Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment (Q27134934)

8

0 references

Martina Summer-Kutmon

6

Martina Kutmon

1 reference

ORCID Public Data File 2021

Lars Eijssen

2

0 references

Anwesha Bohler

1

0 references

Martijn P van Iersel

3

0 references

Christ Leemans

Christ Leemans

full work available at URL

4

0 references

Magali Jaillard

7

0 references

language of work or name

English

0 references

publication date

2015

0 references

number of pages

12

0 references

http://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0708-8

0 references

published in

BMC Bioinformatics

0 references

volume

16

0 references

issue

1

0 references

page(s)

267

0 references

describes a project that uses

Cytoscape

Cytoscape

1 reference

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

GEOquery

GEOquery

1 reference

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

limma

limma

R package limma

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/s12859-015-0708-8

0 references

cites work

Data, information, knowledge and principle: back to metabolism in KEGG

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

NCBI GEO: archive for functional genomics data sets--update

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Pathway Commons, a web resource for biological pathway data

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

NetPath: a public resource of curated signal transduction pathways

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Biopython: freely available Python tools for computational molecular biology and bioinformatics

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

PID: the Pathway Interaction Database

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Presenting and exploring biological pathways with PathVisio

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Pathguide: a pathway resource list

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Bioconductor: open software development for computational biology and bioinformatics

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

The Bioperl toolkit: Perl modules for the life sciences

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

The BioPAX community standard for pathway data sharing

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

WikiPathways: building research communities on biological pathways

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Building models using Reactome pathways as templates

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Mining biological pathways using WikiPathways web services

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Ten years of pathway analysis: current approaches and outstanding challenges

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Integrated visualization of a multi-omics study of starvation in mouse intestine

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Annotating cancer variants and anti-cancer therapeutics in reactome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

WormBase 2014: new views of curated biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Into the eye of the cytokine storm

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

A comprehensive molecular interaction map for Hepatitis B virus and drug designing of a novel inhibitor for Hepatitis B X protein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

Cellularity and adipogenic profile of the abdominal subcutaneous adipose tissue from obese adolescents: association with insulin resistance and hepatic steatosis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

VANTED: a system for advanced data analysis and visualization in the context of biological networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4546821

LOWESS: A Program for Smoothing Scatterplots by Robust Locally Weighted Regression

31 May 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12859-015-0708-8

The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26298294

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Unraveling cancer chemoimmunotherapy mechanisms by gene and protein expression profiling of responses to cyclophosphamide

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26298294

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Integrated visualization of a multi-omics study of starvation in mouse intestine.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26298294

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12859-015-0708-8

1 reference

journals/bmcbi/BohlerEILWKJE15

557495

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1022044587

0 references

557495

1 reference

1 reference

1 reference