InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor (Q30536439)

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English	InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor	scientific article

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scholarly article

1 reference

Europe PubMed Central

15 August 2017

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor (English)

1 reference

Europe PubMed Central

15 August 2017

0 references

author name string

Alain Coletta

1

1 reference

Europe PubMed Central

15 August 2017

Colin Molter

2

1 reference

Europe PubMed Central

15 August 2017

Robin Duqué

3

1 reference

Europe PubMed Central

15 August 2017

David Steenhoff

4

1 reference

Europe PubMed Central

15 August 2017

Jonatan Taminau

5

1 reference

Europe PubMed Central

15 August 2017

Virginie de Schaetzen

6

1 reference

Europe PubMed Central

15 August 2017

Stijn Meganck

7

1 reference

Europe PubMed Central

15 August 2017

Cosmin Lazar

8

1 reference

Europe PubMed Central

15 August 2017

David Venet

9

1 reference

Europe PubMed Central

15 August 2017

Vincent Detours

10

1 reference

Europe PubMed Central

15 August 2017

Ann Nowé

11

1 reference

Europe PubMed Central

15 August 2017

Hugues Bersini

12

1 reference

Europe PubMed Central

15 August 2017

David Y Weiss Solís

13

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Europe PubMed Central

15 August 2017

publication date

18 November 2012

1 reference

Europe PubMed Central

15 August 2017

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Europe PubMed Central

15 August 2017

13

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Europe PubMed Central

15 August 2017

11

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Europe PubMed Central

15 August 2017

R104

1 reference

Europe PubMed Central

15 August 2017

describes a project that uses

object named as

Limma

1 reference

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

https://scigraph.springernature.com/pub.10.1186/gb-2012-13-11-r104

0 references

The limitations of simple gene set enrichment analysis assuming gene independence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Making sense out of massive data by going beyond differential expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Toward interoperable bioscience data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Genomics and privacy: implications of the new reality of closed data for the field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

DNA methylation profiling reveals a predominant immune component in breast cancers.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Discovery and preclinical validation of drug indications using compendia of public gene expression data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Integrated genomic analyses of ovarian carcinoma

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

A framework for variation discovery and genotyping using next-generation DNA sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Integrative genomics viewer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

A global map of human gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Frozen robust multiarray analysis (fRMA).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Computer science. Accessible reproducible research

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Application and evaluation of automated semantic annotation of gene expression experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Gene-expression signatures in breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Human cancer cell lines: Experimental models for cancer cells in situ? For cancer stem cells?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Human thyroid tumor cell lines derived from different tumor types present a common dedifferentiated phenotype

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Reproducible research: a bioinformatics case study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

GenePattern 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Gene expression in human thyrocytes and autonomous adenomas reveals suppression of negative feedbacks in tumorigenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Bioconductor: open software development for computational biology and bioinformatics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Coexpression analysis of human genes across many microarray data sets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

The Unified Medical Language System (UMLS): integrating biomedical terminology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Integration and cross-validation of high-throughput gene expression data: comparing heterogeneous data sets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Multiclass cancer diagnosis using tumor gene expression signatures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

20 June 2018

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

1 reference

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20 June 2018

A general method to derive robust organ-specific gene expression-based differentiation indices: application to thyroid cancer diagnostic.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

26 November 2018

Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group

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26 November 2018

A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers.

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26 November 2018

Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3580496

26 November 2018

inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO

1 reference

https://pubmed.ncbi.nlm.nih.gov/23158523

12 December 2020

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Identifiers

10.1186/GB-2012-13-11-R104

1 reference

Europe PubMed Central

15 August 2017

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1 reference

Europe PubMed Central

15 August 2017

1 reference

Europe PubMed Central

15 August 2017

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