Analyzing gene expression data in terms of gene sets: methodological issues

doi:10.1093/bioinformatics/btm051

PMID: 17303618DOI: 10.1093/bioinformatics/btm051Feb 17, 2007

Analyzing gene expression data in terms of gene sets: methodological issues

Bioinformatics

Jelle Goeman, Peter Bühlmann

Abstract

Many statistical tests have been proposed in recent years for analyzing gene expression data in terms of gene sets, usually from Gene Ontology. These methods are based on widely different methodological assumptions. Some approaches test differential expression of each gene set against differential expression of the rest of the genes, whereas others test each gene set on its own. Also, some methods are based on a model in which the genes are the sampling units, whereas others treat the subjects as the sampling units. This article aims to clarify the assumptions behind different approaches and to indicate a preferential methodology of gene set testing. We identify some crucial assumptions which are needed by the majority of methods. P-values derived from methods that use a model which takes the genes as the sampling unit are easily misinterpreted, as they are based on a statistical model that does not resemble the biological experiment actually performed. Furthermore, because these models are based on a crucial and unrealistic independence assumption between genes, the P-values derived from such methods can be wildly anti-conservative, as a simulation experiment shows. We also argue that methods that competitively test each gene ...Continue Reading

References

KEGG: Kyoto Encyclopedia of Genes and Genomes

Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium

May 10, 2000·Nature Genetics·M AshburnerG Sherlock

GoMiner: a resource for biological interpretation of genomic and proteomic data

Apr 19, 2003·Genome Biology·Barry R ZeebergJohn N Weinstein

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

Jun 17, 2003·Nature Genetics·Vamsi K MoothaLeif C Groop

Identifying biological themes within lists of genes with EASE

Oct 2, 2003·Genome Biology·Douglas A HosackRichard A Lempicki

A global test for groups of genes: testing association with a clinical outcome

Dec 25, 2003·Bioinformatics·Jelle GoemanHans C van Houwelingen

GOstat: find statistically overrepresented Gene Ontologies within a group of genes

Feb 14, 2004·Bioinformatics·Tim Beißbarth, Terence P Speed

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

Feb 21, 2004·BMC Bioinformatics·Bing ZhangJay Snoddy

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Mar 3, 2004·Bioinformatics·Fátima Al-ShahrourJoaquín Dopazo

Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments

Mar 31, 2004·BMC Bioinformatics·Rainer BreitlingPawel Herzyk

Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex

Jun 5, 2004·Neurochemical Research·Paul PavlidisEtienne Sibille

Statistical concerns about the GSEA procedure

Jul 1, 2004·Nature Genetics·Doris Damian, Malka Gorfine

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

Aug 7, 2004·Bioinformatics·Elizabeth I BoyleG Sherlock

Comparing functional annotation analyses with Catmap

Dec 14, 2004·BMC Bioinformatics·Thomas BreslinMorten Krogh

Significance analysis of functional categories in gene expression studies: a structured permutation approach

Jan 14, 2005·Bioinformatics·William T BarryFred A Wright

Testing association of a pathway with survival using gene expression data

Jan 20, 2005·Bioinformatics·Jelle GoemanHans C van Houwelingen

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information

Apr 21, 2005·Bioinformatics·Fátima Al-ShahrourJoaquín Dopazo

Theme discovery from gene lists for identification and viewing of multiple functional groups

Jul 1, 2005·BMC Bioinformatics·Petri PehkonenPetri Törönen

Ontological analysis of gene expression data: current tools, limitations, and open problems

Jul 5, 2005·Bioinformatics·Purvesh Khatri, Sorin Drăghici

Pathway level analysis of gene expression using singular value decomposition

Sep 15, 2005·BMC Bioinformatics·John TomfohrThomas B Kepler

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov

ErmineJ: tool for functional analysis of gene expression data sets

Nov 11, 2005·BMC Bioinformatics·Homin K LeePaul Pavlidis

Microarray data analysis: from disarray to consolidation and consensus

Dec 22, 2005·Nature Reviews. Genetics·David B AllisonMahyar Sabripour

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

Jan 21, 2006·BMC Bioinformatics·Ming YiRobert M Stephens

Group testing for pathway analysis improves comparability of different microarray datasets

Aug 10, 2006·Bioinformatics·Theodora ManoliBenedikt Brors

Citations

Integration of biological networks and pathways with genetic association studies

Jul 11, 2012·Human Genetics·Yan V Sun

Genome-wide pathway analysis of memory impairment in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort implicates gene candidates, canonical pathways, and networks

Aug 7, 2012·Brain Imaging and Behavior·Vijay K RamananAlzheimer’s Disease Neuroimaging Initiative (ADNI)

Multimodel pathway enrichment methods for functional evaluation of expression regulation

Apr 5, 2012·Journal of Proteome Research·Ufuk KirikFredrik Levander

A network-based gene-weighting approach for pathway analysis

Sep 7, 2011·Cell Research·Zhaoyuan FangHongbin Ji

Plasma 25 hydroxyvitamin D level and blood gene expression profiles: a cross-sectional study of the Norwegian Women and Cancer Post-genome Cohort

Mar 7, 2013·European Journal of Clinical Nutrition·K Standahl OlsenE Lund

Use of the gamma method for self-contained gene-set analysis of SNP data

Dec 15, 2011·European Journal of Human Genetics : EJHG·Joanna M BiernackaBrooke L Fridley

Variable set enrichment analysis in genome-wide association studies

Mar 24, 2011·European Journal of Human Genetics : EJHG·Wei YangC Charles Gu

Gene set analysis of SNP data: benefits, challenges, and future directions

Apr 14, 2011·European Journal of Human Genetics : EJHG·Brooke L Fridley, Joanna M Biernacka

Prioritising risk pathways of complex human diseases based on functional profiling

Oct 11, 2012·European Journal of Human Genetics : EJHG·Yan LiYixue Li

DBGSA: a novel method of distance-based gene set analysis

Jul 13, 2012·Journal of Human Genetics·Jin LiXia Li

Gene expression in archived newborn blood spots distinguishes infants who will later develop cerebral palsy from matched controls

Dec 28, 2012·Pediatric Research·Nhan Thi HoNigel Paneth

Development of an integrated metabolomic profiling approach for infectious diseases research

Sep 17, 2011·The Analyst·Haitao LvJeffrey P Henderson

Pathway analysis of microarray data via regression

Mar 12, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Adeniyi J AdewaleYutaka Yasui

Analysis of gene sets based on the underlying regulatory network

Mar 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ali Shojaie, George Michailidis

Estimation of gene induction enables a relevance-based ranking of gene sets

Jul 8, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Kilian BartholoméJens Timmer

Reverse engineering molecular regulatory networks from microarray data with qp-graphs

Jan 31, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Robert Castelo, Alberto Roverato

Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology

Jun 14, 2013·Omics : a Journal of Integrative Biology·Juan C VivarSujoy Ghosh

Gene-set analysis and reduction

Oct 7, 2008·Briefings in Bioinformatics·Irina DinuYutaka Yasui

Literature-aided interpretation of gene expression data with the weighted global test

Dec 25, 2010·Briefings in Bioinformatics·Rob JelierPeter A C 't Hoen

Ontological analysis of gene expression data: current tools, limitations, and open problems

Jul 5, 2005·Bioinformatics·Purvesh Khatri, Sorin Drăghici

GlobalANCOVA: exploration and assessment of gene group effects

Nov 21, 2007·Bioinformatics·Manuela HummelUlrich Mansmann

Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis

Nov 29, 2007·Bioinformatics·Dan NettletonJames M Reecy

Multiple testing on the directed acyclic graph of gene ontology

Jan 22, 2008·Bioinformatics·Jelle Goeman, Ulrich Mansmann

SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy

Dec 23, 2008·Bioinformatics·Daniel M GattiWilliam T Barry

Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection

Jan 27, 2009·Bioinformatics·Michael C WuXihong Lin

A flexible two-stage procedure for identifying gene sets that are differentially expressed

