当前位置： SCI文献检索 > BMC GENOMICS期刊下所有文献 > Discovering large conserved functional components in global network alignment by graph matching.

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

Abstract：

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 https://github.com/yzlwhu/GMAlign .

journal_name

BMC Genomics

journal_title

BMC genomics

authors

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

doi

10.1186/s12864-018-5027-9

subject

Has Abstract

pub_date

2018-09-24 00:00:00

pages

670

issue

Suppl 7

issn

1471-2164

pii

10.1186/s12864-018-5027-9

journal_volume

19

pub_type

杂志文章

相关文献

BMC GENOMICS文献大全
  • A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing.

    abstract：BACKGROUND:CRISPR-Cas9 is a revolutionary genome editing technique that allows for efficient and directed alterations of the eukaryotic genome. This relatively new technology has already been used in a large number of 'loss of function' experiments in cultured cells. Despite its simplicity and efficiency, screening for...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-1002

    authors： Bell CC,Magor GW,Gillinder KR,Perkins AC

    更新日期：2014-11-20 00:00:00

  • Transcriptomic and metabolomic profiling of chicken adipose tissue in response to insulin neutralization and fasting.

    abstract：BACKGROUND:Domestic broiler chickens rapidly accumulate adipose tissue due to intensive genetic selection for rapid growth and are naturally hyperglycemic and insulin resistant, making them an attractive addition to the suite of rodent models used for studies of obesity and type 2 diabetes in humans. Furthermore, chick...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-13-441

    authors： Ji B,Ernest B,Gooding JR,Das S,Saxton AM,Simon J,Dupont J,Métayer-Coustard S,Campagna SR,Voy BH

    更新日期：2012-08-31 00:00:00

  • Genome-wide association and transcriptional studies reveal novel genes for unsaturated fatty acid synthesis in a panel of soybean accessions.

    abstract：BACKGROUND:The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genome-wide association (GWAS) studies along with gene expression studies in soybean [Glycine max (L.) Me...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-019-5449-z

    authors： Zhao X,Jiang H,Feng L,Qu Y,Teng W,Qiu L,Zheng H,Han Y,Li W

    更新日期：2019-01-21 00:00:00

  • Correction to: Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line.

    abstract：:An amendment to this paper has been published and can be accessed via the original article. ...

    journal_title：BMC genomics

    pub_type： 已发布勘误

    doi：10.1186/s12864-020-07211-8

    authors： Levin M,Scheibe M,Butter F

    更新日期：2020-11-12 00:00:00

  • Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling.

    abstract：BACKGROUND:Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the pre...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-14-857

    authors： Chen J,Dong X,Li Q,Zhou X,Gao S,Chen R,Sun L,Zhang L,Chen W

    更新日期：2013-12-05 00:00:00

  • Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni.

    abstract：BACKGROUND:It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of t...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-6-154

    authors： Laha T,Kewgrai N,Loukas A,Brindley PJ

    更新日期：2005-11-04 00:00:00

  • Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

    abstract：BACKGROUND:Cattle and other ruminants have evolved the ability to derive most of their metabolic energy requirement from otherwise indigestible plant matter through a symbiotic relationship with plant fibre degrading microbes within a specialised fermentation chamber, the rumen. The genetic changes underlying the evolu...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-8-75

    authors： Wheeler TT,Hood KA,Maqbool NJ,McEwan JC,Bingle CD,Zhao S

    更新日期：2007-03-15 00:00:00

  • Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research.

    abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. RESULTS:In this study, we investigated ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-019-6347-0

    authors： Liu S,An Y,Tong W,Qin X,Samarina L,Guo R,Xia X,Wei C

    更新日期：2019-12-05 00:00:00

  • Transcriptional responses of PBMC in psychosocially stressed animals indicate an alerting of the immune system in female but not in castrated male pigs.

    abstract：BACKGROUND:Brain and immune system are linked in a bi-directional manner. To date, it remained largely unknown why immune components become suppressed, enhanced, or remain unaffected in relation to psychosocial stress. Therefore, we mixed unfamiliar pigs with different levels of aggressiveness. We separated castrated m...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-967

    authors： Oster M,Muráni E,Ponsuksili S,D'Eath RB,Turner SP,Evans G,Thölking L,Kurt E,Klont R,Foury A,Mormède P,Wimmers K

