主な内容
Bioconductor's page on ToPASeq
Vignette
Rcodes
Summary
Gene-expression data (Microarray, RNA-seq)
Topology-based pathway analysis methods (7 methods in one package)
Procedures
(1) Differential expression analysis
List genes differentially expressed between conditions
(2) Pathway analysis
Listed genes are mapped on pathways that were imported from databases somewhere
(3) Topological evaluation
Use topology of pathways to detect difference between conditions with better sensitivity/specificity performance
Seven methods implemented in ToPASeq -> See Table 1 inVignette
TopologyGSA
DEGraph
clipper
SPIA
TAPPA
PRS or TBS
PWEA
Miscelaneous
ToPASeq offers easy access to multiple methods
Visualization with Graphviz
Details
(1) Differential expression analysis
(i) Preparations (RNA-seq count normalization - TMM, DESeq)
(ii) Differential expression analysis (limma DESeq2)
Or you can do normalization/DE analysis yourself for downstream steps (SPIA,PRS,PWEA).
(2) Pathway analysis
Pathways are Graphs
Use graphite package to import pathways in KEGG, Biocarta, Reactome, NCI, SPIKE, HumanCyc,
G = (V,E)
Clique to handle protein complexes
Gene families are in the shape of parallels
Compound-mediated interaction (A-c-B => A-B)
If your own pathways, use utility functions in ToPASeq
(3) Topology analyses
(i) TopologyGSA
Gaussian Graphical Model on pathway graph with covariance matrix reflecting the pathway topology
Iterative Proportional Scaling for covariance matrix estimate
(ii) DEGraph
Assumes the same direction in the differential expression of genes in a pathway ("Discrete Signal Processing on Graphs")
(iii) clipper
Gaussian Graphical Model on pathway graph with covariance matrix reflecting the pathway topology
Shrinkage procedure of James-Stein-type for covariance matrix estimate
(iv) SPIA
Most well-known
Number of differentially expressed genes in pathway is considered
Pathway information is used as upstream genes in the pathway should be stronger and downstream weaker
Combine two information together to score pathways
(v) TAPPA
A bit classical
Handles genes as chemical atoms and a pathway as a chemical compound
(vi) PRS
Differentially expressed genes' effect should appear in downstream genes in pathway. This idea is used to summarize gene-wise significance.
(vii) PWEA
Pathway-information is used to expand GSEA.
Bioconductor's page on ToPASeq
Vignette
Rcodes
Summary
Gene-expression data (Microarray, RNA-seq)
Topology-based pathway analysis methods (7 methods in one package)
Procedures
(1) Differential expression analysis
List genes differentially expressed between conditions
(2) Pathway analysis
Listed genes are mapped on pathways that were imported from databases somewhere
(3) Topological evaluation
Use topology of pathways to detect difference between conditions with better sensitivity/specificity performance
Seven methods implemented in ToPASeq -> See Table 1 inVignette
TopologyGSA
DEGraph
clipper
SPIA
TAPPA
PRS or TBS
PWEA
Miscelaneous
ToPASeq offers easy access to multiple methods
Visualization with Graphviz
Details
(1) Differential expression analysis
(i) Preparations (RNA-seq count normalization - TMM, DESeq)
(ii) Differential expression analysis (limma DESeq2)
Or you can do normalization/DE analysis yourself for downstream steps (SPIA,PRS,PWEA).
(2) Pathway analysis
Pathways are Graphs
Use graphite package to import pathways in KEGG, Biocarta, Reactome, NCI, SPIKE, HumanCyc,
G = (V,E)
Clique to handle protein complexes
Gene families are in the shape of parallels
Compound-mediated interaction (A-c-B => A-B)
If your own pathways, use utility functions in ToPASeq
(3) Topology analyses
(i) TopologyGSA
Gaussian Graphical Model on pathway graph with covariance matrix reflecting the pathway topology
Iterative Proportional Scaling for covariance matrix estimate
(ii) DEGraph
Assumes the same direction in the differential expression of genes in a pathway ("Discrete Signal Processing on Graphs")
(iii) clipper
Gaussian Graphical Model on pathway graph with covariance matrix reflecting the pathway topology
Shrinkage procedure of James-Stein-type for covariance matrix estimate
(iv) SPIA
Most well-known
Number of differentially expressed genes in pathway is considered
Pathway information is used as upstream genes in the pathway should be stronger and downstream weaker
Combine two information together to score pathways
(v) TAPPA
A bit classical
Handles genes as chemical atoms and a pathway as a chemical compound
(vi) PRS
Differentially expressed genes' effect should appear in downstream genes in pathway. This idea is used to summarize gene-wise significance.
(vii) PWEA
Pathway-information is used to expand GSEA.
コメントをかく