Heading down the wrong pathway: on the influence of correlation within gene sets (Q34966567)

5 August 2017

Heading down the wrong pathway: on the influence of correlation within gene sets (English)

1 reference

5 August 2017

1

Daniel M Gatti

1 reference

5 August 2017

4

Ivan Rusyn

1 reference

5 August 2017

William T Barry

2

1 reference

5 August 2017

Andrew B Nobel

series ordinal

3

1 reference

5 August 2017

Fred A Wright

series ordinal

5

1 reference

5 August 2017

language of work or name

English

0 references

publication date

18 October 2010

1 reference

5 August 2017

1 reference

5 August 2017

11

1 reference

5 August 2017

574

1 reference

describes a project that uses

5 August 2017

GEOquery

object named as

GEOquery

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Testing the additional predictive value of high-dimensional molecular data

1 reference

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Gene set internal coherence in the context of functional profiling

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

A biological evaluation of six gene set analysis methods for identification of differentially expressed pathways in microarray data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

A general modular framework for gene set enrichment analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Microarray-based gene set analysis: a comparison of current methods

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Significance levels for studies with correlated test statistics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Activation of inflammation/NF-kappaB signaling in infants born to arsenic-exposed mothers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Capturing heterogeneity in gene expression studies by surrogate variable analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Improving gene set analysis of microarray data by SAM-GS.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Analyzing gene expression data in terms of gene sets: methodological issues

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Gene expression omnibus: microarray data storage, submission, retrieval, and analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

A multivariate approach for integrating genome-wide expression data and biological knowledge

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Met-regulated expression signature defines a subset of human hepatocellular carcinomas with poor prognosis and aggressive phenotype

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

A new type of stochastic dependence revealed in gene expression data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Microarray data analysis: from disarray to consolidation and consensus

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

ErmineJ: tool for functional analysis of gene expression data sets

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Discovering statistically significant pathways in expression profiling studies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

PAGE: parametric analysis of gene set enrichment

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Significance analysis of functional categories in gene expression studies: a structured permutation approach

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Comparing functional annotation analyses with Catmap

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Bioconductor: open software development for computational biology and bioinformatics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

A global test for groups of genes: testing association with a clinical outcome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

GoMiner: a resource for biological interpretation of genomic and proteomic data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Gene ontology: tool for the unification of biology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

KEGG: Kyoto Encyclopedia of Genes and Genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Cluster analysis and display of genome-wide expression patterns

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

GlobalANCOVA: exploration and assessment of gene group effects.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Future of toxicogenomics and safety signatures: balancing public access to data with proprietary drug discovery

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3091509

Correlation between gene expression levels and limitations of the empirical bayes methodology for finding differentially expressed genes

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20955544

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20955544

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-11-574

1 reference

5 August 2017

1 reference

5 August 2017

1 reference