• Reactome

  • Referenced in 24 articles [sw14952]
  • free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive ... tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome...
  • E-CELL

  • Referenced in 20 articles [sw07917]
  • simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models...
  • CAMERA

  • Referenced in 4 articles [sw30339]
  • tests are commonly used in molecular pathway analysis to test for enrichment of a particular ... excellent power for detecting genuine differential expression. Analysis of breast cancer data shows that CAMERA ... analyze specified sets or as a pathway analysis tool using a database of molecular signatures...
  • KEGGgraph

  • Referenced in 8 articles [sw06934]
  • pathway topology and allows further analysis or dissection of pathway graphs. We demonstrate...
  • GSA

  • Referenced in 37 articles [sw18747]
  • pathways derived from biological databases. Our starting point is the interesting Gene Set Enrichment Analysis...
  • BhGLM

  • Referenced in 3 articles [sw10342]
  • particularly useful for complicated genetic data analysis, for example, QTL mapping in experimental crosses, genetic ... diseases and traits, gene-set and pathway analysis, and gene-gene and gene-environment interactions...
  • Oncomine

  • Referenced in 7 articles [sw17289]
  • Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression ... have been widely applied to cancer transcriptome analysis; however, the majority of such data ... biomedical research community. Our analysis has identified the genes, pathways, and networks deregulated across ... initiative, describe the database and analysis modules, and highlight several notable observations. Results from this...
  • GSVA

  • Referenced in 3 articles [sw17293]
  • pathway or signature summary. The strengths of this approach over single gene analysis include noise ... Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample ... utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously ... bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover...
  • ReactomePA

  • Referenced in 1 article [sw25978]
  • ReactomePA: an R/Bioconductor package for Reactome pathway analysis and visualization. This package provides functions ... pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis...
  • MetaOmics

  • Referenced in 1 article [sw16608]
  • quality control, differentially expressed gene analysis and pathway enrichment detection. Summary: With the rapid advances ... gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides a quantitative ... meta-analysis. MetaDE and MetaPath were developed for candidate marker and pathway detection, which provide ... marker detection, meta-analysis and pathway analysis methods. The system allows flexible input of experimental...
  • GANPA

  • Referenced in 1 article [sw25308]
  • package GANPA: Gene Association Network-based Pathway Analysis. This package implements a network-based gene ... analysis approach for microarray data pathway analysis...
  • COVAIN

  • Referenced in 1 article [sw10556]
  • complex. No single technique for statistical analysis and biological interpretation of these ultracomplex data ... multivariate statistics, network topology and biochemical pathway mapping analysis is in all cases recommended. Therefore ... multivariate statistical analysis, Granger time-series analysis, pathway mapping, correlation network topology analysis and visualization ... such as Granger causality and permutation entropy analysis that are not implemented in other similar...
  • MetaModel

  • Referenced in 4 articles [sw09011]
  • program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles ... calculate the control structure of a pathway: it provides not only an educational tool that ... classic summation relationships of metabolic control analysis but also a research tool for addressing ‘what...
  • EXPANDER

  • Referenced in 8 articles [sw30158]
  • genes (including methods suitable for NGS data analysis); Clustering and biclustering; Down-stream enrichment analyses ... UTRs and; Biological pathways and Chromosomal locations; Network-based analysis of the expression data.EXPANDER provides...
  • topologyGSA

  • Referenced in 1 article [sw15178]
  • topologyGSA: Gene Set Analysis Exploiting Pathway Topology. Using Gaussian graphical models ... propose a novel approach to perform pathway analysis using gene expression. Given the structure...
  • DNA

  • Referenced in 4 articles [sw26923]
  • provide a recipe for conducting a differential analysis of networks constructed from microarray data under ... information about the underlying biochemical pathways. Differential network analysis with appropriate connectivity scores...
  • GSNCA

  • Referenced in 3 articles [sw25309]
  • gene set analysis approaches primarily focus on identifying differentially expressed gene sets (pathways). Methods ... identifying differentially coexpressed pathways also exist but are mostly based on aggregated pairwise correlations ... Instead, we propose Gene Sets Net Correlations Analysis (GSNCA), a multivariate differential coexpression test that ... approach for the analysis of differentially coexpressed pathways that also evaluates the importance...
  • WikiPathways

  • Referenced in 1 article [sw29362]
  • disseminating models of biological pathways for data visualization and analysis. Since our last NAR update ... diversity and depth of the collected pathways are described from the perspective of researchers interested ... extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio ... introduce the Quick Edit feature for pathway authors and curators, in addition to new means...
  • gage

  • Referenced in 1 article [sw25396]
  • gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray ... batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies ... pathways and GO terms. These funtions and data are also useful for gene set analysis...
  • PRS

  • Referenced in 1 article [sw29380]
  • Software. PRS software is a new pathway enrichment analysis tool with a MATLAB graphical user ... gene expression data and run a pathway enrichment analysis using two different approaches ... navigate through the maps of enriched pathways where significant genes are marked with different colours...