellequer</name></author><author><name sortKey="Westhof, E" uniqKey="Westhof E">E Westhof</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alix, Aj" uniqKey="Alix A">AJ Alix</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Odorico, M" uniqKey="Odorico M">M Odorico</name></author><author><name sortKey="Pellequer, Jl" uniqKey="Pellequer J">JL Pellequer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saha, S" uniqKey="Saha S">S Saha</name></author><author><name sortKey="Raghava, Gps" uniqKey="Raghava G">GPS Raghava</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blythe, Mj" uniqKey="Blythe M">MJ Blythe</name></author><author><name sortKey="Flower, Dr" uniqKey="Flower D">DR Flower</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Larsen, Je" uniqKey="Larsen J">JE Larsen</name></author><author><name sortKey="Lund, O" uniqKey="Lund O">O Lund</name></author><author><name sortKey="Nielsen, M" uniqKey="Nielsen M">M Nielsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sollner, J" uniqKey="Sollner J">J Söllner</name></author><author><name sortKey="Mayer, B" uniqKey="Mayer B">B Mayer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saha, S" uniqKey="Saha S">S Saha</name></author><author><name sortKey="Raghava, Gp" uniqKey="Raghava G">GP Raghava</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Liu, H" uniqKey="Liu H">H Liu</name></author><author><name sortKey="Yang, J" uniqKey="Yang J">J Yang</name></author><author><name sortKey="Chou, Kc" uniqKey="Chou K">KC Chou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="El Manzalawy, Y" uniqKey="El Manzalawy Y">Y El-Manzalawy</name></author><author><name sortKey="Dobbs, D" uniqKey="Dobbs D">D Dobbs</name></author><author><name sortKey="Honavar, V" uniqKey="Honavar V">V Honavar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sweredoski, Mj" uniqKey="Sweredoski M">MJ Sweredoski</name></author><author><name sortKey="Baldi, P" uniqKey="Baldi P">P Baldi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rubinstein, Nd" uniqKey="Rubinstein N">ND Rubinstein</name></author><author><name sortKey="Mayrose, I" uniqKey="Mayrose I">I Mayrose</name></author><author><name sortKey="Pupko, T" uniqKey="Pupko T">T Pupko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rubinstein, Nd" uniqKey="Rubinstein N">ND Rubinstein</name></author><author><name sortKey="Mayrose, I" uniqKey="Mayrose I">I Mayrose</name></author><author><name sortKey="Martz, E" uniqKey="Martz E">E Martz</name></author><author><name sortKey="Pupko, T" uniqKey="Pupko T">T Pupko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shen, J" uniqKey="Shen J">J Shen</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Luo, X" uniqKey="Luo X">X Luo</name></author><author><name sortKey="Zhu, W" uniqKey="Zhu W">W Zhu</name></author><author><name sortKey="Yu, K" uniqKey="Yu K">K Yu</name></author><author><name sortKey="Chen, K" uniqKey="Chen K">K Chen</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Jiang, H" uniqKey="Jiang H">H Jiang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, J" uniqKey="Song J">J Song</name></author><author><name sortKey="Burrage, K" uniqKey="Burrage K">K Burrage</name></author><author><name sortKey="Yuan, Z" uniqKey="Yuan Z">Z Yuan</name></author><author><name sortKey="Huber, T" uniqKey="Huber T">T Huber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, J" uniqKey="Song J">J Song</name></author><author><name sortKey="Burrage, K" uniqKey="Burrage K">K Burrage</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saha, S" uniqKey="Saha S">S Saha</name></author><author><name sortKey="Bhasin, M" uniqKey="Bhasin M">M Bhasin</name></author><author><name sortKey="Raghava, Gp" uniqKey="Raghava G">GP Raghava</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shao, J" uniqKey="Shao J">J Shao</name></author><author><name sortKey="Xu, D" uniqKey="Xu D">D Xu</name></author><author><name sortKey="Tsai, Sn" uniqKey="Tsai S">SN Tsai</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Ngai, Sm" uniqKey="Ngai S">SM Ngai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, J" uniqKey="Song J">J Song</name></author><author><name sortKey="Tan, H" uniqKey="Tan H">H Tan</name></author><author><name sortKey="Shen, H" uniqKey="Shen H">H Shen</name></author><author><name sortKey="Mahmood, K" uniqKey="Mahmood K">K Mahmood</name></author><author><name sortKey="Boyd, Se" uniqKey="Boyd S">SE Boyd</name></author><author><name sortKey="Webb, Gi" uniqKey="Webb G">GI Webb</name></author><author><name sortKey="Akutsu, T" uniqKey="Akutsu T">T Akutsu</name></author><author><name sortKey="Whisstock, Jc" uniqKey="Whisstock J">JC Whisstock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="El Manzalawy, Y" uniqKey="El Manzalawy Y">Y EL-Manzalawy</name></author><author><name sortKey="Dobbs, D" uniqKey="Dobbs D">D Dobbs</name></author><author><name sortKey="Honavar, V" uniqKey="Honavar V">V Honavar</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Chang, Cc" uniqKey="Chang C">CC Chang</name></author><author><name sortKey="Lin, Cj" uniqKey="Lin C">CJ Lin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burges, Cjc" uniqKey="Burges C">CJC Burges</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Singapour</li></country><orgName><li>Université nationale de Singapour</li></orgName></list><tree><noCountry><name sortKey="Kam, Yiu Wing" sort="Kam, Yiu Wing" uniqKey="Kam Y" first="Yiu-Wing" last="Kam">Yiu-Wing Kam</name><name sortKey="Simarmata, Diane" sort="Simarmata, Diane" uniqKey="Simarmata D" first="Diane" last="Simarmata">Diane Simarmata</name><name sortKey="Wee, Lawrence Jk" sort="Wee, Lawrence Jk" uniqKey="Wee L" first="Lawrence Jk" last="Wee">Lawrence Jk Wee</name></noCountry><country name="Singapour"><noRegion><name sortKey="Ng, Lisa Fp" sort="Ng, Lisa Fp" uniqKey="Ng L" first="Lisa Fp" last="Ng">Lisa Fp Ng</name></noRegion><name sortKey="Tong, Joo Chuan" sort="Tong, Joo Chuan" uniqKey="Tong J" first="Joo Chuan" last="Tong">Joo Chuan Tong</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002612 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002612 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3005920
|texte= SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:21143805" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |