NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis (Q92735608)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

title

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis (English)

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

1 reference

1 reference

3

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Jianguo Xia

6

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

5

Niladri Basu

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

author name string

Guangyan Zhou

1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Othman Soufan

2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

Robert E W Hancock

4

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1 May 2020

publication date

1 July 2019

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

published in

Nucleic Acids Research

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

volume

47

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1 May 2020

issue

W1

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1 May 2020

page(s)

W234-W241

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Creative Commons Attribution 4.0 International

1 May 2020

copyright license

start time

1 April 2019

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/6602507

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Remove, rather than redefine, statistical significance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Redefine statistical significance

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

The Comparative Toxicogenomics Database: update 2019

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Experimenting with reproducibility: a case study of robustness in bioinformatics

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

DrugBank 5.0: a major update to the DrugBank database for 2018.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

The DifferentialNet database of differential protein-protein interactions in human tissues

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

TCSBN: a database of tissue and cancer specific biological networks

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

PCSF: An R-package for network-based interpretation of high-throughput data.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Ranking metrics in gene set enrichment analysis: do they matter?

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

g:Profiler-a web server for functional interpretation of gene lists (2016 update)

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system.

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Near-optimal probabilistic RNA-seq quantification

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

A review of bioinformatic pipeline frameworks

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

HISAT: a fast spliced aligner with low memory requirements

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Biological network exploration with Cytoscape 3

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Reconstruction of gene co-expression network from microarray data using local expression patterns

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

INVEX--a web-based tool for integrative visualization of expression data

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

INMEX--a web-based tool for integrative meta-analysis of expression data

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

miRTarBase: a database curates experimentally validated microRNA-target interactions

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

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

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

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

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

The ENCODE (ENCyclopedia Of DNA Elements) Project

11 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6602507

11 February 2021

Identifiers

DOI

10.1093/NAR/GKZ240

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30931480%20AND%20SRC:MED&resulttype=core&format=json

1 May 2020

1 reference