Ontological analysis of gene expression data: current tools, limitations, and open problems (Q30993399)

11 September 2017

Ontological analysis of gene expression data: current tools, limitations, and open problems (English)

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11 September 2017

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2

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11 September 2017

1

Purvesh Khatri

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PMCID

2435250

11 September 2017

language of work or name

English

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publication date

30 June 2005

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11 September 2017

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11 September 2017

21

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11 September 2017

18

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11 September 2017

3587-3595

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Recent additions and improvements to the Onto-Tools

11 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

A semantic analysis of the annotations of the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

GOToolBox: functional analysis of gene datasets based on Gene Ontology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

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=2435250

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

GOstat: find statistically overrepresented Gene Ontologies within a group 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=2435250

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

Characterizing gene sets with FuncAssociate

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

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=2435250

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

GeneMerge—post-genomic analysis, data mining, and hypothesis testing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

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=2435250

Predicting gene function from patterns of annotation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

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=2435250

MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from 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=2435250

The Pathway Tools software

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

Pathway Processor: a tool for integrating whole-genome expression results into metabolic 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=2435250

Pieces of the puzzle: expressed sequence tags and the catalog of human 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=2435250

Human heme oxygenase-2: characterization and expression of a full-length cDNA and evidence suggesting that the two HO-2 transcripts may differ by choice of polyadenylation signal

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2435250

The control of the false discovery rate in multiple testing under dependency

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI565

Transcriptional regulation and function during the human cell cycle

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI565

Profiling Gene Expression Using Onto-Express

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI565

The Database of Interacting Proteins: 2004 update

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI565

POWER_SAGE: comparing statistical tests for SAGE experiments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI565

Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15994189

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTI565

1 reference

journals/bioinformatics/KhatriD05

11 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

11 September 2017

1 reference

PMCID

2435250