Feb 14, 2009·Bioinformatics·Ruth HellerWarren J Ewens

Identification of differential gene pathways with principal component analysis

Feb 19, 2009·Bioinformatics·Shuangge Ma, Michael R Kosorok

Multivariate analysis of variance test for gene set analysis

Mar 4, 2009·Bioinformatics·Chen-An Tsai, James J Chen

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

Jul 4, 2009·Bioinformatics·Galina Glazko, Frank Emmert-Streib

Meta-analysis for pathway enrichment analysis when combining multiple genomic studies

Apr 23, 2010·Bioinformatics·Kui Shen, George C Tseng

De-correlating expression in gene-set analysis

Sep 9, 2010·Bioinformatics·Dougu Nam

ROAST: rotation gene set tests for complex microarray experiments

Jul 9, 2010·Bioinformatics·Di WuGordon K Smyth

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data

Sep 3, 2010·Bioinformatics·Elana J FertigMichael F Ochs

Robust and accurate data enrichment statistics via distribution function of sum of weights

Sep 10, 2010·Bioinformatics·Aleksandar Stojmirović, Yi-Kuo Yu

Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes

Mar 29, 2011·Bioinformatics·Klaus JungTim Beißbarth

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

Jun 21, 2011·Bioinformatics·Ludwig GeistlingerRalf Zimmer

A procedure to statistically evaluate agreement of differential expression for cross-species genomics

Jun 24, 2011·Bioinformatics·Stan PoundsRichard J Gilbertson

Contextual analysis of RNAi-based functional screens using interaction networks

Aug 13, 2011·Bioinformatics·Orland Gonzalez, Ralf Zimmer

Rigorous assessment of gene set enrichment tests

Apr 12, 2012·Bioinformatics·Haroon NaeemRobert Küffner

iBBiG: iterative binary bi-clustering of gene sets

Jul 14, 2012·Bioinformatics·Daniel GusenleitnerAedín C Culhane

Gene set analysis for self-contained tests: complex null and specific alternative hypotheses

Oct 10, 2012·Bioinformatics·Yasir RahmatallahGalina Glazko

Pathway hunting by random survival forests

Nov 7, 2012·Bioinformatics·Xi Chen, Hemant Ishwaran

A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies

Feb 19, 2013·Bioinformatics·Min ChenGuanghua Xiao

Testing SNPs and sets of SNPs for importance in association studies

Jul 6, 2010·Biostatistics·Holger SchwenderKatja Ickstadt

Empirical pathway analysis, without permutation

Feb 23, 2013·Biostatistics·Yi-Hui ZhouFred A Wright

GEPAS, a web-based tool for microarray data analysis and interpretation

May 30, 2008·Nucleic Acids Research·Joaquin TarragaJoaquín Dopazo

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

Jun 3, 2008·Nucleic Acids Research·Fátima Al-ShahrourJoaquín Dopazo

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Nov 27, 2008·Nucleic Acids Research·Da Wei HuangRichard A Lempicki

GeneSigDB--a curated database of gene expression signatures

Nov 26, 2009·Nucleic Acids Research·Aedín C CulhaneJohn Quackenbush

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

Jun 9, 2009·Nucleic Acids Research·Ignacio MedinaJoaquín Dopazo

GOing Bayesian: model-based gene set analysis of genome-scale data

Feb 23, 2010·Nucleic Acids Research·Sebastian BauerPeter N Robinson

GSA-SNP: a general approach for gene set analysis of polymorphisms

May 27, 2010·Nucleic Acids Research·Dougu NamSangsoo Kim

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

Nov 24, 2011·Nucleic Acids Research·Aedín C CulhaneJohn Quackenbush

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

Jan 24, 2012·Nucleic Acids Research·Daniela M Witten, William Stafford Noble

Camera: a competitive gene set test accounting for inter-gene correlation

May 29, 2012·Nucleic Acids Research·Di Wu, Gordon K Smyth

Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments

Jul 31, 2012·Nucleic Acids Research·Luz García-AlonsoJoaquín Dopazo

Along signal paths: an empirical gene set approach exploiting pathway topology

Sep 25, 2012·Nucleic Acids Research·Paolo MartiniChiara Romualdi

Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential

Feb 8, 2013·Nucleic Acids Research·Shailesh TripathiFrank Emmert-Streib

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

Feb 28, 2013·Nucleic Acids Research·Leif VäremoIntawat Nookaew

Graphite Web: Web tool for gene set analysis exploiting pathway topology

May 15, 2013·Nucleic Acids Research·Gabriele SalesChiara Romualdi

Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions

Jun 19, 2013·Nucleic Acids Research·Maarten van ItersonJudith M Boer

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations

Aug 8, 2013·Nucleic Acids Research·Gur YaariSteven H Kleinstein

Gene set analysis of purine and pyrimidine antimetabolites cancer therapies

Aug 27, 2011·Pharmacogenetics and Genomics·Brooke L FridleyRichard M Weinshilboum

Differential regulation of the nuclear factor-κB pathway by rabbit antithymocyte globulins in kidney transplantation

Feb 16, 2012·Transplantation·Mariana UrbanovaOndrej Viklicky

Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets

Sep 24, 2011·Genome Research·Qing XiongTerrence S Furey

A multivariate extension of the gene set enrichment analysis

Oct 13, 2007·Journal of Bioinformatics and Computational Biology·Lev KlebanovYuanhui Xiao

Bioinformatic tools for inferring functional information from plant microarray data II: Analysis beyond single gene

Jul 11, 2008·International Journal of Plant Genomics·Issa Coulibaly, Grier P Page

A hypothesis test for equality of bayesian network models

Oct 29, 2010·EURASIP Journal on Bioinformatics & Systems Biology·Anthony Almudevar

Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways

Jan 6, 2010·Statistical Methods in Medical Research·Michael C Wu, Xihong Lin

Diffuse large B-cell lymphomas with CDKN2A deletion have a distinct gene expression signature and a poor prognosis under R-CHOP treatment: a GELA study

May 4, 2010·Blood·Fabrice JardinKaren Leroy

GAGE: generally applicable gene set enrichment for pathway analysis

May 29, 2009·BMC Bioinformatics·Weijun LuoPeter J Woolf

RCMAT: a regularized covariance matrix approach to testing gene sets

Sep 24, 2009·BMC Bioinformatics·Phillip D Yates, Mark A Reimers

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

Sep 25, 2009·BMC Bioinformatics·Petri TörönenLiisa Holm

Generation of Gene Ontology benchmark datasets with various types of positive signal

Oct 9, 2009·BMC Bioinformatics·Petri TörönenLiisa Holm

Quantitative comparison of microarray experiments with published leukemia related gene expression signatures

Dec 17, 2009·BMC Bioinformatics·Hans-Ulrich KleinMartin Dugas

A new permutation strategy of pathway-based approach for genome-wide association study

Dec 22, 2009·BMC Bioinformatics·Yan-Fang GuoHong-Wen Deng

A general modular framework for gene set enrichment analysis

Feb 5, 2009·BMC Bioinformatics·Marit Ackermann, Korbinian Strimmer

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Feb 5, 2009·BMC Bioinformatics·Eran EdenZohar Yakhini

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data

Oct 14, 2009·BMC Bioinformatics·Bart H J van den BergSusan M Bridges

Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets

Jan 13, 2010·BMC Bioinformatics·Esteban CzwanDavid Kipling

Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context

May 27, 2010·BMC Bioinformatics·Gad AbrahamJustin Zobel

Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets

Oct 15, 2010·BMC Bioinformatics·Fabrice BergerEric Depiereux

Investigating the effect of paralogs on microarray gene-set analysis

Jan 26, 2011·BMC Bioinformatics·Andre J FaureNicola J Mulder

Expression cartography of human tissues using self organizing maps

Jul 29, 2011·BMC Bioinformatics·Henry WirthHans Binder

A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype

Sep 29, 2011·BMC Bioinformatics·Seungyeoun LeeSunho Lee

Integrative set enrichment testing for multiple omics platforms

Nov 29, 2011·BMC Bioinformatics·Laila M PoissonDebashis Ghosh

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies

Apr 13, 2011·BMC Bioinformatics·Paolo MartiniStefano Cagnin

Down-weighting overlapping genes improves gene set analysis

Jun 21, 2012·BMC Bioinformatics·Adi L TarcaRoberto Romero

Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data

Jul 26, 2012·BMC Bioinformatics·Wenge GuoShyamal D Peddada

GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network

Aug 11, 2012·BMC Bioinformatics·Dan Jacobson, Guy Emerton

DNA methylation arrays as surrogate measures of cell mixture distribution

May 10, 2012·BMC Bioinformatics·E Andres HousemanKarl T Kelsey

Comparative evaluation of set-level techniques in predictive classification of gene expression samples

