Wikiomics:Pathway analysis - Revision history

Heyi Xiao at 00:43, 26 March 2013

2013-03-26T00:43:26Z

←Older revision		Revision as of 00:43, 26 March 2013
Line 35:		Line 35:
	* [http://www.cytoscape.org/ Cytoscape] leader in the field		* [http://www.cytoscape.org/ Cytoscape] leader in the field
	* [http://www.ondex.org/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques"		* [http://www.ondex.org/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques"
-	* [http://bioconductor.org/packages/2.12/bioc/html/pathview.html Pathview] a tool set for pathway based data integration and visualization in R/Bioconductor.	+	* [http://bioconductor.org/packages/2.12/bioc/html/pathview.html Pathview] a tool set for pathway based data integration and visualization in R/Bioconductor. [http://pathview.r-forge.r-project.org/ R-Forge]has an overview with some nice examples.

	=Protein interactions=		=Protein interactions=

Heyi Xiao at 21:27, 25 March 2013

2013-03-25T21:27:40Z

←Older revision		Revision as of 21:27, 25 March 2013
Line 35:		Line 35:
	* [http://www.cytoscape.org/ Cytoscape] leader in the field		* [http://www.cytoscape.org/ Cytoscape] leader in the field
	* [http://www.ondex.org/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques"		* [http://www.ondex.org/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques"
		+	* [http://bioconductor.org/packages/2.12/bioc/html/pathview.html Pathview] a tool set for pathway based data integration and visualization in R/Bioconductor.

	=Protein interactions=		=Protein interactions=

Heyi Xiao: /* Pathway Databases */

2011-11-16T01:33:38Z

Pathway Databases

←Older revision		Revision as of 01:33, 16 November 2011
Line 53:		Line 53:

	* [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] open curation of biological pathways		* [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] open curation of biological pathways
		+	* [http://www.pathwaycommons.org/pc/ Pathway Commons] access to biological pathway information collected from public pathway databases.

	=Pathway specific languages=		=Pathway specific languages=

Heyi Xiao at 01:28, 16 November 2011

2011-11-16T01:28:36Z

←Older revision		Revision as of 01:28, 16 November 2011
Line 20:		Line 20:

	* [http://www.bioinformatics.ubc.ca/ermineJ/ ErmineJ] "ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background."		* [http://www.bioinformatics.ubc.ca/ermineJ/ ErmineJ] "ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background."
		+
		+	* [http://www.bioconductor.org/packages/release/bioc/html/gage.html GAGE] is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity ( [http://www.biomedcentral.com/1471-2105/10/161 paper]). This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general.

	=Other tools to check=		=Other tools to check=
Line 71:		Line 73:

	=Biography=		=Biography=
		+	#Luo W, Friedman M, Shedden K, Hankenson KD, Woolf JP (2009). "GAGE: generally applicable gene set enrichment for pathway analysis". BMC Bioinformatics 10: 161: http://www.biomedcentral.com/1471-2105/10/161.
	#Aittokallio, Tero, and Benno Schwikowski. “Graph-based methods for analysing networks in cell biology.” Brief Bioinform 7, no. 3 (September 1, 2006): 243-255.		#Aittokallio, Tero, and Benno Schwikowski. “Graph-based methods for analysing networks in cell biology.” Brief Bioinform 7, no. 3 (September 1, 2006): 243-255.
	#Li, Chuan-Yun, Xizeng Mao, and Liping Wei. “Genes and (Common) Pathways Underlying Drug Addiction.” PLoS Computational Biology 4, no. 1 (1, 2008): e2 EP -.		#Li, Chuan-Yun, Xizeng Mao, and Liping Wei. “Genes and (Common) Pathways Underlying Drug Addiction.” PLoS Computational Biology 4, no. 1 (1, 2008): e2 EP -.
Line 78:		Line 81:
	#“Tools for visually exploring biological networks -- Suderman and Hallett 23 (20): 2651 -- Bioinformatics.” http://bioinformatics.oxfordjournals.org/cgi/content/full/23/20/2651.		#“Tools for visually exploring biological networks -- Suderman and Hallett 23 (20): 2651 -- Bioinformatics.” http://bioinformatics.oxfordjournals.org/cgi/content/full/23/20/2651.
	#"Pathways to the analysis of microarray data",Trends in Biotechnology, Volume 23, Issue 8, August 2005, Pages 429-435 R.Keira Curtis, Matej Oresic, Antonio Vidal-Puig		#"Pathways to the analysis of microarray data",Trends in Biotechnology, Volume 23, Issue 8, August 2005, Pages 429-435 R.Keira Curtis, Matej Oresic, Antonio Vidal-Puig
-	#"Bioinformatics applications for pathway analysis of microarray data"	+	#"Bioinformatics applications for pathway analysis of microarray data",Current Opinion in Biotechnology, Volume 19, Issue 1, February 2008, Pages 50-54,Thomas Werner
-	,Current Opinion in Biotechnology, Volume 19, Issue 1, February 2008, Pages 50-54,Thomas Werner	+

Darek Kedra: /* Pathway Databases */

2011-03-03T19:34:13Z

Pathway Databases

←Older revision		Revision as of 19:34, 3 March 2011
Line 50:		Line 50:
	* [http://regulondb.ccg.unam.mx/ RegulonDB] E.coli K12 DB (operons/genes/regulatory elements)		* [http://regulondb.ccg.unam.mx/ RegulonDB] E.coli K12 DB (operons/genes/regulatory elements)

-	[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] open curation of biological pathways	+	* [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] open curation of biological pathways

