Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences
C Manzoni, DA Kia, J Vandrovcova… - Briefings in …, 2018 - academic.oup.com
Advances in the technologies and informatics used to generate and process large biological
data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While …
data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While …
Identifying significantly impacted pathways: a comprehensive review and assessment
Background Many high-throughput experiments compare two phenotypes such as disease
vs. healthy, with the goal of understanding the underlying biological phenomena …
vs. healthy, with the goal of understanding the underlying biological phenomena …
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets
Y Zhou, B Zhou, L Pache, M Chang… - Nature …, 2019 - nature.com
A critical component in the interpretation of systems-level studies is the inference of enriched
biological pathways and protein complexes contained within OMICs datasets. Successful …
biological pathways and protein complexes contained within OMICs datasets. Successful …
rGREAT: an R/bioconductor package for functional enrichment on genomic regions
Z Gu, D Hübschmann - Bioinformatics, 2023 - academic.oup.com
Abstract Summary GREAT (Genomic Regions Enrichment of Annotations Tool) is a widely
used tool for functional enrichment on genomic regions. However, as an online tool, it has …
used tool for functional enrichment on genomic regions. However, as an online tool, it has …
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results
Z Gu, D Hübschmann - Genomics, Proteomics & Bioinformatics, 2023 - academic.oup.com
Functional enrichment analysis or gene set enrichment analysis is a basic bioinformatics
method that evaluates the biological importance of a list of genes of interest. However, it may …
method that evaluates the biological importance of a list of genes of interest. However, it may …
GREAT improves functional interpretation of cis-regulatory regions
Abstract We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to
analyze the functional significance of cis-regulatory regions identified by localized …
analyze the functional significance of cis-regulatory regions identified by localized …
GSVA: gene set variation analysis for microarray and RNA-seq data
Background Gene set enrichment (GSE) analysis is a popular framework for condensing
information from gene expression profiles into a pathway or signature summary. The …
information from gene expression profiles into a pathway or signature summary. The …
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
DW Huang, BT Sherman, RA Lempicki - Nature protocols, 2009 - nature.com
DAVID bioinformatics resources consists of an integrated biological knowledgebase and
analytic tools aimed at systematically extracting biological meaning from large gene/protein …
analytic tools aimed at systematically extracting biological meaning from large gene/protein …
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
DW Huang, BT Sherman, RA Lempicki - Nucleic acids research, 2009 - academic.oup.com
Functional analysis of large gene lists, derived in most cases from emerging high-throughput
genomic, proteomic and bioinformatics scanning approaches, is still a challenging and …
genomic, proteomic and bioinformatics scanning approaches, is still a challenging and …
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation
Background Gene-set enrichment analysis is a useful technique to help functionally
characterize large gene lists, such as the results of gene expression experiments. This …
characterize large gene lists, such as the results of gene expression experiments. This …