(Q35129397)

6 August 2017

title

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis (English)

1 reference

6 August 2017

main subject

Medical Subject Headings

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Koki Tsuyuzaki

1

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Takeru Nakazato

object named as

Takeru Nakazato

4

0 references

Itoshi Nikaido

object named as

Itoshi Nikaido

6

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author name string

Gota Morota

2

1 reference

6 August 2017

Manabu Ishii

3

1 reference

6 August 2017

Satoru Miyazaki

5

1 reference

6 August 2017

publication date

15 February 2015

1 reference

6 August 2017

1 reference

6 August 2017

volume

16

1 reference

6 August 2017

page(s)

45

1 reference

Creative Commons Attribution 4.0 International

6 August 2017

copyright license

start time

15 February 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/4343279

based on heuristic

inferred from PubMed Central ID database lookup

SQL

1 reference

26 June 2022

https://europepmc.org/article/PMC/PMC4343279

based on heuristic

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1186/s12859-015-0453-z

0 references

cites work

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Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis

13 July 2018

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InterProScan 5: genome-scale protein function classification

13 July 2018

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FIDEA: a server for the functional interpretation of differential expression analysis

13 July 2018

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The UCSC Genome Browser database: extensions and updates 2013.

13 July 2018

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EnrichNet: network-based gene set enrichment analysis.

13 July 2018

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GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

13 July 2018

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Caloric restriction-associated remodeling of rat white adipose tissue: effects on the growth hormone/insulin-like growth factor-1 axis, sterol regulatory element binding protein-1, and macrophage infiltration.

13 July 2018

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Metab2MeSH: annotating compounds with medical subject headings

13 July 2018

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Ten years of pathway analysis: current approaches and outstanding challenges

13 July 2018

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Disease Ontology: a backbone for disease semantic integration

13 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Differential expression in RNA-seq: a matter of depth

13 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

A powerful and flexible approach to the analysis of RNA sequence count data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

RAPSearch: a fast protein similarity search tool for short reads

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Molecular signatures database (MSigDB) 3.0.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq

13 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Differential expression analysis for sequence count data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Independent filtering increases detection power for high-throughput experiments

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

An introduction to effective use of enrichment analysis software

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

A genome-wide association study identifies susceptibility variants for type 2 diabetes in Han Chinese

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Gene ontology analysis for RNA-seq: accounting for selection bias

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Gene set enrichment analysis made simple

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Gendoo: functional profiling of gene and disease features using MeSH vocabulary.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Testing significance relative to a fold-change threshold is a TREAT.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Reactome knowledgebase of human biological pathways and processes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

The impact of next-generation sequencing technology on genetics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Using GOstats to test gene lists for GO term association

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Bioconductor: open software development for computational biology and bioinformatics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

The MeSH translation maintenance system: structure, interface design, and implementation

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Identifying biological themes within lists of genes with EASE

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Statistical significance for genomewide studies

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Summaries of Affymetrix GeneChip probe level data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Nonparametric methods for identifying differentially expressed genes in microarray data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Significance analysis of microarrays applied to the ionizing radiation response

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Functional annotation of a full-length mouse cDNA collection

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Gene ontology: tool for the unification of biology

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

KEGG: kyoto encyclopedia of genes and genomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Basic local alignment search tool

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

Empirical bayes methods and false discovery rates for microarrays

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4343279

The positive false discovery rate: a Bayesian interpretation and the q -value

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12859-015-0453-Z

Empirical Bayes Analysis of a Microarray Experiment

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12859-015-0453-Z

10.1186/S12859-015-0453-Z

21 January 2018

Identifiers

DOI

1 reference

journals/bmcbi/TsuyuzakiMINMN15

6 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

6 August 2017

1 reference