	=Pathway specific languages=		=Pathway specific languages=

Darek Kedra: /* Protein interactions */

2011-03-03T19:32:47Z

Protein interactions

←Older revision		Revision as of 19:32, 3 March 2011
Line 35:		Line 35:

	=Protein interactions=		=Protein interactions=
-	* [http://sbi.imim.es/~~piana~~/ ~~PIANA~~] ~~Protein Interactions And Network Analysis) ** integrates data from multiple sources in a centralized~~ database,	+	* [http://sbi.imim.es/web/BIANA.php BIANA] biological database integration and network management framework, successor of PIANA
-	*[http://acgt.cs.tau.ac.il/matisse MATISSE]Modular Analysis for Topology of Interactions and Similarity SEts	+
		+	*[http://acgt.cs.tau.ac.il/matisse MATISSE] Modular Analysis for Topology of Interactions and Similarity SEts
	** automating the analysis of protein-protein interactions networks.		** automating the analysis of protein-protein interactions networks.

Darek Kedra: /* Pathway/graph visualisation */

2011-03-03T19:30:09Z

Pathway/graph visualisation

←Older revision		Revision as of 19:30, 3 March 2011
Line 32:		Line 32:
	=Pathway/graph visualisation=		=Pathway/graph visualisation=
	* [http://www.cytoscape.org/ Cytoscape] leader in the field		* [http://www.cytoscape.org/ Cytoscape] leader in the field
-	* [http://~~ondex~~.~~sourceforge~~.~~net~~/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques"	+	* [http://www.ondex.org/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques"

	=Protein interactions=		=Protein interactions=

Darek Kedra: /* Other tools to check */

2011-03-03T19:29:18Z

Other tools to check

←Older revision		Revision as of 19:29, 3 March 2011
Line 26:		Line 26:
	* [http://www.biomedcentral.com/1471-2105/6/144#B12 PAGE] Parametric Analysis of Gene Set Enrichment		* [http://www.biomedcentral.com/1471-2105/6/144#B12 PAGE] Parametric Analysis of Gene Set Enrichment
	* [http://cbio.mskcc.org/software/cpath/ CPath] database and software suite for storing, visualizing, and analyzing biological pathways [http://cbio.mskcc.org/cpath/ demo page]		* [http://cbio.mskcc.org/software/cpath/ CPath] database and software suite for storing, visualizing, and analyzing biological pathways [http://cbio.mskcc.org/cpath/ demo page]
-	* EASE (old?) http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=14519205	+	* EASE (old but highly cited) http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=14519205

-	* nonparametric multivariate analysis Nettleton et al. [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/2/192 HTML]. R code ~~availebla~~ from author.	+	* nonparametric multivariate analysis Nettleton et al. [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/2/192 HTML]. R code available from author.

	=Pathway/graph visualisation=		=Pathway/graph visualisation=

Darek Kedra: /* Other tools to check */

2011-03-03T19:27:03Z

Other tools to check

←Older revision		Revision as of 19:27, 3 March 2011
Line 23:		Line 23:
	=Other tools to check=		=Other tools to check=
	* [http://gepat.sourceforge.net/ GEPAT] Genome Expression Pathway Analysis Tool. Performs standard microarray analyzes plus "Ensembl database and provides information about gene names, chromosomal location, GO categories and enzymatic activity for each probe on the chip.". Complex installation of java jars/MySQL etc.		* [http://gepat.sourceforge.net/ GEPAT] Genome Expression Pathway Analysis Tool. Performs standard microarray analyzes plus "Ensembl database and provides information about gene names, chromosomal location, GO categories and enzymatic activity for each probe on the chip.". Complex installation of java jars/MySQL etc.
-	* [http://www.bioinformatics.ubc.ca/ermineJ/ ErmineJ] Java stand-alone program "designed to be used by biologists with little or no informatics background" + command line for expert	+
	* [http://www.biomedcentral.com/1471-2105/6/144#B12 PAGE] Parametric Analysis of Gene Set Enrichment		* [http://www.biomedcentral.com/1471-2105/6/144#B12 PAGE] Parametric Analysis of Gene Set Enrichment
	* [http://cbio.mskcc.org/software/cpath/ CPath] database and software suite for storing, visualizing, and analyzing biological pathways [http://cbio.mskcc.org/cpath/ demo page]		* [http://cbio.mskcc.org/software/cpath/ CPath] database and software suite for storing, visualizing, and analyzing biological pathways [http://cbio.mskcc.org/cpath/ demo page]

Darek Kedra: /* Recommended */

2011-03-03T19:25:40Z

Recommended

←Older revision		Revision as of 19:25, 3 March 2011
Line 14:		Line 14:
	*** only about 1/3 of genes will get annotated in the first step		*** only about 1/3 of genes will get annotated in the first step
	** Li, Chuan-Yun, Xizeng Mao, and Liping Wei. “Genes and (Common) Pathways Underlying Drug Addiction.” PLoS Computational Biology 4, no. 1 (1, 2008) [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0040002 HTML]		** Li, Chuan-Yun, Xizeng Mao, and Liping Wei. “Genes and (Common) Pathways Underlying Drug Addiction.” PLoS Computational Biology 4, no. 1 (1, 2008) [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0040002 HTML]
-	* [http://www.broad.mit.edu/gsea/index.jsp GSEA] "Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states"	+	* [http://www.broad.mit.edu/gsea/index.jsp GSEA] withMSigDB "Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states"

	objections (Damian D, Gorfine M. Statistical concerns about the GSEA procedure): http://www.nature.com/ng/journal/v36/n7/full/ng0704-663a.html		objections (Damian D, Gorfine M. Statistical concerns about the GSEA procedure): http://www.nature.com/ng/journal/v36/n7/full/ng0704-663a.html