gene-set
A Hierarchical Gene-Set Genetic Algorithm
... The gene-set size in the proposed approach was long at the beginning generations, which were regarded as a rough optimization ...the gene-set size becoming smaller, the local search in HGSGA ...
9
Gene set analysis controlling for length bias in RNA-seq experiments
... for gene set analysis with RNA-seq ...the gene-set-level ...the gene length bias. It works with any gene-level DE test ...significant gene sets and controls type I ...for ...
18
Finding pathway regulators: gene set approach using peak identification algorithms
... 'gene set', we consider a two-step procedure to the analysis of the Genetic Analysis Work- shop 15 (GAW15) Problem 1 data to identify regulators controlling the functional pathways in lymphoblast ...
6
A Two Sample Test for High Dimensional Data with Applications to Gene set Testing
... 4. Gene-set ...each gene does not function individually in isolation. Rather, one gene tends to work with other genes to achieve certain biological ...
33
A cross-study gene set enrichment analysis identifies critical pathways in endometriosis
... performed gene set enrichment analysis of six independent publicly available gene expression data sets to understand in depth the common biological mecha- nisms involved in ...the gene ...
9
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype
... GO: Gene ontology; GoDARTS: Genetics of Diabetes and Audit Research Tayside Study; GSEA: Gene set enrichment analysis; GWAS: Genome wide association study; HF: Heart failure; HLA: Human leukocyte ...
11
Estimating the Empirical Null Distribution of Maxmean Statistics in Gene Set Analysis
... data set, our method has fewer gene sets with unadjusted p-value < ...more gene sets after controlling for FDR. A reason is that in GSA, gene-set p-values are limited by the number ...
7
Integration of a priori gene set information into genome wide association studies
... of gene set information into ...and gene sets. The chance of a gene appearing in more than one of our final gene lists is only ...for gene sets. Although the top 100 gene ...
5
Gene set analysis methods applied to chicken microarray expression data
... the gene in the gene set ...between gene set test based on individual oligonucleotides or genes it is diffi- cult to generalize to other ...genes. Gene set tests taking GO ...
6
GSEPD: A Bioconductor Package for RNA-seq Gene Set Enrichment and Projection Display
... (gene set enrichment and projection display). GSEPD produces DE gene lists, significantly enriched gene ontology (GO) terms, and importantly their cross-product: a mapping of which genes are ...
7
Apriori Gene Set-based Microarray Analysis for Disease Classification Using Unlabeled Data
... each gene set in order to find the gene subset that response to disease or condition of interest (PCOGs set) as ...PCOGs set of the unlabeled set, we simply use the same PCOGs ...
9
A review on the effect of sulphur mustard on gene expression alterations, finding the most important molecular functions using gene set functional enrichment analysis
... on gene expression alterations caused by SM, however, there is still no integrated understanding of this ...using gene set enrichment analysis, we tried to find the most central functions that are ...
7
Importance of collection in gene set enrichment analysis of drug response in cancer cell lines
... Co-expression gene set collection based on cancer cell line ...of gene sets, we created a new collection based on a fully data- driven analysis of cancer cell ...using gene co- expression data ...
8
LnCompare: gene set feature analysis for human long non-coding RNAs.
... lncRNA gene sets. The Gene Set Feature Comparison mode tests for enrichment amongst a panel of quantitative and categorical fea- tures, spanning gene structure, evolutionary conser- vation, ...
7
Size matters: how sample size affects the reproducibility and specificity of gene set analysis
... The systematic methodology described in this paper can be successfully used to evaluate the reproducibility of results from gene set analysis methods, allowing compar- ison across methods and sample sizes. ...
12
Machine learning identifies a compact gene set for monitoring the circadian clock in human blood
... One limitation of this study is that, because not all of the datasets included individual-level information about DLMO, we had no direct measurement for the internal time of each individual’s central circadian clock. ...
11
Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection
... of gene inter- action and gene-set GWAS offers great promise in the charac- terization of the biological pathway of genetic determination of complex ...known gene (Maurano et ...each ...
14
FDR-FET: an optimizing gene set enrichment analysis method
... requires gene sets to be sufficiently large, we only examined those gene sets with sizes ...three gene sets (ie, GO:0006418, GO:0004812, and KEGG:hsa00970) are set to 20 because they all have ...
6
Principal component gene set enrichment (PCGSE)
... functional gene sets, researchers currently lack meth- ods that competitively test the association between gene sets and PCs with correct handling of inter-gene ...ponent gene set ...
18
Gene Set Enrichment Analysis using Linear Models and Diagnostics
... the gene-set defined as the 11 non-autosomal Y chromosome genes in our filtered dataset, reveals the expected strong sex-related pattern – albeit with some noise ...
7