Jul 13, 2012·BMC Bioinformatics·Matěj HolecJakub Tolar

THINK Back: KNowledge-based Interpretation of High Throughput data

May 2, 2012·BMC Bioinformatics·Fernando FarfánHosagrahar V Jagadish

Gene set analysis using variance component tests

Jun 29, 2013·BMC Bioinformatics·Yen-Tsung Huang, Xihong Lin

Linear combination test for gene set analysis of a continuous phenotype

Jul 3, 2013·BMC Bioinformatics·Irina DinuSaumyadipta Pyne

Pathway-PDT: a flexible pathway analysis tool for nuclear families

Sep 7, 2013·BMC Bioinformatics·Yo Son ParkRen-Hua Chung

GSVA: gene set variation analysis for microarray and RNA-seq data

Jan 18, 2013·BMC Bioinformatics·Sonja HänzelmannJustin Guinney

Improving gene set analysis of microarray data by SAM-GS

Jul 7, 2007·BMC Bioinformatics·Irina DinuYutaka Yasui

ProbCD: enrichment analysis accounting for categorization uncertainty

Oct 16, 2007·BMC Bioinformatics·Ricardo Z N Vêncio, Ilya Shmulevich

Comparative evaluation of gene-set analysis methods

Nov 9, 2007·BMC Bioinformatics·Qi LiuYutaka Yasui

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'

Jan 19, 2008·BMC Bioinformatics·Alexandre KuhnMauro Delorenzi

Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models

Jun 26, 2008·BMC Bioinformatics·Dawei LiuXihong Lin

Testing gene set enrichment for subset of genes: Sub-GSE

Sep 4, 2008·BMC Bioinformatics·Xiting Yan, Fengzhu Sun

Gene set analyses for interpreting microarray experiments on prokaryotic organisms

Nov 7, 2008·BMC Bioinformatics·Nathan TintleRonald C Taylor

Gene set enrichment analysis for non-monotone association and multiple experimental categories

Nov 19, 2008·BMC Bioinformatics·Rongheng LinLeping Li

Microarray-based gene set analysis: a comparison of current methods

Nov 29, 2008·BMC Bioinformatics·Sarah Song, Michael A Black

Building pathway clusters from Random Forests classification using class votes

Feb 8, 2008·BMC Bioinformatics·Herbert Pang, Hongyu Zhao

Gene set internal coherence in the context of functional profiling

Apr 29, 2009·BMC Genomics·David MontanerJoaquín Dopazo

A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets

Jan 17, 2009·BMC Genomics·Chien-Yi TungChi-Hung Lin

Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development

Jan 13, 2010·BMC Genomics·Wen HuangHasan Khatib

Heading down the wrong pathway: on the influence of correlation within gene sets

Oct 20, 2010·BMC Genomics·Daniel M GattiFred A Wright

Chipster: user-friendly analysis software for microarray and other high-throughput data

Oct 18, 2011·BMC Genomics·M Aleksi KallioEija I Korpelainen

Improving gene expression data interpretation by finding latent factors that co-regulate gene modules with clinical factors

Nov 18, 2011·BMC Genomics·Tianwei Yu, Yun Bai

Can subtle changes in gene expression be consistently detected with different microarray platforms?

Mar 12, 2008·BMC Genomics·Paola PedottiRenée X de Menezes

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

Jun 27, 2008·BMC Genomics·Seraya MaoucheFrançois Cambien

In vivo rescue of alveolar macrophages from SP-A knockout mice with exogenous SP-A nearly restores a wild type intracellular proteome; actin involvement

Nov 1, 2011·Proteome Science·David S PhelpsJoanna Floros

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

Dec 12, 2012·Biology Direct·Frank Emmert-StreibRicardo de Matos Simoes

PathNet: a tool for pathway analysis using topological information

Sep 26, 2012·Source Code for Biology and Medicine·Bhaskar DuttaJaques Reifman

Gene regulatory networks in lactation: identification of global principles using bioinformatics

Nov 28, 2007·BMC Systems Biology·Danielle G LemayJ Bruce German

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes

Jun 8, 2012·BMC Systems Biology·Zuguang GuJin Wang

Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer

Jan 11, 2013·BMC Systems Biology·Peilin JiaZhongming Zhao

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Jul 21, 2009·BMC Proceedings·Jakob HedegaardMichael Watson

Gene set analysis methods applied to chicken microarray expression data

Jul 21, 2009·BMC Proceedings·Axel SkarmanPeter Sørensen

Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16

Dec 19, 2009·BMC Proceedings·Nathan TintleAirat Bekmetjev

Does pathway analysis make it easier for common variants to tag rare ones?

Mar 1, 2012·BMC Proceedings·Hae-Won UhJeanine J Houwing-Duistermaat

Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis

May 13, 2009·BMC Medical Genomics·Erik F HensenCees J Cornelisse

Pathway analysis comparison using Crohn's disease genome wide association studies

Jun 30, 2010·BMC Medical Genomics·David BallardHongyu Zhao

A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression

May 10, 2011·BMC Medical Genomics·Eva AllozaJoaquín Dopazo

Mining SOM expression portraits: feature selection and integrating concepts of molecular function

Oct 10, 2012·BioData Mining·Henry WirthHans Binder

Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

Apr 28, 2009·Genome Biology·Reuben ThomasChristopher J Portier

Patient-oriented gene set analysis for cancer mutation data

Nov 26, 2010·Genome Biology·Simina M BocaGiovanni Parmigiani

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging

Feb 5, 2010·Genome Biology·Kristen FortneyIgor Jurisica

Identification of functional modules that correlate with phenotypic difference: the influence of network topology

Mar 2, 2010·Genome Biology·Jui-Hung HungCharles DeLisi

Pathway analysis of expression data: deciphering functional building blocks of complex diseases

Jun 4, 2011·PLoS Computational Biology·Frank Emmert-Streib, Galina Glazko

Ten years of pathway analysis: current approaches and outstanding challenges

Mar 3, 2012·PLoS Computational Biology·Purvesh KhatriAtul J Butte

Chapter 8: Biological knowledge assembly and interpretation

Jan 10, 2013·PLoS Computational Biology·Ju Han Kim

Differential expression analysis for pathways

Mar 22, 2013·PLoS Computational Biology·Winston A HaynesEugene Kolker

Finding novel molecular connections between developmental processes and disease

May 31, 2014·PLoS Computational Biology·Jisoo ParkDonna K Slonim

CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis

Aug 15, 2009·PLoS Genetics·Ernst AichingerClaudia Köhler

Pathways-driven sparse regression identifies pathways and genes associated with high-density lipoprotein cholesterol in two Asian cohorts

Nov 28, 2013·PLoS Genetics·Matt SilverGiovanni Montana

Integrated pathway-based approach identifies association between genomic regions at CTCF and CACNB2 and schizophrenia

Jun 6, 2014·PLoS Genetics·Dilafruz JuraevaBenedikt Brors

Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy

Oct 7, 2008·PloS One·Ki-Hong JungPamela C Ronald

Assessing statistical significance in microarray experiments using the distance between microarrays

Jun 17, 2009·PloS One·Douglas HaydenInflammation and the Host Response to Injury Investigators

A systems biology-based gene expression classifier of glioblastoma predicts survival with solid tumors

