Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425400
G. Nicosia, E. Sciacca, L. Zammataro
The detection of protein characters that could reveal how protein chains are constituted, is an important step to understand the main functions of specific classes of proteins. We made use of the concept of "HP pattern-based" grammars to study the connection between protein chains and protein functions. In order to consider the structure of the proteins the HP models were used. Amino acid sequences were treated as a formal language, and it was built a set of HP pattern-based grammars to describe this language by means the Teiresiaspattern discovery tool. First, this methodology was tested on the class of antimicrobial peptides (AmPs). The deduced derivation rules of HP pattern-based grammars were validated by the regular grammar designed by [Loose, C., et al., 2006] which was used to create new, unnatural, AmPs sequences. Then, our approach was applied to characterize a function of the Pleckstrin homology domain (PH Domain) which represents an important three dimensional domain which bind to phosphoinositides. Nowadays, interactions among PH domain amino acids and inositol phosphate are not well characterized. For the first time, by means of an HP pattern-based grammar, we highlight that this binding function can be described in terms of hydrophocity patterns. Our approach points out some fundamental aspects regarding the relationship between sequence, structure and function of proteins.
{"title":"Detecting constituent sequences by means of HP pattern-based grammars to synthesize proteins: Inferring sequence-structure-function relationship","authors":"G. Nicosia, E. Sciacca, L. Zammataro","doi":"10.1109/BIBMW.2007.4425400","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425400","url":null,"abstract":"The detection of protein characters that could reveal how protein chains are constituted, is an important step to understand the main functions of specific classes of proteins. We made use of the concept of \"HP pattern-based\" grammars to study the connection between protein chains and protein functions. In order to consider the structure of the proteins the HP models were used. Amino acid sequences were treated as a formal language, and it was built a set of HP pattern-based grammars to describe this language by means the Teiresiaspattern discovery tool. First, this methodology was tested on the class of antimicrobial peptides (AmPs). The deduced derivation rules of HP pattern-based grammars were validated by the regular grammar designed by [Loose, C., et al., 2006] which was used to create new, unnatural, AmPs sequences. Then, our approach was applied to characterize a function of the Pleckstrin homology domain (PH Domain) which represents an important three dimensional domain which bind to phosphoinositides. Nowadays, interactions among PH domain amino acids and inositol phosphate are not well characterized. For the first time, by means of an HP pattern-based grammar, we highlight that this binding function can be described in terms of hydrophocity patterns. Our approach points out some fundamental aspects regarding the relationship between sequence, structure and function of proteins.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"119 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123249966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425403
Jing He, K. Al Nasr
We have developed an algorithm to assemble a loop in between two helices using the idea of the cyclic coordinate descent (CCD) that is an inverse kinematics approach in the field of robotics. Our method is a variant of the original CCD. It uses both the forward walk and the backward walk with different targets. A test of 20 cases suggests that the minimum root mean square deviation to native for the 500 assembled loops is comparable to that of the original CCD method but less number of the loops is needed. The results of the test suggest that the number of walks needed to reach the required accuracy can be significantly smaller than 50, the maximum number allowed in our method.
{"title":"An approximate robotics algorithm to assemble a loop between two helices","authors":"Jing He, K. Al Nasr","doi":"10.1109/BIBMW.2007.4425403","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425403","url":null,"abstract":"We have developed an algorithm to assemble a loop in between two helices using the idea of the cyclic coordinate descent (CCD) that is an inverse kinematics approach in the field of robotics. Our method is a variant of the original CCD. It uses both the forward walk and the backward walk with different targets. A test of 20 cases suggests that the minimum root mean square deviation to native for the 500 assembled loops is comparable to that of the original CCD method but less number of the loops is needed. The results of the test suggest that the number of walks needed to reach the required accuracy can be significantly smaller than 50, the maximum number allowed in our method.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"48 10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129705084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425399
Weitao Sun
Conditioned self-avoiding walk (CSAW) is a novel ab initio protein folding simulation model based on Langevin equation and Monte-Carlo method. The polypeptide chain is divided into effectively rigid crank units lined by covalent bonds. The only degrees of the freedom are rotations around these bonds. Instead of a hard sphere, the amino acid side chains are modeled by real atom conformation in this paper. The particular feathers of each side chain are considered in calculating the hydrophobic and electrostatic energy in all-atom CSAW. By introducing long range electrostatic interactions, not only the alpha helixes in 1A7W but also beta sheets/strands in 3AIT are successfully simulated for the first time by improved CSAW.
