Discovering large conserved functional components in global network alignment by graph matching.


BACKGROUND:Aligning protein-protein interaction (PPI) networks is very important to discover the functionally conserved sub-structures between different species. In recent years, the global PPI network alignment problem has been extensively studied aiming at finding the one-to-one alignment with the maximum matching score. However, finding large conserved components remains challenging due to its NP-hardness. RESULTS:We propose a new graph matching method GMAlign for global PPI network alignment. It first selects some pairs of important proteins as seeds, followed by a gradual expansion to obtain an initial matching, and then it refines the current result to obtain an optimal alignment result iteratively based on the vertex cover. We compare GMAlign with the state-of-the-art methods on the PPI network pairs obtained from the largest BioGRID dataset and validate its performance. The results show that our algorithm can produce larger size of alignment, and can find bigger and denser common connected subgraphs as well for the first time. Meanwhile, GMAlign can achieve high quality biological results, as measured by functional consistency and semantic similarity of the Gene Ontology terms. Moreover, we also show that GMAlign can achieve better results which are structurally and biologically meaningful in the detection of large conserved biological pathways between species. CONCLUSIONS:GMAlign is a novel global network alignment tool to discover large conserved functional components between PPI networks. It also has many potential biological applications such as conserved pathway and protein complex discovery across species. The GMAlign software and datasets are avaialbile at .


BMC Genomics


BMC genomics


Zhu Y,Li Y,Liu J,Qin L,Yu JX




Has Abstract


2018-09-24 00:00:00




Suppl 7








  • A Caenorhabditis motif compendium for studying transcriptional gene regulation.

    abstract:BACKGROUND:Controlling gene expression is fundamental to biological complexity. The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dieterich C,Sommer RJ

    更新日期:2008-01-23 00:00:00

  • Effect of sample stratification on dairy GWAS results.

    abstract:BACKGROUND:Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for s...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma L,Wiggans GR,Wang S,Sonstegard TS,Yang J,Crooker BA,Cole JB,Van Tassell CP,Lawlor TJ,Da Y

    更新日期:2012-10-06 00:00:00

  • Efficient depletion of ribosomal RNA for RNA sequencing in planarians.

    abstract:BACKGROUND:The astounding regenerative abilities of planarian flatworms prompt steadily growing interest in examining their molecular foundation. Planarian regeneration was found to require hundreds of genes and is hence a complex process. Thus, RNA interference followed by transcriptome-wide gene expression analysis b...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim IV,Ross EJ,Dietrich S,Döring K,Sánchez Alvarado A,Kuhn CD

    更新日期:2019-11-29 00:00:00

  • Reconstruction of evolutionary trajectories of chromosomes unraveled independent genomic repatterning between Triticeae and Brachypodium.

    abstract:BACKGROUND:After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers amo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang Z,Wang J,Pan Y,Lei T,Ge W,Wang L,Zhang L,Li Y,Zhao K,Liu T,Song X,Zhang J,Yu J,Hu J,Wang X

    更新日期:2019-03-07 00:00:00

  • Characterization of the transcriptome and temperature-induced differential gene expression in QPX, the thraustochytrid parasite of hard clams.

    abstract:BACKGROUND:The hard clam or northern quahog, Mercenaria mercenaria, is one of the most valuable seafood products in the United States representing the first marine resource in some Northeastern states. Severe episodes of hard clam mortality have been consistently associated with infections caused by a thraustochytrid p...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rubin E,Tanguy A,Perrigault M,Pales Espinosa E,Allam B

    更新日期:2014-03-28 00:00:00

  • Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus.

    abstract:BACKGROUND:Several in vitro studies document the function of the transcriptional regulator TrmBL1 of Pyrococcus furiosus. These data indicate that the protein can act as repressor or activator and is mainly involved in transcriptional control of sugar uptake and in the switch between glycolysis and gluconeogenesis. The...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Reichelt R,Gindner A,Thomm M,Hausner W

    更新日期:2016-01-08 00:00:00

  • A hybrid imputation approach for microarray missing value estimation.