    更新日期：2014-11-08 00:00:00

  • Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters.

    abstract：BACKGROUND:The transformation of a developing epithelium into an adult structure is a complex process, which often involves coordinated changes in cell proliferation, metabolism, adhesion, and shape. To identify genetic mechanisms that control epithelial differentiation, we analyzed the temporal patterns of gene expres...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-13-498

    authors： O'Keefe DD,Thomas SR,Bolin K,Griggs E,Edgar BA,Buttitta LA

    更新日期：2012-09-20 00:00:00

  • The developmental transcriptomes of two sea biscuit species with differing larval types.

    abstract：BACKGROUND:Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-018-4768-9

    authors： Armstrong AF,Grosberg RK

    更新日期：2018-05-18 00:00:00

  • Integrated proteomic and metabolomic analysis to study the effects of spaceflight on Candida albicans.

    abstract：BACKGROUND:Candida albicans is an opportunistic pathogenic yeast, which could become pathogenic in various stressful environmental factors including the spaceflight environment. In this study, we aim to explore the phenotypic changes and possible mechanisms of C. albicans after exposure to spaceflight conditions. RESU...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-020-6476-5

    authors： Wang J,Liu Y,Zhao G,Gao J,Liu J,Wu X,Xu C,Li Y

    更新日期：2020-01-17 00:00:00

  • Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations.

    abstract：BACKGROUND:Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy langu...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-015-1394-7

    authors： Kusuma P,Cox MP,Pierron D,Razafindrazaka H,Brucato N,Tonasso L,Suryadi HL,Letellier T,Sudoyo H,Ricaut FX

    更新日期：2015-03-17 00:00:00

  • Microarray analysis of response of Salmonella during infection of HLA-B27- transfected human macrophage-like U937 cells.

    abstract：BACKGROUND:Human leukocyte antigen (HLA)-B27 is strongly associated with the development of reactive arthritis (ReA) in humans after salmonellosis. Human monocytic U937 cells transfected with HLA-B27 are less able to eliminate intracellular Salmonella enterica serovar Enteritidis than those transfected with control HLA...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-11-456

    authors： Ge S,Danino V,He Q,Hinton JC,Granfors K

    更新日期：2010-07-30 00:00:00

  • ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

    abstract：BACKGROUND:ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-018-4559-3

    authors： Ou J,Liu H,Yu J,Kelliher MA,Castilla LH,Lawson ND,Zhu LJ

    更新日期：2018-03-01 00:00:00

  • Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

    abstract：BACKGROUND:Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. RESULTS:In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-9-36

    authors： Zhou F,Olman V,Xu Y

    更新日期：2008-01-24 00:00:00

  • Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome.

    abstract：BACKGROUND:Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-12-202

    authors： Fraser BA,Weadick CJ,Janowitz I,Rodd FH,Hughes KA

    更新日期：2011-04-20 00:00:00

  • A comparative approach to elucidate chloroplast genome replication.

    abstract：BACKGROUND:Electron microscopy analyses of replicating chloroplast molecules earlier predicted bidirectional Cairns replication as the prevalent mechanism, perhaps followed by rounds of a rolling circle mechanism. This standard model is being challenged by the recent proposition of homologous recombination-mediated rep...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-10-237

    authors： Krishnan NM,Rao BJ

    更新日期：2009-05-20 00:00:00

  • Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells.

    abstract：BACKGROUND:Although profiling of RNA in single cells has broadened our understanding of development, cancer biology and mechanisms of disease dissemination, it requires the development of reliable and flexible methods. Here we demonstrate that the EpiStem RNA-Amp™ methodology reproducibly generates microgram amounts of...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-1129

    authors： Rothwell DG,Li Y,Ayub M,Tate C,Newton G,Hey Y,Carter L,Faulkner S,Moro M,Pepper S,Miller C,Blackhall F,Bertolini G,Roz L,Dive C,Brady G

    更新日期：2014-12-17 00:00:00

  • Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group.

    abstract：BACKGROUND:The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing s...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-12-430

    authors： Schmidt TR,Scott EJ 2nd,Dyer DW

    更新日期：2011-08-24 00:00:00

  • Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping.

