A gene sets approach for identifying prognostic gene signatures for outcome prediction.


BACKGROUND:Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. RESULTS:We applied a gene sets approach to develop a prognostic gene set from multiple gene expression datasets. By analyzing 12 independent breast cancer gene expression datasets comprising 1,756 tissues with 2,411 pre-defined gene sets including gene ontology categories and pathways, we found many gene sets that were prognostic in most of the analyzed datasets. Those prognostic gene sets were related to biological processes such as cell cycle and proliferation and had additional prognostic values over conventional clinical parameters such as tumor grade, lymph node status, estrogen receptor (ER) status, and tumor size. We then estimated the prediction accuracy of each gene set by performing external validation using six large datasets and identified a gene set with an average prediction accuracy of 67.55%. CONCLUSION:A gene sets approach is an effective method to develop prognostic gene sets to predict patient outcome and to understand the underlying biology of the developed gene set. Using the gene sets approach we identified many prognostic gene sets in breast cancer.


BMC Genomics


BMC genomics


Kim SY,Kim YS




Has Abstract


2008-04-16 00:00:00










  • Unsupervised genome-wide recognition of local relationship patterns.

    abstract:BACKGROUND:Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zamani N,Russell P,Lantz H,Hoeppner MP,Meadows JR,Vijay N,Mauceli E,di Palma F,Lindblad-Toh K,Jern P,Grabherr MG

    更新日期:2013-05-24 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


    authors: Krishnan NM,Rao BJ

    更新日期:2009-05-20 00:00:00

  • Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs.

    abstract:BACKGROUND:Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang M,Han W,Tang H,Li G,Zhang M,Xu R,Liu Y,Yang T,Li W,Zou J,Wu K

    更新日期:2018-08-09 00:00:00

  • Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features.

    abstract:BACKGROUND:The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura-2 parameter (K-2-P) analysis based on the nucleotide sequence of three genes in this isolate, po...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Huang YF,Chen TH,Chang ZT,Wang TC,Lee SJ,Kim JC,Kim JS,Chiu KP,Nai YS

    更新日期:2019-05-27 00:00:00

  • Drosophila melanogaster retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations.

    abstract:BACKGROUND:Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon mobility in Drosophila somatic cells by poorly understood mechanisms. 21 nucleotide esiRNAs are primarily generated from retrotransposons and two inverted repeat (hairpin) loci in Drosophila culture cells in a Dicer2 dependent man...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Harrington AW,McKain MR,Michalski D,Bauer KM,Daugherty JM,Steiniger M

    更新日期:2017-04-17 00:00:00

  • The genome of the emerging barley pathogen Ramularia collo-cygni.

    abstract:BACKGROUND:Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and he...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McGrann GR,Andongabo A,Sjökvist E,Trivedi U,Dussart F,Kaczmarek M,Mackenzie A,Fountaine JM,Taylor JM,Paterson LJ,Gorniak K,Burnett F,Kanyuka K,Hammond-Kosack KE,Rudd JJ,Blaxter M,Havis ND

    更新日期:2016-08-09 00:00:00

  • Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton.

    abstract:BACKGROUND:Low iron bioavailability is a common feature of ocean surface water and therefore micro-algae developed original strategies to optimize iron uptake and metabolism. The marine picoeukaryotic green alga Ostreococcus tauri is a very good model for studying physiological and genetic aspects of the adaptation of ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lelandais G,Scheiber I,Paz-Yepes J,Lozano JC,Botebol H,Pilátová J,Žárský V,Léger T,Blaiseau PL,Bowler C,Bouget FY,Camadro JM,Sutak R,Lesuisse E

    更新日期:2016-05-03 00:00:00

  • Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomes.

    abstract:BACKGROUND:Many gram-negative bacteria use type III secretion systems (T3SSs) to translocate effector proteins into host cells. T3SS effectors can give some bacteria a competitive edge over others within the same environment and can help bacteria to invade the host cells and allow them to multiply rapidly within the ho...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hobbs CK,Porter VL,Stow ML,Siame BA,Tsang HH,Leung KY

    更新日期:2016-12-19 00:00:00

  • Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cao X,Wu Z,Jiang F,Zhou R,Yang Z

    更新日期:2014-12-17 00:00:00

  • Transcriptome profiling of litchi leaves in response to low temperature reveals candidate regulatory genes and key metabolic events during floral induction.

    abstract:BACKGROUND:Litchi (Litchi chinensis Sonn.) is an economically important evergreen fruit tree widely cultivated in subtropical areas. Low temperature is absolutely required for floral induction of litchi, but its molecular mechanism is not fully understood. Leaves of litchi played a key role during floral induction and ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang H,Shen J,Wei Y,Chen H

    更新日期:2017-05-10 00:00:00

  • Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor.

    abstract:BACKGROUND:Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize second...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bobek J,Strakova E,Zikova A,Vohradsky J

    更新日期:2014-12-23 00:00:00

  • The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster.

    abstract:BACKGROUND:Genetic association studies that seek to explain the inheritance of complex traits typically fail to explain a majority of the heritability of the trait under study. Thus, we are left with a gap in the map from genotype to phenotype. Several approaches have been used to fill this gap, including those that at...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Harrison BR,Wang L,Gajda E,Hoffman EV,Chung BY,Pletcher SD,Raftery D,Promislow DEL

    更新日期:2020-05-04 00:00:00

  • De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray.

    abstract:BACKGROUND:Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a comple...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Benzekri H,Armesto P,Cousin X,Rovira M,Crespo D,Merlo MA,Mazurais D,Bautista R,Guerrero-Fernández D,Fernandez-Pozo N,Ponce M,Infante C,Zambonino JL,Nidelet S,Gut M,Rebordinos L,Planas JV,Bégout ML,Claros MG,Manchado