    abstract:BACKGROUND:Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most existing approaches suffer from this prevalent problem. Imputation is one of the frequently used metho...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li H,Zhao C,Shao F,Li GZ,Wang X

    更新日期:2015-01-01 00:00:00

  • Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis.

    abstract:BACKGROUND:The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence i...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dong N,Bandura J,Zhang Z,Wang Y,Labadie K,Noel B,Davison A,Koene JM,Sun HS,Coutellec MA,Feng ZP

    更新日期:2021-01-06 00:00:00

  • Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands.

    abstract:BACKGROUND:Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecula...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma L,Ma Q,Li X,Cheng L,Li K,Li S

    更新日期:2014-03-09 00:00:00

  • Global analysis of the ovarian microRNA transcriptome: implication for miR-2 and miR-133 regulation of oocyte meiosis in the Chinese mitten crab, Eriocheir sinensis (Crustacea:Decapoda).

    abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNA molecules that downregulate gene expression by base pairing to the 3'-untranslated region (UTR) of target messenger RNAs (mRNAs). Up to now, rare information for the miRNAs is available in decapod crustaceans. Our previous studies showed that many miRNA-binding sit...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Song YN,Shi LL,Liu ZQ,Qiu GF

    更新日期:2014-07-01 00:00:00

  • Quantitative proteomic analysis of host--pathogen interactions: a study of Acinetobacter baumannii responses to host airways.

    abstract:BACKGROUND:Acinetobacter baumannii is a major health problem. The most common infection caused by A. baumannii is hospital acquired pneumonia, and the associated mortality rate is approximately 50%. Neither in vivo nor ex vivo expression profiling has been performed at the proteomic or transcriptomic level for pneumoni...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Méndez JA,Mateos J,Beceiro A,Lopez M,Tomás M,Poza M,Bou G

    更新日期:2015-05-30 00:00:00

  • Genome-wide survey and expression profiles of the AP2/ERF family in castor bean (Ricinus communis L.).

    abstract:BACKGROUND:The AP2/ERF transcription factor, one of the largest gene families in plants, plays a crucial role in the regulation of growth and development, metabolism, and responses to biotic and abiotic stresses. Castor bean (Ricinus communis L., Euphobiaceae) is one of most important non-edible oilseed crops and its s...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Xu W,Li F,Ling L,Liu A

    更新日期:2013-11-13 00:00:00

  • Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme.

    abstract:BACKGROUND:The development of microarrays permits us to monitor transcriptomes on a genome-wide scale. To validate microarray measurements, quantitative-real time-reverse transcription PCR (Q-RT-PCR) is one of the most robust and commonly used approaches. The new challenge in gene quantification analysis is how to expl...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Su LJ,Chang CW,Wu YC,Chen KC,Lin CJ,Liang SC,Lin CH,Whang-Peng J,Hsu SL,Chen CH,Huang CY

    更新日期:2007-06-01 00:00:00

  • σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

    abstract:BACKGROUND:The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequen...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kazakov AE,Rajeev L,Chen A,Luning EG,Dubchak I,Mukhopadhyay A,Novichkov PS

    更新日期:2015-11-10 00:00:00

  • Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system.

    abstract:BACKGROUND:Sugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causing severe losses to the sugarcane industry. The use of PCR reference genes is essential to the no...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Huang N,Ling H,Liu F,Su Y,Su W,Mao H,Zhang X,Wang L,Chen R,Que Y

    更新日期:2018-06-19 00:00:00

  • Genome sequence of an aflatoxigenic pathogen of Argentinian peanut, Aspergillus arachidicola.

    abstract:BACKGROUND:Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. This aflatoxigenic species is capable of secreting both B and G aflatoxins, similar to A. parasit...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Moore GG,Mack BM,Beltz SB,Puel O

    更新日期:2018-03-09 00:00:00

  • Histological and global gene expression analysis of the 'lactating' pigeon crop.

    abstract:BACKGROUND:Both male and female pigeons have the ability to produce a nutrient solution in their crop for the nourishment of their young. The production of the nutrient solution has been likened to lactation in mammals, and hence the product has been called pigeon 'milk'. It has been shown that pigeon 'milk' is essenti...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gillespie MJ,Haring VR,McColl KA,Monaghan P,Donald JA,Nicholas KR,Moore RJ,Crowley TM

