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Protocols

ALIGATOR specifications

Information


Unique identifier OMICS_04383
Name ALIGATOR
Alternative name Association LIst Go AnnoTatOR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data SNP p-values
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

Versioning


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Maintainer


This tool is not available anymore.

Publication for Association LIst Go AnnoTatOR

ALIGATOR citations

 (35)
library_books

Gene set meta analysis of lung cancer identifies pathway related to systemic lupus erythematosus

2017
PLoS One
PMCID: 5342225
PMID: 28273134
DOI: 10.1371/journal.pone.0173339

[…] e remaining studies NCI, deCODE, and HARVARD were combined to investigate only those pathways whose findings in the screening phase proved promising. If necessary, GSA was performed using the program ALIGATOR []. The method META-GSA [] was performed to pool GSA results (p-values pGS,s) at each stage. The aim of META-GSA is to increase statistical evidence by pooling the p-values pGS,s of GSAs, tak […]

call_split

snpGeneSets: An R Package for Genome Wide Study Annotation

2016
PMCID: 5144977
PMID: 27807048
DOI: 10.1534/g3.116.034694
call_split See protocol

[…] tions for annotation and postanalysis include msigdb_build() for building a local knowledge base of gene sets from MSigDB, uscore() for calculating genome-wide U-scores from gene effect measures, and aligator() for enrichment analysis of GWAS by the ALIGATOR method (). […]

library_books

Pathway analysis of bladder cancer genome wide association study identifies novel pathways involved in bladder cancer development

2016
PMCID: 5059113
PMID: 27738493
DOI: 10.18632/genesandcancer.113

[…] Aligator utilizes a predefined threshold P-value of 0.01 wherein significant SNPs were defined on the basis of less than the predefined threshold. If a gene had one or more than one significant SNP, t […]

library_books

Gene Prioritization for Imaging Genetics Studies Using Gene Ontology and a Stratified False Discovery Rate Approach

2016
Front Neuroinform
PMCID: 4823264
PMID: 27092072
DOI: 10.3389/fninf.2016.00014

[…] In contrast to existing approaches, our novel method provides a systematic integration framework for previous knowledge with the GO database. Alternatives such as Aligator and INRICH both rely on the identification of over-represented GO categories among significant hits. These approaches use GO as the last step to identify which biological domains are enriched […]

library_books

Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study

2015
Sci Rep
PMCID: 4663496
PMID: 26616738
DOI: 10.1038/srep17447

[…] ALIGATOR was performed using the SNPath R package (linchen.fhcrc.org/grass.html) and 1345 Reactome pathways (www.reactome.org, accessed April 2013), also known as “events”. The input data were the P v […]

library_books

META GSA: Combining Findings from Gene Set Analyses across Several Genome Wide Association Studies

2015
PLoS One
PMCID: 4621033
PMID: 26501144
DOI: 10.1371/journal.pone.0140179

[…] such as Sidak's correction []; decorrelation tests []; or omnibus tests, such as Fisher’s inverse Chi2-method (e.g. SLAT []) are used. To be robust against a), b) and c) permutation procedures (e.g. ALIGATOR []) or single model approaches comprising all SNPs allocated to a gene-set and correcting for the number of effective markers (e.g. kernel methods[]) can be used. An additional source of bias […]

Citations

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ALIGATOR institution(s)
MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Heath Park, Cardiff, UK

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