Jul 18, 2009·PloS One·Jing ZhangSonya Wei Song

Identifying gene interaction enrichment for gene expression data

Dec 4, 2009·PloS One·Jigang ZhangHong-Wen Deng

Multidimensional gene set analysis of genomic data

May 4, 2010·PloS One·David Montaner, Joaquín Dopazo

Prediction and testing of biological networks underlying intestinal cancer

Sep 9, 2010·PloS One·Vishal N PatelMark R Chance

Self-contained gene-set analysis of expression data: an evaluation of existing and novel methods

Sep 24, 2010·PloS One·Brooke L FridleyJoanna M Biernacka

Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties

Mar 17, 2011·PloS One·Pablo Minguez, Joaquín Dopazo

A systems biology-based classifier for hepatocellular carcinoma diagnosis

Aug 11, 2011·PloS One·Yanqiong ZhangFuchu He

Uniform approximation is more appropriate for Wilcoxon Rank-Sum Test in gene set analysis

Feb 22, 2012·PloS One·Zhide FangXiangqin Cui

pcaGoPromoter--an R package for biological and regulatory interpretation of principal components in genome-wide gene expression data

Mar 3, 2012·PloS One·Morten HansenJørgen Olsen

Assessment method for a power analysis to identify differentially expressed pathways

May 26, 2012·PloS One·Shailesh Tripathi, Frank Emmert-Streib

Detection of simultaneous group effects in microRNA expression and related target gene sets

Jun 23, 2012·PloS One·Stephan ArtmannTim Beißbarth

Comparison of methods for competitive tests of pathway analysis

Aug 4, 2012·PloS One·Marina EvangelouFrank Dudbridge

Identifying the genetic variation of gene expression using gene sets: application of novel gene Set eQTL approach to PharmGKB and KEGG

Aug 21, 2012·PloS One·Ryan AboBrooke L Fridley

Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules

Oct 23, 2013·PloS One·Quan WangZhongming Zhao

A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity

Nov 22, 2013·PloS One·Adi L TarcaRoberto Romero

Transcriptome analysis reveals differential splicing events in IPF lung tissue

Mar 22, 2014·PloS One·Tracy NanceStephen B Montgomery

The core mouse response to infection by neospora caninum defined by gene set enrichment analyses

Sep 27, 2012·Bioinformatics and Biology Insights·John EllisStephen Bush

timeClip: pathway analysis for time course data without replicates

Aug 1, 2014·BMC Bioinformatics·Paolo MartiniChiara Romualdi

Sporadic early-onset colorectal cancer is a specific sub-type of cancer: a morphological, molecular and genetics study

Aug 2, 2014·PloS One·Sylvain KirzinJanick Selves

Physical activity and prostate gene expression in men with low-risk prostate cancer

Feb 8, 2014·Cancer Causes & Control : CCC·Mark Jesus M MagbanuaJune M Chan

Integrative gene set analysis: application to platinum pharmacogenomics

Nov 10, 2013·Omics : a Journal of Integrative Biology·Brooke L FridleyLiewei Wang

Finding consistent disease subnetworks using PFSNet

Dec 3, 2013·Bioinformatics·Kevin Lim, Limsoon Wong

Two novel pathway analysis methods based on a hierarchical model

Oct 15, 2013·Bioinformatics·Marina EvangelouLorenz Wernisch

Tubular atrophy and low netrin-1 gene expression are associated with delayed kidney allograft function

Oct 5, 2013·Transplantation·Mariana WohlfahrtovaOndrej Viklicky

Gene-based GWAS and biological pathway analysis of the resilience of executive functioning

Sep 28, 2013·Brain Imaging and Behavior·Shubhabrata MukherjeeAlzheimer’s Disease Neuroimaging Initiative

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway

Oct 30, 2013·Bioinformatics·Pengyi YangYee Hwa Yang

Breaking free from the chains of pathway annotation: de novo pathway discovery for the analysis of disease processes

Dec 12, 2012·Pharmacogenomics·Benjamin Lehne, Thomas Schlitt

Integrative gene set analysis of multi-platform data with sample heterogeneity

Feb 4, 2014·Bioinformatics·Jun Hu, Jung-Ying Tzeng

Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets

Dec 3, 2013·Bioinformatics·Yasir RahmatallahGalina Glazko

Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle

Mar 29, 2014·BMC Genomics·Aideen P KilleenSinead M Waters

Characterizing human stem cell-derived sensory neurons at the single-cell level reveals their ion channel expression and utility in pain research

May 17, 2014·Molecular Therapy : the Journal of the American Society of Gene Therapy·Gareth T YoungEdward B Stevens

Human longevity and variation in DNA damage response and repair: study of the contribution of sub-processes using competitive gene-set analysis

Feb 13, 2014·European Journal of Human Genetics : EJHG·Birgit DebrabantLene Christiansen

SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing

Feb 19, 2014·Bioinformatics·Xi Wang, Murray J Cairns

Gene set analysis methods: statistical models and methodological differences

Feb 16, 2013·Briefings in Bioinformatics·Henryk Maciejewski

Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways

Nov 25, 2011·Age·Joris DeelenMarian Beekman

Gene set analysis: limitations in popular existing methods and proposed improvements

Jun 7, 2014·Bioinformatics·Pashupati P MishraLiisa Holm

The multivariate nonparametric methods for identifying gene sets with differential expression

Sep 10, 2014·Gene·Soheila KhodakarimHamid AlaviMajd

Scientific research in the age of omics: the good, the bad, and the sloppy

Oct 6, 2012·Journal of the American Medical Informatics Association : JAMIA·Daniela M Witten, Robert Tibshirani

Multivariate inference of pathway activity in host immunity and response to therapeutics

Aug 26, 2014·Nucleic Acids Research·Gautam GoelRamnik J Xavier

Transcriptomic profiles of high and low antibody responders to smallpox vaccine

Apr 19, 2013·Genes and Immunity·Richard B KennedyGregory A Poland

Analysing biological pathways in genome-wide association studies

Nov 19, 2010·Nature Reviews. Genetics·Kai WangHakon Hakonarson

Functional genomics and networks: new approaches in the extraction of complex gene modules

Feb 4, 2010·Expert Review of Proteomics·Pablo Minguez, Joaquín Dopazo

JAG: A Computational Tool to Evaluate the Role of Gene-Sets in Complex Traits

Jun 26, 2015·Genes·Esther S LipsDanielle Posthuma

Validation and integration of gene-expression signatures in cancer

Mar 28, 2008·Expert Review of Molecular Diagnostics·Abhijit MazumderYixin Wang

Integrating fragmented software applications into holistic solutions: focus on drug discovery

Apr 1, 2011·Expert Opinion on Drug Discovery·Anton Yuryev

Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data

Jan 22, 2013·Expert Opinion on Medical Diagnostics·Jason E McDermottKarin D Rodland

GiANT: gene set uncertainty in enrichment analysis

Feb 3, 2016·Bioinformatics·Florian SchmidHans A Kestler

Increased prediction accuracy using a genomic feature model including prior information on quantitative trait locus regions in purebred Danish Duroc pigs

Jan 6, 2016·BMC Genetics·Pernille SarupPeter Sørensen

Understanding disease mechanisms with models of signaling pathway activities

Oct 26, 2014·BMC Systems Biology·Patricia Sebastian-LeonJoaquín Dopazo

Gene set analysis using sufficient dimension reduction

Feb 8, 2016·BMC Bioinformatics·Huey-Miin Hsueh, Chen-An Tsai

Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood

Feb 19, 2016·Epigenetics : Official Journal of the DNA Methylation Society·Yen-Tsung HuangKarl T Kelsey

A novel bi-level meta-analysis approach: applied to biological pathway analysis

Oct 17, 2015·Bioinformatics·Tin NguyenSorin Drăghici

Methylomic analysis of salivary DNA in childhood ADHD identifies altered DNA methylation in VIPR2

Aug 26, 2015·Journal of Child Psychology and Psychiatry, and Allied Disciplines·Beth WilmotJoel T Nigg

