Assessing and predicting protein interactions by combining manifold embedding with multiple information integration.

Abstract:

BACKGROUND:Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism. Over the last decade, the development of novel high-throughput techniques has resulted in enormous amounts of data and provided valuable resources for studying protein interactions. However, these high-throughput protein interaction data are often associated with high false positive and false negative rates. It is therefore highly desirable to develop scalable methods to identify these errors from the computational perspective. RESULTS:We have developed a robust computational technique for assessing the reliability of interactions and predicting new interactions by combining manifold embedding with multiple information integration. Validation of the proposed method was performed with extensive experiments on densely-connected and sparse PPI networks of yeast respectively. Results demonstrate that the interactions ranked top by our method have high functional homogeneity and localization coherence. CONCLUSIONS:Our proposed method achieves better performances than the existing methods no matter assessing or predicting protein interactions. Furthermore, our method is general enough to work over a variety of PPI networks irrespectively of densely-connected or sparse PPI network. Therefore, the proposed algorithm is a much more promising method to detect both false positive and false negative interactions in PPI networks.

journal_name

BMC Bioinformatics

journal_title

BMC bioinformatics

authors

Lei YK,You ZH,Ji Z,Zhu L,Huang DS

doi

10.1186/1471-2105-13-S7-S3

subject

Has Abstract

pub_date

2012-05-08 00:00:00

pages

S3

issn

1471-2105

pii

1471-2105-13-S7-S3

journal_volume

13 Suppl 7

pub_type

杂志文章
  • EGenBio: a data management system for evolutionary genomics and biodiversity.

    abstract:BACKGROUND:Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; http://egenbio.lsu.edu) to begin to address this....

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-S2-S7

    authors: Nahum LA,Reynolds MT,Wang ZO,Faith JJ,Jonna R,Jiang ZJ,Meyer TJ,Pollock DD

    更新日期:2006-09-06 00:00:00

  • Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology.

    abstract:BACKGROUND:An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biolo...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-94

    authors: Hill SM,Neve RM,Bayani N,Kuo WL,Ziyad S,Spellman PT,Gray JW,Mukherjee S

    更新日期:2012-05-11 00:00:00

  • Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes.

    abstract:BACKGROUND:A major goal of the analysis of high-dimensional RNA expression data from tumor tissue is to identify prognostic signatures for discriminating patient subgroups. For this purpose genome-wide identification of bimodally expressed genes from gene array data is relevant because distinguishability of high and lo...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-276

    authors: Hellwig B,Hengstler JG,Schmidt M,Gehrmann MC,Schormann W,Rahnenführer J

    更新日期:2010-05-25 00:00:00

  • Ferret: a sentence-based literature scanning system.

    abstract:BACKGROUND:The rapid pace of bioscience research makes it very challenging to track relevant articles in one's area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to se...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0630-0

    authors: Srinivasan P,Zhang XN,Bouten R,Chang C

    更新日期:2015-06-20 00:00:00

  • Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics.

    abstract:BACKGROUND:We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, ma...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-5-101

    authors: Cherkasov A,Ho Sui SJ,Brunham RC,Jones SJ

    更新日期:2004-07-26 00:00:00

  • Ontology driven integration platform for clinical and translational research.

    abstract::Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H)...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S2-S2

    authors: Mirhaji P,Zhu M,Vagnoni M,Bernstam EV,Zhang J,Smith JW

    更新日期:2009-02-05 00:00:00

  • MOSBIE: a tool for comparison and analysis of rule-based biochemical models.

    abstract:BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-316

    authors: Wenskovitch JE Jr,Harris LA,Tapia JJ,Faeder JR,Marai GE

    更新日期:2014-09-25 00:00:00

  • Missing genes in the annotation of prokaryotic genomes.

    abstract:BACKGROUND:Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs have problems with small genes (either over-predicting or under-predicting). Therefore the question ari...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-131

    authors: Warren AS,Archuleta J,Feng WC,Setubal JC

    更新日期:2010-03-15 00:00:00

  • GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA).

    abstract:BACKGROUND:The goal of metabolomics analyses is a comprehensive and systematic understanding of all metabolites in biological samples. Many useful platforms have been developed to achieve this goal. Gas chromatography coupled to mass spectrometry (GC/MS) is a well-established analytical method in metabolomics study, an...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-131

    authors: Tsugawa H,Tsujimoto Y,Arita M,Bamba T,Fukusaki E

    更新日期:2011-05-04 00:00:00

  • Local search for the generalized tree alignment problem.

    abstract:BACKGROUND:A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-14-66

    authors: Varón A,Wheeler WC

    更新日期:2013-02-26 00:00:00

  • Discovering biological connections between experimental conditions based on common patterns of differential gene expression.

    abstract:BACKGROUND:Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expression alterations. The growing volume of gene expression data in open data repositories such as the N...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-381

    authors: Gower AC,Spira A,Lenburg ME

    更新日期:2011-09-27 00:00:00

  • PuFFIN--a parameter-free method to build nucleosome maps from paired-end reads.

    abstract:BACKGROUND:We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that require users to optimize several parameters according to t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-S9-S11

    authors: Polishko A,Bunnik EM,Le Roch KG,Lonardi S

    更新日期:2014-01-01 00:00:00

  • Automated peptide mapping and protein-topographical annotation of proteomics data.

