Literature DB >> 21917718

Introduction to statistical methods for analyzing large data sets: gene-set enrichment analysis.

Neil R Clark1, Avi Ma'ayan.   

Abstract

This Teaching Resource provides lecture notes, slides, and a problem set for a series of lectures introducing the mathematical concepts behind gene-set enrichment analysis (GSEA) and were part of a course entitled "Systems Biology: Biomedical Modeling." GSEA is a statistical functional enrichment analysis commonly applied to identify enrichment of biological functional categories in sets of ranked differentially expressed genes from genome-wide mRNA expression data sets.

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Year:  2011        PMID： 21917718      PMCID： PMC3205944          DOI： 10.1126/scisignal.2001966

Source DB:  PubMed          Journal:  Sci Signal        ISSN： 1945-0877            Impact factor:   8.192


  3 in total

1.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

2.  PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.

Authors:  Vamsi K Mootha; Cecilia M Lindgren; Karl-Fredrik Eriksson; Aravind Subramanian; Smita Sihag; Joseph Lehar; Pere Puigserver; Emma Carlsson; Martin Ridderstråle; Esa Laurila; Nicholas Houstis; Mark J Daly; Nick Patterson; Jill P Mesirov; Todd R Golub; Pablo Tamayo; Bruce Spiegelman; Eric S Lander; Joel N Hirschhorn; David Altshuler; Leif C Groop
Journal:  Nat Genet       Date:  2003-07       Impact factor: 38.330

3.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Authors:  Da Wei Huang; Brad T Sherman; Richard A Lempicki
Journal:  Nucleic Acids Res       Date:  2008-11-25       Impact factor: 16.971
  3 in total
  15 in total

1.  Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation.

Authors:  Erna S Arnardottir; Elena V Nikonova; Keith R Shockley; Alexei A Podtelezhnikov; Ron C Anafi; Keith Q Tanis; Greg Maislin; David J Stone; John J Renger; Christopher J Winrow; Allan I Pack
Journal:  Sleep       Date:  2014-10-01       Impact factor: 5.849

2.  Introduction to network analysis in systems biology.

Authors:  Avi Ma'ayan
Journal:  Sci Signal       Date:  2011-09-06       Impact factor: 8.192

3.  Genomic diversity and post-admixture adaptation in the Uyghurs.

Authors:  Yuwen Pan; Chao Zhang; Yan Lu; Zhilin Ning; Dongsheng Lu; Yang Gao; Xiaohan Zhao; Yajun Yang; Yaqun Guan; Dolikun Mamatyusupu; Shuhua Xu
Journal:  Natl Sci Rev       Date:  2021-09-11       Impact factor: 17.275

4.  HiCDB: a sensitive and robust method for detecting contact domain boundaries.

Authors:  Fengling Chen; Guipeng Li; Michael Q Zhang; Yang Chen
Journal:  Nucleic Acids Res       Date:  2018-11-30       Impact factor: 16.971

5.  A new method for identifying causal genes of schizophrenia and anti-tuberculosis drug-induced hepatotoxicity.

Authors:  Tao Huang; Cheng-Lin Liu; Lin-Lin Li; Mei-Hong Cai; Wen-Zhong Chen; Yi-Feng Xu; Paul F O'Reilly; Lei Cai; Lin He
Journal:  Sci Rep       Date:  2016-09-01       Impact factor: 4.379

6.  Beyond differential expression: the quest for causal mutations and effector molecules.

Authors:  Nicholas J Hudson; Brian P Dalrymple; Antonio Reverter
Journal:  BMC Genomics       Date:  2012-07-31       Impact factor: 3.969

7.  Gene expression changes in subcutaneous adipose tissue due to Cushing's disease.

Authors:  Irit Hochberg; Innocence Harvey; Quynh T Tran; Erin J Stephenson; Ariel L Barkan; Alan R Saltiel; William F Chandler; Dave Bridges
Journal:  J Mol Endocrinol       Date:  2015-07-06       Impact factor: 5.098

8.  Transcriptional changes induced by candidate malaria vaccines and correlation with protection against malaria in a human challenge model.

Authors:  Susanna Dunachie; Tamara Berthoud; Adrian V S Hill; Helen A Fletcher
Journal:  Vaccine       Date:  2015-08-07       Impact factor: 3.641

9.  Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples.

Authors:  Xiangtian Yu; Tao Zeng; Guojun Li
Journal:  BMC Genomics       Date:  2015-11-10       Impact factor: 3.969

10.  Transcriptional changes in organoculture of full-thickness human skin following topical application of all-trans retinoic acid.

Authors:  J M Gillbro; T Al-Bader; M Westman; M J Olsson; A Mavon
Journal:  Int J Cosmet Sci       Date:  2014-03-27       Impact factor: 2.970
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