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

Jan 23, 2016·BMC Bioinformatics·Ludwig GeistlingerRalf Zimmer

Adaptive Set-Based Methods for Association Testing

Dec 29, 2015·Genetic Epidemiology·Yu-Chen SuJuan Pablo Lewinger

Pathway analysis of genomic data: concepts, methods, and prospects for future development

Apr 7, 2012·Trends in Genetics : TIG·Vijay K RamananAndrew J Saykin

Pathway Analysis: State of the Art

Jan 7, 2016·Frontiers in Physiology·Miguel A García-CamposEnrique Hernández-Lemus

A Powerful Pathway-Based Adaptive Test for Genetic Association with Common or Rare Variants

Jun 30, 2015·American Journal of Human Genetics·Wei PanPeng Wei

Matrix metalloproteinase 1 in pre-eclampsia and fetal growth restriction: reduced gene expression in decidual tissue and protein expression in extravillous trophoblasts

May 11, 2010·Placenta·I A LianR Austgulen

MicroRNA expression is altered in lateral septum across reproductive stages

Nov 25, 2015·Neuroscience·M C SaulS C Gammie

Metabolomics for phytochemical discovery: development of statistical approaches using a cranberry model system

Mar 10, 2015·Journal of Natural Products·Christina E TuriPaula N Brown

Comparative evaluation of gene set analysis approaches for RNA-Seq data

Dec 6, 2014·BMC Bioinformatics·Yasir RahmatallahGalina Glazko

A shortcut for multiple testing on the directed acyclic graph of gene ontology

Nov 5, 2014·BMC Bioinformatics·Garrett SaundersS Clay Isom

Know your limits: assumptions, constraints and interpretation in systems biology

May 15, 2009·Biochimica Et Biophysica Acta·Garth R IlsleyRolf Apweiler

Formulating and testing hypotheses in functional genomics

Sep 16, 2008·Artificial Intelligence in Medicine·Joaquín Dopazo

Gene module level analysis: identification to networks and dynamics

Aug 30, 2008·Current Opinion in Biotechnology·Xuewei WangChristina Chan

Interpretation of genomic data: questions and answers

Jun 28, 2008·Seminars in Hematology·Richard Simon

Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis

Nov 29, 2014·Proteomics·Kris LaukensWim Vanden Berghe

Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study

Oct 10, 2013·Scientific Reports·Brooke L FridleyAnn L Oberg

Inclusion of a priori information in genome-wide association analysis

Nov 20, 2009·Genetic Epidemiology·Nathan TintleHeike Bickeböller

Effects of Systemically Administered Hydrocortisone on the Human Immunome

Mar 15, 2016·Scientific Reports·Matthew J OlnesCHI Consortium

Mining transcriptome data for function-trait relationship of hyper productivity of recombinant antibody

Jan 10, 2009·Biotechnology and Bioengineering·Salim CharaniyaWei-Shou Hu

A decision-theory approach to interpretable set analysis for high-dimensional data

Aug 6, 2013·Biometrics·Simina M BocaGiovanni Parmigiani

A SATS algorithm for jointly identifying multiple differentially expressed gene sets

Apr 8, 2011·Statistics in Medicine·Tae Young Yang

CD8-alpha T-cell infiltration in human papillomavirus-related oropharyngeal carcinoma correlates with improved patient prognosis

Aug 15, 2012·International Journal of Cancer. Journal International Du Cancer·Alain C JungJoseph Abecassis

Pathway-based analysis for genome-wide association studies using supervised principal components

Sep 16, 2010·Genetic Epidemiology·Xi ChenXiaofeng Zhu

Differential methylation tests of regulatory regions

Mar 17, 2016·Statistical Applications in Genetics and Molecular Biology·Duchwan RyuRobert H Podolsky

The transcriptional response to chronic stress and glucocorticoid receptor blockade in the hippocampal dentate gyrus

Dec 25, 2010·Hippocampus·Nicole A DatsonPaul J Lucassen

Secondary analysis of publicly available data reveals superoxide and oxygen radical pathways are enriched for associations between type 2 diabetes and low-frequency variants

Aug 15, 2013·Annals of Human Genetics·Mojgan YazdanpanahJinko Graham

DINGO: differential network analysis in genomics

Jul 8, 2015·Bioinformatics·Min Jin HaKim-Anh Do

Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies

Dec 14, 2011·Genetic Epidemiology·Daniel J SchaidRichard M Weinshilboum

Global analysis of methylation profiles from high resolution CpG data

Dec 30, 2014·Genetic Epidemiology·Ni ZhaoMichael C Wu

A Bayesian extension of the hypergeometric test for functional enrichment analysis

Dec 11, 2013·Biometrics·Jing Cao, Song Zhang

Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of hepatic tissue in cattle

Mar 18, 2016·BMC Genomics·Kate KeoghSinead M Waters

Human variation in alcohol response is influenced by variation in neuronal signaling genes

Mar 6, 2010·Alcoholism, Clinical and Experimental Research·Geoff JoslynRaymond L White

Rotation gene set testing for longitudinal expression data

Sep 23, 2014·Biometrical Journal. Biometrische Zeitschrift·Guro DørumSolve Saebø

Gene, region and pathway level analyses in whole-genome studies

Dec 17, 2009·Genetic Epidemiology·Omar De la CruzDan L Nicolae

The role of empirical Bayes methodology as a leading principle in modern medical statistics

Sep 11, 2014·Biometrical Journal. Biometrische Zeitschrift·Hans C van Houwelingen

Power calculation for overall hypothesis testing with high-dimensional commensurate outcomes

Oct 15, 2013·Statistics in Medicine·Yueh-Yun ChiKeith E Muller

Empirical evidence of the applicability of functional clustering through gene expression classification

Feb 1, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Milos Krejník, Jirí Kléma

Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls

Oct 9, 2015·Briefings in Bioinformatics·Rosa J Meijer, Jelle Goeman

Pathway analysis for RNA-Seq data using a score-based approach

Aug 12, 2015·Biometrics·Yi-Hui Zhou

htsint: a Python library for sequencing pipelines that combines data through gene set generation

Sep 25, 2015·BMC Bioinformatics·Adam J RichardsCamille Bonneaud

Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential

Sep 24, 2015·BMC Systems Biology·Claudia CavaIsabella Castiglioni

Lessons learned in the analysis of high-dimensional data in vaccinomics

May 10, 2015·Vaccine·Ann L ObergGregory A Poland

High-throughput data analysis and data integration for vaccine trials

May 16, 2015·Vaccine·January WeinerJeroen Maertzdorf

Integrative analysis of micro-RNA, gene expression, and survival of glioblastoma multiforme

Dec 30, 2014·Genetic Epidemiology·Yen-Tsung HuangChien-Ling Lin

Comparison of univariate and multivariate gene set analysis in acute lymphoblastic leukemia

May 18, 2013·Asian Pacific Journal of Cancer Prevention : APJCP·Khodakarim SoheilaTajalli Vahide

Gene set analysis: A step-by-step guide

Jun 11, 2015·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Michael A Mooney, Beth Wilmot

Linking Phenotypes and Modes of Action Through High-Content Screen Fingerprints

Aug 11, 2015·Assay and Drug Development Technologies·Felix ReisenPaul Selzer

Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates

Sep 1, 2015·BMC Bioinformatics·Jacob A TurnerDerek M Blankenship

Commentary: The seven plagues of epigenetic epidemiology

Jan 25, 2012·International Journal of Epidemiology·Bastiaan T Heijmans, Jonathan Mill

Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data

Apr 14, 2012·Genomics·Laila M PoissonDebashis Ghosh

Random forests-based differential analysis of gene sets for gene expression data

Dec 12, 2012·Gene·Huey-Miin HsuehChen-An Tsai

Increased endoplasmic reticulum stress in decidual tissue from pregnancies complicated by fetal growth restriction with and without pre-eclampsia

Sep 13, 2011·Placenta·I A LianR Austgulen

Capturing changes in gene expression dynamics by gene set differential coordination analysis