    abstract:BACKGROUND:In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS:We developed ImproViser...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-207

    authors: Videm P,Gunasekaran D,Schröder B,Mayer B,Biniossek ML,Schilling O

    更新日期:2014-06-19 00:00:00

  • Googling DNA sequences on the World Wide Web.

    abstract:BACKGROUND:New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bio...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S14-S4

    authors: Hajibabaei M,Singer GA

    更新日期:2009-11-10 00:00:00

  • SitesIdentify: a protein functional site prediction tool.

    abstract:BACKGROUND:The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function i...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-379

    authors: Bray T,Chan P,Bougouffa S,Greaves R,Doig AJ,Warwicker J

    更新日期:2009-11-18 00:00:00

  • An integrated approach to the prediction of domain-domain interactions.

    abstract:BACKGROUND:The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain i...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-269

    authors: Lee H,Deng M,Sun F,Chen T

    更新日期:2006-05-25 00:00:00

  • Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.

    abstract:BACKGROUND:A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging ty...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0875-7

    authors: Dubinkina VB,Ischenko DS,Ulyantsev VI,Tyakht AV,Alexeev DG

    更新日期:2016-01-16 00:00:00

  • BioIMAX: a Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data.

    abstract:BACKGROUND:Innovations in biological and biomedical imaging produce complex high-content and multivariate image data. For decision-making and generation of hypotheses, scientists need novel information technology tools that enable them to visually explore and analyze the data and to discuss and communicate results or f...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-297

    authors: Loyek C,Rajpoot NM,Khan M,Nattkemper TW

    更新日期:2011-07-21 00:00:00

  • Big data analysis for evaluating bioinvasion risk.

    abstract:BACKGROUND:Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area through ballast water and biofouling. Aiming at aquatic bioinvasion issue, people proposed various sug...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-018-2272-5

    authors: Wang S,Wang C,Wang S,Ma L

    更新日期:2018-08-13 00:00:00

  • Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays.

    abstract:BACKGROUND:Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematica...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-344

    authors: Chain B,Bowen H,Hammond J,Posch W,Rasaiyaah J,Tsang J,Noursadeghi M

    更新日期:2010-06-24 00:00:00

  • Analysis of cancer metabolism with high-throughput technologies.

    abstract:BACKGROUND:Recent advances in genomics and proteomics have allowed us to study the nuances of the Warburg effect--a long-standing puzzle in cancer energy metabolism--at an unprecedented level of detail. While modern next-generation sequencing technologies are extremely powerful, the lack of appropriate data analysis to...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-S10-S8

    authors: Markovets AA,Herman D

    更新日期:2011-10-18 00:00:00

  • Pathogenic Bacillus anthracis in the progressive gene losses and gains in adaptive evolution.

    abstract:BACKGROUND:Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss-of-function mutations and/o...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-S1-S3

    authors: Yu GX

    更新日期:2009-01-30 00:00:00

  • Taking U out, with two nucleases?

    abstract:BACKGROUND:REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and the consequences of the presence of two related proteins are not fully understood. Here, a variety of computational studies were p...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-305

    authors: Mian IS,Worthey EA,Salavati R

    更新日期:2006-06-16 00:00:00

  • Accelerating a cross-correlation score function to search modifications using a single GPU.

    abstract:BACKGROUND:A cross-correlation (XCorr) score function is one of the most popular score functions utilized to search peptide identifications in databases, and many computer programs, such as SEQUEST, Comet, and Tide, currently use this score function. Recently, the HiXCorr algorithm was developed to speed up this score ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-018-2559-6

    authors: Kim H,Han S,Um JH,Park K

    更新日期:2018-12-12 00:00:00

  • Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks.

    abstract:BACKGROUND:Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. RESULTS:Here, we weighted edges of a human protein interaction network and a transcriptional r...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-392

    authors: Chen L,Wang H,Zhang L,Li W,Wang Q,Shang Y,He Y,He W,Li X,Tai J,Li X

    更新日期:2010-07-22 00:00:00

  • In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.

    abstract:BACKGROUND:Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-461

    authors: Casneuf T,Van de Peer Y,Huber W

    更新日期:2007-11-26 00:00:00

  • Detection of biological switches using the method of Gröebner bases.

    abstract:BACKGROUND:Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS:In this wor...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-019-3155-0

    authors: Arkun Y

    更新日期:2019-11-28 00:00:00

  • Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery.

    abstract:BACKGROUND:As a novel cancer diagnostic paradigm, mass spectroscopic serum proteomic pattern diagnostics was reported superior to the conventional serologic cancer biomarkers. However, its clinical use is not fully validated yet. An important factor to prevent this young technology to become a mainstream cancer diagnos...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-S1-S1

    authors: Han H

    更新日期:2010-01-18 00:00:00

  • Multi-label literature classification based on the Gene Ontology graph.

    abstract:BACKGROUND:The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-9-525

    authors: Jin B,Muller B,Zhai C,Lu X

    更新日期:2008-12-08 00:00:00

  • 'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools.

    abstract:BACKGROUND:Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the eukaryotic cell. Each tool performs well on certain data sets, but their predictions often disagree for ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-420

    authors: Shen YQ,Burger G

    更新日期:2007-10-29 00:00:00