{"title":"Protein folding simulation by all-atom CSAW method","authors":"Weitao Sun","doi":"10.1109/BIBMW.2007.4425399","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425399","url":null,"abstract":"Conditioned self-avoiding walk (CSAW) is a novel ab initio protein folding simulation model based on Langevin equation and Monte-Carlo method. The polypeptide chain is divided into effectively rigid crank units lined by covalent bonds. The only degrees of the freedom are rotations around these bonds. Instead of a hard sphere, the amino acid side chains are modeled by real atom conformation in this paper. The particular feathers of each side chain are considered in calculating the hydrophobic and electrostatic energy in all-atom CSAW. By introducing long range electrostatic interactions, not only the alpha helixes in 1A7W but also beta sheets/strands in 3AIT are successfully simulated for the first time by improved CSAW.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123347889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425419
Hongling Wang, Yungui Huang, V. Vieland, Alberto Maria Segre, J. O’Connell
This paper introduces a new method for computing large numbers of LOD scores in linkage analysis. The LOD score method is commonly used in genetic linkage analysis to associate functionality of genes to their locations on chromosomes. A LOD score is a log 10 likelihood ratio of linkage to no linkage. Instead of calculating values of likelihoods of linkage and no linkage under given values of genetic parameters directly from pedigree data, we construct expressions for likelihoods of linkage and no linkage as polynomials of genetic parameters. These likelihood polynomials of pedigrees don't change for different parameter values. After the likelihood polynomials are constructed, the values of likelihoods of linkage and no linkage can be computed by evaluating the likelihood polynomials with specific parameter values. The likelihood polynomials are optimized during construction so that repeated terms within the expressions are shared. Moreover, we find that the likelihood polynomials of different pedigrees also often share terms. This term-sharing feature leads us to an evaluation strategy where shared terms are evaluated only once and reused by all the polynomials that share them. The reuse of shared terms in polynomial evaluation greatly decreases the re- computation in calculation of large numbers of LOD scores and improves the computing efficiency. Our results show that this approach can speed up the traditional genetic linkage computation by 10~1200 times. This approached has been applied to the computation of the posterior probability of linkage (PPL) where calculation of large numbers of LOD scores is required.