    更新日期:2014-11-03 00:00:00

  • Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis.

    abstract:BACKGROUND:Propionibacterium acnes and Staphylococcus epidermidis live in close proximity on human skin, and both bacterial species can be isolated from normal and acne vulgaris-affected skin sites. The antagonistic interactions between the two species are poorly understood, as well as the potential significance of bac...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Christensen GJ,Scholz CF,Enghild J,Rohde H,Kilian M,Thürmer A,Brzuszkiewicz E,Lomholt HB,Brüggemann H

    更新日期:2016-02-29 00:00:00

  • Genome-wide mapping of Hif-1α binding sites in zebrafish.

    abstract:BACKGROUND:Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved, allowing the use of zebrafish (Danio rerio) as a model for studying the hypoxic response. Activati...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Greenald D,Jeyakani J,Pelster B,Sealy I,Mathavan S,van Eeden FJ

    更新日期:2015-11-11 00:00:00

  • Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum.

    abstract:BACKGROUND:It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene m...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: López-Barragán MJ,Lemieux J,Quiñones M,Williamson KC,Molina-Cruz A,Cui K,Barillas-Mury C,Zhao K,Su XZ

    更新日期:2011-11-30 00:00:00

  • Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome.

    abstract:BACKGROUND:Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Morishige DT,Klein PE,Hilley JL,Sahraeian SM,Sharma A,Mullet JE

    更新日期:2013-07-05 00:00:00

  • An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern.

    abstract:BACKGROUND:Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the p...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zimmerman SJ,Aldridge CL,Oyler-McCance SJ

    更新日期:2020-06-01 00:00:00

  • Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq.

    abstract:BACKGROUND:Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix-loop-helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD rep...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kodama M,Brinch-Pedersen H,Sharma S,Holme IB,Joernsgaard B,Dzhanfezova T,Amby DB,Vieira FG,Liu S,Gilbert MTP

    更新日期:2018-11-08 00:00:00

  • Heritability and genome-wide association analyses of fasting plasma glucose in Chinese adult twins.

    abstract:BACKGROUND:Currently, diabetes has become one of the leading causes of death worldwide. Fasting plasma glucose (FPG) levels that are higher than optimal, even if below the diagnostic threshold of diabetes, can also lead to increased morbidity and mortality. Here we intend to study the magnitude of the genetic influence...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang W,Zhang C,Liu H,Xu C,Duan H,Tian X,Zhang D

    更新日期:2020-07-18 00:00:00

  • RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit.

    abstract:BACKGROUND:There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limit...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Garcia-Seco D,Zhang Y,Gutierrez-Mañero FJ,Martin C,Ramos-Solano B

    更新日期:2015-01-22 00:00:00

  • Altered gene expression in the superior temporal gyrus in schizophrenia.

    abstract:BACKGROUND:The superior temporal gyrus (STG), which encompasses the primary auditory cortex, is believed to be a major anatomical substrate for speech, language and communication. The STG connects to the limbic system (hippocampus and amygdala), the thalamus and neocortical association areas in the prefrontal cortex, a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bowden NA,Scott RJ,Tooney PA

    更新日期:2008-04-29 00:00:00

  • Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.

    abstract:BACKGROUND:The MHC and KIR loci are clinically relevant regions of the genome. Typing the sequence of these loci has a wide range of applications including organ transplantation, drug discovery, pharmacogenomics and furthering fundamental research in immune genetics. Rapid advances in biochemical and next-generation se...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Selvaraj S,Schmitt AD,Dixon JR,Ren B

    更新日期:2015-11-05 00:00:00

  • Cell population-specific expression analysis of human cerebellum.

    abstract:BACKGROUND:Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kuhn A,Kumar A,Beilina A,Dillman A,Cookson MR,Singleton AB

    更新日期:2012-11-12 00:00:00

  • Profiling expression changes caused by a segmental aneuploid in maize.

    abstract:BACKGROUND:While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS:We employed a segmental aneup...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Makarevitch I,Phillips RL,Springer NM

    更新日期:2008-01-10 00:00:00

  • DAWN: a resource for yielding insights into the diversity among wheat genomes.

    abstract:BACKGROUND:Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysing these data sets. RESULTS:DAWN (Diversity Among Wheat geNomes) integrates data from the T. aes...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Watson-Haigh NS,Suchecki R,Kalashyan E,Garcia M,Baumann U

    更新日期:2018-12-17 00:00:00

  • Finishing monkeypox genomes from short reads: assembly analysis and a neural network method.

    abstract:BACKGROUND:Poxviruses constitute one of the largest and most complex animal virus families known. The notorious smallpox disease has been eradicated and the virus contained, but its simian sister, monkeypox is an emerging, untreatable infectious disease, killing 1 to 10 % of its human victims. In the case of poxviruses...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhao K,Wohlhueter RM,Li Y

    更新日期:2016-08-31 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


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

    更新日期:2005-11-04 00:00:00

  • RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior.

    abstract:BACKGROUND:Invasive aspergillosis is started after germination of Aspergillus fumigatus conidia that are inhaled by susceptible individuals. Fungal hyphae can grow in the lung through the epithelial tissue and disseminate hematogenously to invade into other organs. Low fungaemia indicates that fungal elements do not re...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Irmer H,Tarazona S,Sasse C,Olbermann P,Loeffler J,Krappmann S,Conesa A,Braus GH

    更新日期:2015-08-27 00:00:00

  • Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates.

    abstract:BACKGROUND:Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gavelis GS,White RA,Suttle CA,Keeling PJ,Leander BS

    更新日期:2015-07-17 00:00:00