    abstract：BACKGROUND:Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplas...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-019-5662-9

    authors： Do TD,Vuong TD,Dunn D,Clubb M,Valliyodan B,Patil G,Chen P,Xu D,Nguyen HT,Shannon JG

    更新日期：2019-04-25 00:00:00

  • Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1.

    abstract：BACKGROUND:We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we transferred this respiratory phenotype in the presence of up to 50 g/L glucose to a yeast strai...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-9-365

    authors： Bonander N,Ferndahl C,Mostad P,Wilks MD,Chang C,Showe L,Gustafsson L,Larsson C,Bill RM

    更新日期：2008-07-31 00:00:00

  • Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns.

    abstract：BACKGROUND:Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with a higher than normal risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. While arsenic-induced biological changes play a role in disea...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-015-1295-9

    authors： Riedmann C,Ma Y,Melikishvili M,Godfrey SG,Zhang Z,Chen KC,Rouchka EC,Fondufe-Mittendorf YN

    更新日期：2015-03-19 00:00:00

  • Regulation of microRNAs miR-30a and miR-143 in cerebral vasculature after experimental subarachnoid hemorrhage in rats.

    abstract：BACKGROUND:microRNAs (miRNAs) are important regulators of translation and have been implicated in the pathogenesis of a number of cardiovascular diseases, including stroke, and suggested as possible prognostic biomarkers. Our aim was to identify miRNAs that are differentially regulated in cerebral arteries after subara...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-015-1341-7

    authors： Müller AH,Povlsen GK,Bang-Berthelsen CH,Kruse LS,Nielsen J,Warfvinge K,Edvinsson L

    更新日期：2015-02-22 00:00:00

  • Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401.

    abstract：BACKGROUND:Cyanobacteria are major primary producers in extreme cold ecosystems. Many lineages of cyanobacteria thrive in these harsh environments, but it is not fully understood how they survive in these conditions and whether they have evolved specific mechanisms of cold adaptation. Phormidesmis priestleyi is a cyano...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-016-2846-4

    authors： Chrismas NA,Barker G,Anesio AM,Sánchez-Baracaldo P

    更新日期：2016-08-02 00:00:00

  • Transposon libraries identify novel Mycobacterium bovis BCG genes involved in the dynamic interactions required for BCG to persist during in vivo passage in cattle.

    abstract：BACKGROUND:BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its incompatibility with current tuberculin testing regimens remains unlicensed. BCG's efficacy relates...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-019-5791-1

    authors： Mendum TA,Chandran A,Williams K,Vordermeier HM,Villarreal-Ramos B,Wu H,Singh A,Smith AA,Butler RE,Prasad A,Bharti N,Banerjee R,Kasibhatla SM,Bhatt A,Stewart GR,McFadden J

    更新日期：2019-05-28 00:00:00

  • Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation.

    abstract：BACKGROUND:The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-015-1699-6

    authors： Ryan PT,Ó'Maoiléidigh DS,Drost HG,Kwaśniewska K,Gabel A,Grosse I,Graciet E,Quint M,Wellmer F

    更新日期：2015-07-01 00:00:00

  • Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelial-mesenchymal transition.

    abstract：BACKGROUND:DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biological significance of DNA methylation in lung cancer. RESULTS:We integrated the gene expression pr...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-1079

    authors： Lin SH,Wang J,Saintigny P,Wu CC,Giri U,Zhang J,Menju T,Diao L,Byers L,Weinstein JN,Coombes KR,Girard L,Komaki R,Wistuba II,Date H,Minna JD,Heymach JV

    更新日期：2014-12-08 00:00:00

  • Differential gene expression and Hog1 interaction with osmoresponsive genes in the extremely halotolerant black yeast Hortaea werneckii.

    abstract：BACKGROUND:Fluctuations in external salinity force eukaryotic cells to respond by changes in the gene expression of proteins acting in protective biochemical processes, thus counteracting the changing osmotic pressure. The high-osmolarity glycerol (HOG) signaling pathway is essential for the efficient up-regulation of ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-8-280

    authors： Vaupotic T,Plemenitas A

    更新日期：2007-08-16 00:00:00

  • Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database.

    abstract：BACKGROUND:The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genom...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-10-454

    authors： Scaglione D,Acquadro A,Portis E,Taylor CA,Lanteri S,Knapp SJ

    更新日期：2009-09-28 00:00:00