(Q35994811)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

title

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

0 references

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Anthony R Soltis

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Anthony Gitter

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Nurcan Tuncbag

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Ernest Fraenkel

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

Sara Gosline

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

author name string

Sara J C Gosline

2

1 reference

11 August 2017

language of work or name

1 reference

20 April 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

2 April 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

volume

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

page(s)

e1004879

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

2 April 2020

copyright license

start time

20 April 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

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

cites work

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Identification of a PEAK1/ZEB1 signaling axis during TGFβ/fibronectin-induced EMT in breast cancer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Gene expression. Statistics requantitates the central dogma

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Integrative analysis of 111 reference human epigenomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

SAMNetWeb: identifying condition-specific networks linking signaling and transcription

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Pathway connectivity and signaling coordination in the yeast stress-activated signaling network.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Sharing information to reconstruct patient-specific pathways in heterogeneous diseases

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

STITCH 4: integration of protein-chemical interactions with user data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Identifying proteins controlling key disease signaling pathways

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Extensive changes in DNA methylation are associated with expression of mutant huntingtin.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

The BioGRID interaction database: 2013 update

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

HMDB 3.0--The Human Metabolome Database in 2013

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

EGFR and c-Met Cross Talk in Glioblastoma and Its Regulation by Human Cord Blood Stem Cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

An expansive human regulatory lexicon encoded in transcription factor footprints

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

MINT, the molecular interaction database: 2012 update

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Global quantification of mammalian gene expression control

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Molecular signatures database (MSigDB) 3.0.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

The Biomolecular Interaction Network Database in PSI-MI 2.5.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

A systems view of epithelial-mesenchymal transition signaling states

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Finding undetected protein associations in cell signaling by belief propagation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Discovering pathways by orienting edges in protein interaction networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Suppression of TGFβ-induced epithelial-mesenchymal transition like phenotype by a PIAS1 regulated sumoylation pathway in NMuMG epithelial cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

ConsensusPathDB: toward a more complete picture of cell biology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

The output of Hedgehog signaling is controlled by the dynamic association between Suppressor of Fused and the Gli proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

iRefIndex: a consolidated protein interaction database with provenance

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

DrugBank: a knowledgebase for drugs, drug actions and drug targets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Hedgehog signaling pathway is inactive in colorectal cancer cell lines

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

A direct comparison of protein interaction confidence assignment schemes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

The ENCODE (ENCyclopedia Of DNA Elements) Project

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Integrating regulatory motif discovery and genome-wide expression analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Comparative assessment of large-scale data sets of protein-protein interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Gene ontology: tool for the unification of biology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Algorithms for detecting significantly mutated pathways in cancer.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Identifying functional modules using expression profiles and confidence-scored protein interactions.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Protein-protein interaction networks and biology--what's the connection?

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4838263

Potential artefacts in protein-interaction networks

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004879

10.1371/JOURNAL.PCBI.1004879

21 January 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/TuncbagGKSGF16

2 April 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json

2 April 2020

PubMed publication ID

27096930

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27096930%20AND%20SRC:MED&resulttype=core&format=json