{"title":"Rapid computation of large numbers of LOD scores in linkage analysis through polynomial expression of genetic likelihoods","authors":"Hongling Wang, Yungui Huang, V. Vieland, Alberto Maria Segre, J. O’Connell","doi":"10.1109/BIBMW.2007.4425419","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425419","url":null,"abstract":"This paper introduces a new method for computing large numbers of LOD scores in linkage analysis. The LOD score method is commonly used in genetic linkage analysis to associate functionality of genes to their locations on chromosomes. A LOD score is a log 10 likelihood ratio of linkage to no linkage. Instead of calculating values of likelihoods of linkage and no linkage under given values of genetic parameters directly from pedigree data, we construct expressions for likelihoods of linkage and no linkage as polynomials of genetic parameters. These likelihood polynomials of pedigrees don't change for different parameter values. After the likelihood polynomials are constructed, the values of likelihoods of linkage and no linkage can be computed by evaluating the likelihood polynomials with specific parameter values. The likelihood polynomials are optimized during construction so that repeated terms within the expressions are shared. Moreover, we find that the likelihood polynomials of different pedigrees also often share terms. This term-sharing feature leads us to an evaluation strategy where shared terms are evaluated only once and reused by all the polynomials that share them. The reuse of shared terms in polynomial evaluation greatly decreases the re- computation in calculation of large numbers of LOD scores and improves the computing efficiency. Our results show that this approach can speed up the traditional genetic linkage computation by 10~1200 times. This approached has been applied to the computation of the posterior probability of linkage (PPL) where calculation of large numbers of LOD scores is required.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114872985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425415
O. Huseth, T. Brox Rost
We have developed a tool for annotation of electronic health record (EHR) data. Currently, we are in the process of manually annotating a corpus of Norwegian general practitioners EHRs with mainly linguistic information. The purpose of this project is to attain a lingustically annotated corpus of patient histories from general practice. This corpus will be put to future use in medical language processing and information extraction applications. This paper outlines some of our practical experiences from developing such a corpus and, in particular, the effects of semi-automated annotation. We have also done some preliminary experiments with part-of-speech tagging based on our corpus. The results indicate that relevant training data from the clinical domain gives better results for the tagging task in this domain than training the tagger on a corpus from a more general domain. We are planning to expand the corpus annotations with medical information at a later stage.
{"title":"Developing an annotated corpus of patient histories from the primary care health record","authors":"O. Huseth, T. Brox Rost","doi":"10.1109/BIBMW.2007.4425415","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425415","url":null,"abstract":"We have developed a tool for annotation of electronic health record (EHR) data. Currently, we are in the process of manually annotating a corpus of Norwegian general practitioners EHRs with mainly linguistic information. The purpose of this project is to attain a lingustically annotated corpus of patient histories from general practice. This corpus will be put to future use in medical language processing and information extraction applications. This paper outlines some of our practical experiences from developing such a corpus and, in particular, the effects of semi-automated annotation. We have also done some preliminary experiments with part-of-speech tagging based on our corpus. The results indicate that relevant training data from the clinical domain gives better results for the tagging task in this domain than training the tagger on a corpus from a more general domain. We are planning to expand the corpus annotations with medical information at a later stage.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"91 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129002481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425410
Feng Ji, Jack Fu, R. Elmasri, N. Stojanovic, Geoffrey Grant
In biomedical/biological research fields, scientists usually face the problem of information explosion. Once a query is issued, a collection of data instance IDs such as protein accession numbers are returned. Each protein must be checked for the features of interest. This paper addresses the characterization and differentiating of biological data in the context of mediated domain ontology based on the multilevel abstraction framework. Our mediator system features hybrid ontologies (internal core ontology concept and external classification/annotation concepts) for the interpretation of protein and gene instance data in the context of interaction, pathway and process, which achieve the goal of data integration at the instance level.
{"title":"Mediated taxonomy system for bioinformatics data integration","authors":"Feng Ji, Jack Fu, R. Elmasri, N. Stojanovic, Geoffrey Grant","doi":"10.1109/BIBMW.2007.4425410","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425410","url":null,"abstract":"In biomedical/biological research fields, scientists usually face the problem of information explosion. Once a query is issued, a collection of data instance IDs such as protein accession numbers are returned. Each protein must be checked for the features of interest. This paper addresses the characterization and differentiating of biological data in the context of mediated domain ontology based on the multilevel abstraction framework. Our mediator system features hybrid ontologies (internal core ontology concept and external classification/annotation concepts) for the interpretation of protein and gene instance data in the context of interaction, pathway and process, which achieve the goal of data integration at the instance level.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126882312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Because of its appealing simplicity, the anisotropic network model (ANM) has been widely accepted and applied to study many molecular motion problems: such as the molecular mechanisms of GroEL-GroES function, allosteric changes in hemoglobin, ribosome motion, motor-protein motions, and conformational changes in general, etc. However, the validity of the ANM has not been closely examined. In this work, we use ANM to predict the anisotropic temperature factors of proteins. On the flip side, the rich, directional anisotropic temperature factor data available for hundreds of proteins in the protein data bank (PDB) are used as validation data to closely test the ANM model. The significance of this work is that it presents a timely, important evaluation of the model, shows the extent of its accuracy in reproducing experimental anisotropic temperature factors, and suggests ways to improve the model. An improved model will help us better understand the internal dynamics of proteins, which in turn can greatly expand the usefulness of the models, which has already been demonstrated in many applications.