    更新日期:2011-09-19 00:00:00

  • Identification of microRNA-mRNA modules using microarray data.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA expression and are involved in numerous cellular processes. Consequently, miRNAs are an important component of gene regulatory networks and an improved understanding of miRNAs will further our knowledge of these networks. There is a many-to-many ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jayaswal V,Lutherborrow M,Ma DD,Yang YH

    更新日期:2011-03-06 00:00:00

  • Comparative transcriptomics of early petal development across four diverse species of Aquilegia reveal few genes consistently associated with nectar spur development.

    abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ballerini ES,Kramer EM,Hodges SA

    更新日期:2019-08-22 00:00:00

  • ICPD-a new peak detection algorithm for LC/MS.

    abstract:BACKGROUND:The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang J,Haskins W

    更新日期:2010-12-01 00:00:00

  • RNA sequencing identifies common pathways between cigarette smoke exposure and replicative senescence in human airway epithelia.

    abstract:BACKGROUND:Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be beneficial for cell survival in response to cigarette smoke and thereby may contribute to development o...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Voic H,Li X,Jang JH,Zou C,Sundd P,Alder J,Rojas M,Chandra D,Randell S,Mallampalli RK,Tesfaigzi Y,Ryba T,Nyunoya T

    更新日期:2019-01-09 00:00:00

  • Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement.

    abstract:BACKGROUND:Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Huang J,Gao Y,Jia H,Liu L,Zhang D,Zhang Z

    更新日期:2015-05-08 00:00:00

  • Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation.

    abstract:BACKGROUND:Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on ho...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pasookhush P,Hindmarch C,Sithigorngul P,Longyant S,Bendena WG,Chaivisuthangkura P

    更新日期:2019-10-22 00:00:00

  • Core and accessory genome architecture in a group of Pseudomonas aeruginosa Mu-like phages.

    abstract:BACKGROUND:Bacteriophages that infect the opportunistic pathogen Pseudomonas aeruginosa have been classified into several groups. One of them, which includes temperate phage particles with icosahedral heads and long flexible tails, bears genomes whose architecture and replication mechanism, but not their nucleotide seq...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cazares A,Mendoza-Hernández G,Guarneros G

    更新日期:2014-12-19 00:00:00

  • Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity.

    abstract:BACKGROUND:Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying phy...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sun RX,Chong LC,Simmons TT,Houlahan KE,Prokopec SD,Watson JD,Moffat ID,Lensu S,Lindén J,P'ng C,Okey AB,Pohjanvirta R,Boutros PC

    更新日期:2014-12-03 00:00:00

  • Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.

    abstract:BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cho YB,Lee EJ,Cho S,Kim TY,Park JH,Cho BK

    更新日期:2016-02-29 00:00:00

  • "Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)".

    abstract:BACKGROUND:Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters. RESULTS:We used bioinformat...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ferreira Filho JA,Horta MAC,Dos Santos CA,Almeida DA,Murad NF,Mendes JS,Sforça DA,Silva CBC,Crucello A,de Souza AP

    更新日期:2020-11-02 00:00:00

  • Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses.

    abstract:BACKGROUND:Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang J,Liu B,Li J,Zhang L,Wang Y,Zheng H,Lu M,Chen J

    更新日期:2015-03-14 00:00:00

  • Genetic architecture and genomic selection of female reproduction traits in rainbow trout.

    abstract:BACKGROUND:Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: D'Ambrosio J,Morvezen R,Brard-Fudulea S,Bestin A,Acin Perez A,Guéméné D,Poncet C,Haffray P,Dupont-Nivet M,Phocas F

    更新日期:2020-08-14 00:00:00

  • Concurrent host-pathogen gene expression in the lungs of pigs challenged with Actinobacillus pleuropneumoniae.

    abstract:BACKGROUND:Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcin...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Brogaard L,Klitgaard K,Heegaard PM,Hansen MS,Jensen TK,Skovgaard K

    更新日期:2015-05-28 00:00:00