Oct 6, 2011·Genomics·Tianwei Yu, Yun Bai

Gene set analysis of genome-wide association studies: methodological issues and perspectives

May 14, 2011·Genomics·Lily WangZhongming Zhao

Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival

Jun 15, 2015·Bioinformatics·A Grant SchisslerYves A Lussier

Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs

Jul 29, 2015·BMC Genomics·Carlos Villacorta-MartinMichele Zaccai

Partitioning of genomic variance reveals biological pathways associated with udder health and milk production traits in dairy cattle

Jul 15, 2015·Genetics, Selection, Evolution : GSE·Stefan M EdwardsPeter Sørensen

Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients

Jul 11, 2015·Nature Communications·Mark SausenVictor E Velculescu

Gene Expression Associated with Early and Late Chronotypes in Drosophila melanogaster

Jun 23, 2015·Frontiers in Neurology·Mirko PegoraroEran Tauber

Genomic investigation of etiologic heterogeneity: methodologic challenges

Dec 24, 2014·BMC Medical Research Methodology·Colin B BeggJames J Hsieh

A glance at the applications of Singular Spectrum Analysis in gene expression data

Apr 15, 2016·Biomolecular Detection and Quantification·Hossein Hassani, Zara Ghodsi

DECODE: an integrated differential co-expression and differential expression analysis of gene expression data

Jun 1, 2015·BMC Bioinformatics·Thomas W H LuiBenjamin Y M Yung

dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis

Jan 23, 2015·Bioinformatics·Chao YeJun S Liu

Moment based gene set tests

May 1, 2015·BMC Bioinformatics·Jessica L Larson, Art B Owen

Neonatal DNA methylation patterns associate with gestational age

Dec 6, 2011·Epigenetics : Official Journal of the DNA Methylation Society·James W SchroederA K Smith

Assessment of gene set analysis methods based on microarray data

Sep 10, 2013·Gene·Hamid Alavi-MajdMaryam Heydarpour-Meymeh

Effect of prenatal arsenic exposure on DNA methylation and leukocyte subpopulations in cord blood

Feb 15, 2014·Epigenetics : Official Journal of the DNA Methylation Society·Molly L KileDavid C Christiani

A novel gene expression index (GEI) with software support for comparing microarray gene signatures

Oct 13, 2012·Gene·Haseeb Ahmad Khan

Multiset Statistics for Gene Set Analysis

Apr 29, 2015·Annual Review of Statistics and Its Application·Michael A Newton, Zhishi Wang

Principal component gene set enrichment (PCGSE)

Aug 25, 2015·BioData Mining·H Robert FrostJason H Moore

Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress

Feb 13, 2014·Methods : a Companion to Methods in Enzymology·Kyuri JoSun Kim

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data

Oct 18, 2014·Bioinformatics·Shining MaRui Jiang

uGPA: unified Gene Pathway Analyzer package for high-throughput genome-wide screening data provides mechanistic overview on human diseases

Jan 1, 2015·Clinica Chimica Acta; International Journal of Clinical Chemistry·Daniel W H Ho, Irene O L Ng

Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets

Sep 4, 2014·Bioinformatics·Yotsawat PomyenHector C Keun

Discovering main genetic interactions with LABNet LAsso-based network inference

Nov 5, 2014·PloS One·Francesco Gadaleta, Kristel Van Steen

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data

Jun 26, 2015·PLoS Computational Biology·Boris P HejblumRodolphe Thiébaut

MeDiA: Mean Distance Association and Its Applications in Nonlinear Gene Set Analysis

Apr 29, 2015·PloS One·Hesen PengTianwei Yu

Network and Pathway-Based Analyses of Genes Associated with Parkinson's Disease

Jun 29, 2016·Molecular Neurobiology·Yanshi HuJu Wang

Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome

Jul 1, 2016·Scientific Reports·Heath A MacMillanBrent J Sinclair

A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations

Jul 1, 2016·PLoS Genetics·Han ZhangKai Yu

A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer

Sep 19, 2014·PLoS Computational Biology·Sijia HuangLana X Garmire

GSA-Lightning: ultra-fast permutation-based gene set analysis

Jun 15, 2016·Bioinformatics·Billy Heung Wing Chang, Weidong Tian

Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases

Sep 14, 2016·PloS One·Peng-Lin LinRen-Hua Chung

Self-Contained Statistical Analysis of Gene Sets

Oct 7, 2016·PloS One·David J TorresChristopher Johnson

Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research

Oct 8, 2016·Scientific Reports·Christopher S HughesGregg B Morin

Monte Carlo simulation of OLS and linear mixed model inference of phenotypic effects on gene expression

Oct 21, 2016·PeerJ·Jeffrey A Walker

Comparative study on gene set and pathway topology-based enrichment methods

Oct 23, 2015·BMC Bioinformatics·Michaela BayerlováTim Beißbarth

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data

Oct 31, 2015·BMC Bioinformatics·Ivana Ihnatova, Eva Budinska

Spectral gene set enrichment (SGSE)

Apr 17, 2015·BMC Bioinformatics·H Robert FrostJason H Moore

RichMind: A Tool for Improved Inference from Large-Scale Neuroimaging Results

Jul 28, 2016·PloS One·Adi Maron-KatzRon Shamir

Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle

Feb 13, 2016·PloS One·Kate KeoghSinead M Waters

Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates

Nov 10, 2016·PloS One·Sora YoonDougu Nam

Genome-wide analysis of blood gene expression in migraine implicates immune-inflammatory pathways

Jan 7, 2017·Cephalalgia : an International Journal of Headache·Zachary F GerringDale R Nyholt

Combining multiple tools outperforms individual methods in gene set enrichment analyses

Oct 4, 2016·Bioinformatics·Monther AlhamdooshMatthew E Ritchie

The limitations of simple gene set enrichment analysis assuming gene independence

Oct 17, 2012·Statistical Methods in Medical Research·Pablo TamayoJill P Mesirov

Testing for differentially expressed genetic pathways with single-subject N-of-1 data in the presence of inter-gene correlation

May 30, 2017·Statistical Methods in Medical Research·A Grant SchisslerYves A Lussier

Effect of the absolute statistic on gene-sampling gene-set analysis methods

Mar 4, 2015·Statistical Methods in Medical Research·Dougu Nam

Gene ORGANizer: linking genes to the organs they affect

Apr 27, 2017·Nucleic Acids Research·David GokhmanLiran Carmel

Variance component score test for time-course gene set analysis of longitudinal RNA-seq data

Mar 24, 2017·Biostatistics·Denis Agniel, Boris P Hejblum

Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia

Feb 8, 2018·Genetic Epidemiology·Chong Wu, Wei Pan

Portraying the Expression Landscapes of B-CellLymphoma-Intuitive Detection of Outlier Samples and of Molecular Subtypes

Jan 1, 2013·Biology·Lydia HoppHenry Wirth

Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine jejunal epithelium

Mar 20, 2018·PloS One·Kate KeoghDavid A Kenny

Distance-correlation based gene set analysis in longitudinal studies.