{"title":"Comparison of experimental and computed protein anisotropic temperature factors","authors":"Lei Yang, Guang Song, R. Jernigan","doi":"10.1002/prot.22328","DOIUrl":"https://doi.org/10.1002/prot.22328","url":null,"abstract":"Because of its appealing simplicity, the anisotropic network model (ANM) has been widely accepted and applied to study many molecular motion problems: such as the molecular mechanisms of GroEL-GroES function, allosteric changes in hemoglobin, ribosome motion, motor-protein motions, and conformational changes in general, etc. However, the validity of the ANM has not been closely examined. In this work, we use ANM to predict the anisotropic temperature factors of proteins. On the flip side, the rich, directional anisotropic temperature factor data available for hundreds of proteins in the protein data bank (PDB) are used as validation data to closely test the ANM model. The significance of this work is that it presents a timely, important evaluation of the model, shows the extent of its accuracy in reproducing experimental anisotropic temperature factors, and suggests ways to improve the model. An improved model will help us better understand the internal dynamics of proteins, which in turn can greatly expand the usefulness of the models, which has already been demonstrated in many applications.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127169504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425413
Y. Uzunay, K. Bicakci
One of the most promising technologies to enhance the quality of life of quadriplegia patients is smart home environments. Security has a paramount importance for all health information systems, but it is generally overlooked until a major security breach occurs. Especially in an application specifically targeting people with disabilities, ignoring security might have dire consequences therefore we think that proactive measures should be taken by system designers. In this paper, we present SHA, a secure voice activated smart home for quadriplegia patients. The principal contribution of our system lies behind the security mechanisms incorporated in the proposed smart home architecture which has an integrated framework including ambient assistance and remote health monitoring.
{"title":"SHA: A secure voice activated smart home for quadriplegia patients","authors":"Y. Uzunay, K. Bicakci","doi":"10.1109/BIBMW.2007.4425413","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425413","url":null,"abstract":"One of the most promising technologies to enhance the quality of life of quadriplegia patients is smart home environments. Security has a paramount importance for all health information systems, but it is generally overlooked until a major security breach occurs. Especially in an application specifically targeting people with disabilities, ignoring security might have dire consequences therefore we think that proactive measures should be taken by system designers. In this paper, we present SHA, a secure voice activated smart home for quadriplegia patients. The principal contribution of our system lies behind the security mechanisms incorporated in the proposed smart home architecture which has an integrated framework including ambient assistance and remote health monitoring.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127342311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425404
M. P. Costa, H. Ribeiro, A. Pacheco, D. Pinheiro, M. Kamimura, R. Araujo-Filho, D. M. de Oliveira
Leishmania are uniflagellate protozoa, whose flagellum plays a key role in motility, being essential for parasite migration, invasion and persistence on host tissues. Actin is the major cytoskeleton protein, while polymerization and depolymerization of parasite actin and actin motor-associated proteins during both processes of motility and host cell entry might be key events for successful infection. In search for genomic and/or proteomic evidences of actin-interacting proteins (AIPs) involved in flagellar activities of Leishmania spp., we have applied computational tools (hidden Markov models, Viterbi algorithm and comparative modeling) to infer biological meaning through detailed sequence-structural-functional analyses on Leishmania AIPs, such as coronin and Arp2/3 complex proteins, two important elements on phagosome formation after parasite phagocytosis by macrophages. Results presented here provide the first integrated bioinformatics analyses of Leishmania coronin and Arp2/3 genes and their gene products, a direct contribution to genome annotation of these important actin-regulating proteins yet to be properly in vitro characterized in flagellate trypanosomatids towards their putative virulence.
