Hello.
On my way to read and run a pathway/gene set analysis on some microarray data, I realized that besides the fact that there are many different ways (statistical methods) to do the analysis, all of them (at least as far as I know) stays at statistic and as you already know returns a p-value or/and an enrichment score for each pathway/gene set.
Today, I was wondering if there is any approach ever implemented to do pathway analysis but to take into account also information from systems biology and not only on statistical inferences.
Such information could be the role of each gene inside the gene set, like inducer , inhibitor. Also it could be info about the topology of that specific gene set and maybe gene's inter-correlations.
Does anyone have in mind any research article on such an approach ? Any info or even idea is welcomed.
Thank you.
1 answer
There ia a pahway review:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
Purvesh Khatri , Marina Sirota,Atul J. Butte
There were some biostar-posts:
Tools For Pathway/Gene Set Analysis Of Gwas (Genome-Wide Association Study) Data
How Do You Deal With Biological Context During Pathway Analysis?
A: Comparison Of Pathways Between Microbial Genomes
There was this review:
Analysing biological pathways in genome-wide association studies
Kai Wang, Mingyao Li & Hakon Hakonarson
Tools:
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Mario Latendresse, Joseph M. Dale, Thomas J. Lee, Pallavi Kaipa, Fred Gilham, Aaron Spaulding, Liviu Popescu, Tomer Altman, Ian Paulsen, Ingrid M. Keseler, Ron Caspi
Brief Bioinform. 2010 Jan; 11(1): 40–79. Published online 2009 Dec 2. doi: 10.1093/bib/bbp043
PeTTSy: a computational tool for perturbation analysis of complex systems biology models Mirela Domijan, Paul E. Brown, Boris V. Shulgin, David A. Rand
BMC Bioinformatics. 2016; 17: 124. Published online 2016 Mar 10. doi: 10.1186/s12859-016-0972-2
Log in to answer this question.
-
Choosing the right pathways among gene set enrichment analysis results
written by jabbari.parnian •
-
Co-expression analysis of single cell RNA seq data to identify pathway associations
written by james.drew101 •
-
How to do pathway analysis on kinome Drosophila dataset
written by m98
-
News: Gene set enrichment and pathway analysis in HT data
written by Physalia-courses
-
News: Squeezing biology out of statistics: Gene set and pathway analysis in HT data. Berlin, 11-15 …
written by Physalia-courses
-
News: Course. Squeezing biology out of statistics: Gene set and pathway analysis in HT data
written by Physalia-courses
-
Correlating gene expression with qualitative variables
written by fr
-
Calculating variable importance in model for microarray dataset
written by arronar
-
Creating the gene sets for GSEA in R
written by arronar
-
Figure out outliers in microarray dataset with z-scores
written by arronar