Feb 6, 2018·Statistical Applications in Genetics and Molecular Biology·Jiehuan SunHongyu Zhao

Computation and application of tissue-specific gene set weights

Apr 17, 2018·Bioinformatics·H Robert Frost

Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology

Nov 11, 2017·BMC Genomics·Daragh MatthewsSinead M Waters

Analysis and correction of crosstalk effects in pathway analysis

Aug 13, 2013·Genome Research·Michele DonatoSorin Drăghici

Alcohol consumption and breast tumor gene expression

Sep 14, 2017·Breast Cancer Research : BCR·Jun WangSusan E Hankinson

Overlapping Group Logistic Regression with Applications to Genetic Pathway Selection

Sep 30, 2016·Cancer Informatics·Yaohui Zeng, Patrick Breheny

Evaluating gene set enrichment analysis via a hybrid data model

Feb 22, 2014·Cancer Informatics·Jianping HuaEdward R Dougherty

Plasma metabolite abundances are associated with urinary enterolactone excretion in healthy participants on controlled diets

Aug 16, 2017·Food & Function·Fayth L MilesJohanna W Lampe

Learning dysregulated pathways in cancers from differential variability analysis

Nov 14, 2014·Cancer Informatics·Bahman AfsariElana J Fertig

Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes

Dec 23, 2017·Briefings in Bioinformatics·Francesca VitaliYves A Lussier

Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage

May 24, 2007·Human Molecular Genetics·Alexandre KuhnRuth Luthi-Carter

A Method to Detect Differential Gene Expression in Cross-Species Hybridization Experiments at Gene and Probe Level

Mar 5, 2010·Biomedical Informatics Insights·Ying ChenAnu Chakicherla

Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells

Dec 24, 2017·Skeletal Muscle·Natalia PietrosemoliShahragim Tajbakhsh

Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome

Jul 20, 2018·PloS One·Roberta RovitoAnn C T M Vossen

Microprocessor-dependent processing of splice site overlapping microRNA exons does not result in changes in alternative splicing

Jun 14, 2018·RNA·Giulia PianigianiFranco Pagani

Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance

Feb 7, 2018·ELife·Daniel J FazakerleyDavid E James

A simple null model for inferences from network enrichment analysis

Nov 10, 2018·PloS One·Gustavo S Jeuken, Lukas Käll

Untargeted Plasma Metabolomics Identifies Endogenous Metabolite with Drug-like Properties in Chronic Animal Model of Multiple Sclerosis.

Nov 8, 2015·The Journal of Biological Chemistry·Laila M PoissonShailendra Giri

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

Jan 22, 2019·Nature Protocols·Jüri ReimandGary D Bader

Gene set enrichment analysis for multiple continuous phenotypes

Aug 5, 2014·BMC Bioinformatics·Xiaoming WangIrina Dinu

Statistical Approach for Gene Set Analysis with Trait Specific Quantitative Trait Loci

Feb 7, 2018·Scientific Reports·Samarendra DasShesh N Rai

Conducting gene set tests in meta-analyses of transcriptome expression data

Dec 29, 2018·Research Synthesis Methods·Robin Kosch, Klaus Jung

Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes

Mar 22, 2019·Briefings in Bioinformatics·Fabio FabrisAlex A Freitas

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)

Apr 3, 2019·PLoS Computational Biology·Hailong MengSteven H Kleinstein

Expression of socially sensitive genes: The multi-ethnic study of atherosclerosis

Apr 12, 2019·PloS One·Kristen M BrownSharon L R Kardia

Serum Metabolomic Alterations Associated with Proteinuria in CKD

Feb 9, 2019·Clinical Journal of the American Society of Nephrology : CJASN·Shengyuan LuoChronic Kidney Disease Biomarkers Consortium Investigators

A framework to identify physiological responses in microarray-based gene expression studies: selection and interpretation of biologically relevant genes

Dec 29, 2007·Physiological Genomics·Wendy RodenburgJaap Keijer

Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

Jun 6, 2019·Bioinformatics·Joanna ZylaJanuary Weiner

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Jul 3, 2019·Genes·Elisa BuchbergerNico Posnien

Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods

Jul 13, 2019·Briefings in Bioinformatics·Mitra EbrahimpoorJelle Goeman

Proteome-transcriptome alignment of molecular portraits achieved by self-contained gene set analysis: Consensus colon cancer subtypes case study

Aug 23, 2019·PloS One·Galina GlazkoYasir Rahmatallah

Estimation strategies for reacting to the identification of an association between the genome and adverse drug reactions

Dec 31, 2010·Journal of Biopharmaceutical Statistics·Helene ThygesenClive Bowman

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias

Nov 13, 2019·PLoS Biology·Shir MandelboumRan Elkon

Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles

Jan 1, 2020·Nucleic Acids Research·Andrea LauriaMatteo Cereda

A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales

Oct 2, 2019·Proceedings of the National Academy of Sciences of the United States of America·Amir MarcovitzGill Bejerano

Toward a gold standard for benchmarking gene set enrichment analysis.

Feb 7, 2020·Briefings in Bioinformatics·Ludwig GeistlingerLevi Waldron

Characterizing the Macrophage Response to Immunomodulatory Biomaterials Through Gene Set Analyses

Feb 20, 2020·Tissue Engineering. Part C, Methods·Sarah E BlattKara L Spiller

STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

Apr 24, 2020·Molecular Systems Biology·Monika OberhuberLukas Kenner

Assessing the clinical utility of genomic expression data across human cancers

Jun 21, 2016·Oncotarget·Xinsen XuChang Liu

Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification

Jun 9, 2016·Oncotarget·Salvatore AlaimoAlfredo Pulvirenti

Nuclear magnetic resonance-based tissue metabolomic analysis clarifies molecular mechanisms of gastric carcinogenesis

May 6, 2020·Cancer Science·Jinping GuDonghai Lin

Four cypermethrin isomers induced stereoselective metabolism in H295R cells

Jun 24, 2020·Chirality·Chenyang JiMeirong Zhao

Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study

Jun 26, 2020·Bioscience Reports·Pashupati P MishraTerho Lehtimäki

Gene set analysis methods for the functional interpretation of non-mRNA data-Genomic range and ncRNA data

Oct 16, 2019·Briefings in Bioinformatics·Antonio Mora

Pathway-Structured Predictive Model for Cancer Survival Prediction: A Two-Stage Approach

Jan 5, 2017·Genetics·Xinyan ZhangNengjun Yi

The application of omics-based human liver platforms for investigating the mechanism of drug-induced hepatotoxicity in vitro

Oct 6, 2019·Archives of Toxicology·Jian JiangTheo M C M de Kok

Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes

Jun 19, 2016·Genetics·Palle Duun RohdePeter Sørensen

Unsupervised gene set testing based on random matrix theory

Nov 5, 2016·BMC Bioinformatics·H Robert Frost, Christopher I Amos

Robust multi-group gene set analysis with few replicates

Dec 13, 2016·BMC Bioinformatics·Pashupati P MishraPetri Törönen

Integrated genomic analysis of biological gene sets with applications in lung cancer prognosis

Jul 13, 2017·BMC Bioinformatics·Su Hee Chu, Yen-Tsung Huang

Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma

Apr 19, 2018·PeerJ·Chaoxing LiValentin Dinu

Identification of Discriminating Metabolic Pathways and Metabolites in Human PBMCs Stimulated by Various Pathogenic Agents

Mar 15, 2018·Frontiers in Physiology·Xiang ZhangAlbert K Groen

CEA: Combination-based gene set functional enrichment analysis

Sep 1, 2018·Scientific Reports·Duanchen SunLing-Yun Wu

Integrating Selection Mapping With Genetic Mapping and Functional Genomics

Jan 9, 2019·Frontiers in Genetics·Martin Johnsson

Transcriptomics and differential gene expression in Whitmania pigra (Annelida: Clitellata: Hirudinida: Hirudinidae): Contrasting feeding and fasting modes

Apr 30, 2019·Ecology and Evolution·Muhammad Salabat KhanSheng-Quan Xu

A Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes

May 31, 2019·Frontiers in Genetics·A Grant SchisslerYves A Lussier

A Bayesian hierarchical variable selection prior for pathway-based GWAS using summary statistics

Nov 29, 2019·Statistics in Medicine·Yi YangLin Zhang

Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring

Jul 8, 2020·Nucleic Acids Research·H Robert Frost

A biological evaluation of six gene set analysis methods for identification of differentially expressed pathways in microarray data

Jan 1, 2008·Cancer Informatics·Irina DinuYutaka Yasui

Protein kinase C epsilon and genetic networks in osteosarcoma metastasis

Nov 13, 2013·Cancers·Atta GoudarziIrene L Andrulis

Gene expression elucidates functional impact of polygenic risk for schizophrenia

Oct 28, 2016·Nature Neuroscience·Menachem FromerPamela Sklar

Identifying Significantly Impacted Pathways and Putative Mechanisms with iPathwayGuide