{"title":"Flagellar proteins prediction after sequence-structure alignments of coronin and Arp2/3 complex in Leishmania spp.","authors":"M. P. Costa, H. Ribeiro, A. Pacheco, D. Pinheiro, M. Kamimura, R. Araujo-Filho, D. M. de Oliveira","doi":"10.1109/BIBMW.2007.4425404","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425404","url":null,"abstract":"Leishmania are uniflagellate protozoa, whose flagellum plays a key role in motility, being essential for parasite migration, invasion and persistence on host tissues. Actin is the major cytoskeleton protein, while polymerization and depolymerization of parasite actin and actin motor-associated proteins during both processes of motility and host cell entry might be key events for successful infection. In search for genomic and/or proteomic evidences of actin-interacting proteins (AIPs) involved in flagellar activities of Leishmania spp., we have applied computational tools (hidden Markov models, Viterbi algorithm and comparative modeling) to infer biological meaning through detailed sequence-structural-functional analyses on Leishmania AIPs, such as coronin and Arp2/3 complex proteins, two important elements on phagosome formation after parasite phagocytosis by macrophages. Results presented here provide the first integrated bioinformatics analyses of Leishmania coronin and Arp2/3 genes and their gene products, a direct contribution to genome annotation of these important actin-regulating proteins yet to be properly in vitro characterized in flagellate trypanosomatids towards their putative virulence.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116758463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-11-01DOI: 10.1109/BIBMW.2007.4425409
N. A. Yousri, M. Kamel, M. Ismail
Connectivity based clustering can reveal the continuity of gene expression patterns, and thus can discover interrelations between tumor types, as well as regulatory relations between genes that can lead to discovering gene pathways. Pattern cores are a subset of expression patterns that are representatives of the whole set of patterns and can be used to reveal the structure of the data as well as that of the clusters, especially in the presence of huge data sets. This work presents a fuzzy approach that starts by finding the density-based expression pattern cores. Those cores are then clustered into core clusters and fuzzy memberships to those cores are calculated for all patterns in the data set. The whole data set is then clustered into pattern clusters using a connectivity-based algorithm, where a pattern cluster might contain one or more core clusters. The fuzzy memberships to core clusters in each pattern cluster are used to interpret the connectedness of the pattern cluster using the structure of core clusters, as well as to identify how each pattern is related to one or more tumor types.
{"title":"Using fuzzy memberships to core patterns to interpret connectedness in gene expression clusters","authors":"N. A. Yousri, M. Kamel, M. Ismail","doi":"10.1109/BIBMW.2007.4425409","DOIUrl":"https://doi.org/10.1109/BIBMW.2007.4425409","url":null,"abstract":"Connectivity based clustering can reveal the continuity of gene expression patterns, and thus can discover interrelations between tumor types, as well as regulatory relations between genes that can lead to discovering gene pathways. Pattern cores are a subset of expression patterns that are representatives of the whole set of patterns and can be used to reveal the structure of the data as well as that of the clusters, especially in the presence of huge data sets. This work presents a fuzzy approach that starts by finding the density-based expression pattern cores. Those cores are then clustered into core clusters and fuzzy memberships to those cores are calculated for all patterns in the data set. The whole data set is then clustered into pattern clusters using a connectivity-based algorithm, where a pattern cluster might contain one or more core clusters. The fuzzy memberships to core clusters in each pattern cluster are used to interpret the connectedness of the pattern cluster using the structure of core clusters, as well as to identify how each pattern is related to one or more tumor types.","PeriodicalId":260286,"journal":{"name":"2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114848340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：