SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency (Q33372132)

26 July 2017

SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency (English)

1 reference

26 July 2017

Ming Yi

1

0 references

author name string

Robert M Stephens

series ordinal

2

1 reference

PubMed ID

18818771

26 July 2017

language of work or name

English

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publication date

26 September 2008

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26 July 2017

1 reference

26 July 2017

3

1 reference

26 July 2017

9

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26 July 2017

e3288

1 reference

Creative Commons Attribution 4.0 International

26 July 2017

start time

26 September 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Identification of key processes underlying cancer phenotypes using biologic pathway analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Hubs in biological interaction networks exhibit low changes in expression in experimental asthma

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Identification of functional modules using network topology and high-throughput data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Integrin-mediated cell-matrix interactions for prosurvival and antiapoptotic signaling after genotoxic injury

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Oncogenic pathway signatures in human cancers as a guide to targeted therapies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Discovering statistically significant pathways in expression profiling studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Pathway level analysis of gene expression using singular value decomposition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

T-profiler: scoring the activity of predefined groups of genes using gene expression data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

PAGE: parametric analysis of gene set enrichment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Integrative analysis of the cancer transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Linking disease-associated genes to regulatory networks via promoter organization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

A module map showing conditional activity of expression modules in cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Tests for finding complex patterns of differential expression in cancers: towards individualized medicine

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

A gene atlas of the mouse and human protein-encoding transcriptomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Mixed-Model Reanalysis of Primate Data Suggests Tissue and Species Biases in Oligonucleotide-Based Gene Expression Profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Identifying biological themes within lists of genes with EASE

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Statistical significance for genomewide studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Gene expression phenotypic models that predict the activity of oncogenic pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Statistical Issues in cDNA Microarray Data Analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Global functional profiling of gene expression.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

c-Myc is essential for vasculogenesis and angiogenesis during development and tumor progression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Statistical issues with microarrays: processing and analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Exploring gene expression data with class scores.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Experimental design, analysis of variance and slide quality assessment in gene expression arrays.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Analysis of variance for gene expression microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Significance analysis of microarrays applied to the ionizing radiation response

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Genomics and medicine. Dissecting human disease in the postgenomic era.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Cluster analysis and display of genome-wide expression patterns

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0003288

Using ANOVA for gene selection from microarray studies of the nervous system

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0003288

Forensic genetics and ethical, legal and social implications beyond the clinic

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0003288

Group testing for pathway analysis improves comparability of different microarray datasets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0003288

Cancer outlier differential gene expression detection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0003288

MOST: detecting cancer differential gene expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0003288

Complete genomic screen in Parkinson disease: evidence for multiple genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0003288

An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2546449

Statistical concerns about the GSEA procedure

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18818771

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Outlier sums for differential gene expression analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18818771

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0003288

1 reference

release_bet7eppyarbspnfuz4p4qode6y

26 July 2017

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1 reference

Fatcat

https://api.fatcat.wiki/v0/release/bet7eppyarbspnfuz4p4qode6y

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

2546449

1 reference

26 July 2017

1 reference

PubMed ID

18818771