Jun 28, 2017·Current Protocols in Bioinformatics·Sidra Ahsan, Sorin Drăghici

Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster

May 27, 2017·Scientific Reports·Izel Fourie SørensenPeter Sørensen

Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine ruminal epithelium

May 26, 2017·PloS One·Kate KeoghDavid A Kenny

Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2

Mar 22, 2018·Nucleic Acids Research·Sora YoonDougu Nam

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

Jan 11, 2019·BMC Genomics·Hannah VoicToru Nyunoya

Association between DNA methylation in obesity-related genes and body mass index percentile in adolescents

Feb 16, 2019·Scientific Reports·Fan HeDuanping Liao

Incorporating Pathway Information into Feature Selection towards Better Performed Gene Signatures

May 11, 2019·BioMed Research International·Suyan TianBing Wang

Extensive metabolic remodeling after limiting mitochondrial lipid burden is consistent with an improved metabolic health profile

May 18, 2019·The Journal of Biological Chemistry·Sujoy GhoshRobert C Noland

Transcriptional Network Analysis Implicates Altered Hepatic Immune Function in NASH development and resolution

Nov 9, 2019·Nature Metabolism·Joel T HaasDavid Dombrowicz

Gene-expression profiles of abdominal perivascular adipose tissue distinguish aortic occlusive from stenotic atherosclerotic lesions and denote different pathogenetic pathways

Apr 12, 2020·Scientific Reports·Luca PiacentiniJosé Pablo Werba

Network and pathway-based analyses of genes associated with osteoporosis

Feb 22, 2020·Medicine·Huijie GuXiaofan Yin

Does Protein Glycation Impact on the Drought-Related Changes in Metabolism and Nutritional Properties of Mature Pea (Pisum sativum L.) Seeds?

Jan 19, 2020·International Journal of Molecular Sciences·Tatiana LeonovaAndrej Frolov

Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions

Feb 14, 2020·NAR Genomics and Bioinformatics·Christopher T LeeMaureen A Sartor

Gene Set Analysis: Challenges, Opportunities, and Future Research

Jul 23, 2020·Frontiers in Genetics·Farhad MalekiAnthony J Kusalik

Multivariate genomic scan implicates novel loci and haem metabolism in human ageing

Jul 18, 2020·Nature Communications·Paul R H J TimmersJoris Deelen

Analysis of the real EADGENE data set: multivariate approaches and post analysis (open access publication)

Dec 7, 2007·Genetics, Selection, Evolution : GSE·Peter SørensenHolm Zerbe

Adaptive gene- and pathway-trait association testing with GWAS summary statistics

Dec 15, 2015·Bioinformatics·Il-Youp Kwak, Wei Pan

Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots

May 4, 2017·BMC Bioinformatics·Jochen Kruppa, Klaus Jung

Gene set selection via LASSO penalized regression (SLPR)

May 5, 2017·Nucleic Acids Research·H Robert Frost, Christopher I Amos

N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes

Jun 8, 2017·BMC Medical Genomics·Qike LiYves A Lussier

A comparison of mechanistic signaling pathway activity analysis methods

Jun 6, 2018·Briefings in Bioinformatics·Alicia AmadozJoaquín Dopazo

Transcriptome signature for dietary fructose-specific changes in rat renal cortex: A quantitative approach to physiological relevance

Aug 2, 2018·PloS One·Agustin Gonzalez-VicenteUlrich Hopfer

Metabolomics Analysis in Serum from Patients with Colorectal Polyp and Colorectal Cancer by 1 H-NMR Spectrometry

May 16, 2019·Disease Markers·Jinping GuHua Li

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data

Sep 12, 2019·F1000Research·J Javier Diaz-MejiaJohn H Morris

Exploratory Gene Ontology Analysis with Interactive Visualization

May 28, 2019·Scientific Reports·Junjie ZhuChiara Sabatti

Longitudinal linear combination test for gene set analysis

Dec 12, 2019·BMC Bioinformatics·Elham Khodayari MoezIrina Dinu

Covariance thresholding to detect differentially co-expressed genes from microarray gene expression data

Apr 28, 2020·Journal of Bioinformatics and Computational Biology·Mingyu OhHokeun Sun

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

Sep 6, 2015·Briefings in Bioinformatics·Yasir RahmatallahGalina Glazko

A DNA methylation biomarker of alcohol consumption

Nov 16, 2016·Molecular Psychiatry·C LiuD Levy

Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients

Mar 7, 2017·Medical Science Monitor : International Medical Journal of Experimental and Clinical Research·Zhengyuan XuWeiguo Wu

A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data

Jun 18, 2017·PLoS Computational Biology·En-Yu LaiKun-Pin Wu

Probabilistic prioritization of candidate pathway association with pathway score

Oct 26, 2018·BMC Bioinformatics·Shu-Ju LinChuhsing Kate Hsiao

Gene set analysis methods: a systematic comparison

Jun 9, 2018·BioData Mining·Ravi MathurAlison Motsinger-Reif

Fecal Metabolomics and Potential Biomarkers for Systemic Lupus Erythematosus

May 28, 2019·Frontiers in Immunology·Qiong ZhangYurong Qiu

Network hub-node prioritization of gene regulation with intra-network association

Mar 14, 2020·BMC Bioinformatics·Hung-Ching ChangChuhsing Kate Hsiao

A comparative study of topology-based pathway enrichment analysis methods

Nov 7, 2019·BMC Bioinformatics·Jing MaGeorge Michailidis

Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans' Gene Expression Data

Aug 8, 2020·G3 : Genes - Genomes - Genetics·Michael CaryCynthia Kenyon

Identification of Candidate Genes Associated with Charcot-Marie-Tooth Disease by Network and Pathway Analysis

Oct 9, 2020·BioMed Research International·Min ZhongJinBo Liu

Differential Gene Set Enrichment Analysis: A statistical approach to quantify the relative enrichment of two gene sets.

Jul 22, 2020·Bioinformatics·James H JolyNicholas A Graham

DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data

Dec 11, 2020·GigaScience·Lukas M SimonZhongming Zhao

Molecular classification of malignant pleural mesothelioma: identification of a poor prognosis subgroup linked to the epithelial-to-mesenchymal transition

Jan 21, 2014·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Aurélien de ReynièsDidier Jean

Pathway analysis of renal cell carcinoma genome-wide association studies identifies novel associations

Aug 1, 2020·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Mark P PurdueKai Yu

Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer

Oct 7, 2017·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kumardeep ChaudharyLana X Garmire

Concentrations of legacy and new contaminants are related to metabolite profiles in Hudson Bay polar bears

Nov 2, 2018·Environmental Research·A D MorrisJ Cosgrove

FLAGS: A Flexible and Adaptive Association Test for Gene Sets Using Summary Statistics

Jan 17, 2016·Genetics·Jianfei HuangShizhong Han

Proteome profiling of repeated drought stress reveals genotype-specific responses and memory effects in maize.

Dec 20, 2020·Plant Physiology and Biochemistry : PPB·Waltraud X SchulzeChristian Zörb

Synaptic processes and immune-related pathways implicated in Tourette syndrome.

Jan 20, 2021·Translational Psychiatry·Fotis TsetsosSamuel Zinner

Mutational landscape and evolutionary pattern of liver and brain metastasis in lung adenocarcinoma

Nov 15, 2020·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Tao JiangCaicun Zhou

CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models.

Jan 30, 2021·PLoS Computational Biology·Lillian R ThistlethwaiteAleksandar Milosavljevic

Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges

Dec 9, 2020·Entropy·Samarendra DasShesh N Rai

Metabolic impact of weight variations in Icelandic horses.

Feb 13, 2021·PeerJ·Julien DelarocqueTobias Warnken

Placental genomic risk scores and early neurodevelopmental outcomes.

Feb 10, 2021·Proceedings of the National Academy of Sciences of the United States of America·Gianluca UrsiniDaniel R Weinberger

Compare Expression Profiles for Pre-defined Gene Groups with C-REx

May 1, 2019·Peng LiuMingze He

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