Evidence map›Paper›PMID 28651964›Full record

ArticleMethods (San Diego, Calif.)2017

Protein network construction using reverse phase protein array data.

Rency S Varghese, Yiming Zuo, Yi Zhao, Yong-Wei Zhang, Sandra A Jablonski, Mariaelena Pierobon, Emanuel F Petricoin, Habtom W Ressom, Louis M Weiner

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods (San Diego, Calif.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Panomics for Precision Medicine.Trends in molecular medicine · 2018
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Rency S VargheseDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
Yiming ZuoDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA; Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA.
Yi ZhaoDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA; Department of Biostatistics, School of Public Health, Brown University, Rhode Island, Providence, USA.
Yong-Wei ZhangDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
Sandra A JablonskiDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
Mariaelena PierobonCenter for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
Emanuel F PetricoinCenter for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
Habtom W RessomDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA. Electronic address: hwr@georgetown.edu.
Louis M WeinerDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA. Electronic address: weinerl@georgetown.edu.

Funding

Tissue Culture Shared ResourceP30CA051008 · NCI · GEORGETOWN UNIVERSITY · PI Louis M Weiner · 1990 to 2026
$71.5M
Novel Targets in Endocrine ResponsivenessU54CA149147 · NCI · GEORGETOWN UNIVERSITY · PI MADHAVAN, SUBHA · 2010 to 2014
$6.9M
TARGETED IMMUNOTHERAPY USING BISPECIFIC ANTIBODIESR01CA050633 · NCI · GEORGETOWN UNIVERSITY · PI WEINER, LOUIS M. · 1989 to 2018
$6.5M
Analysis of Racial Disparities in HCC by Systems MetabolomicsU01CA185188 · NCI · GEORGETOWN UNIVERSITY · PI RESSOM, HABTOM W · 2015 to 2019
$1.7M
Analysis of LC-MS data to identify peptide and glycan biomarkers for hepatocellulR01CA143420 · NCI · GEORGETOWN UNIVERSITY · PI RESSOM, HABTOM W · 2010 to 2014
$1.4M
Quantitative analysis of LC-MS data for peptide and glycan biomarker discoveryR01GM086746 · NIGMS · GEORGETOWN UNIVERSITY · PI RESSOM, HABTOM W · 2010 to 2014
$1.3M
NCI NIH HHS P30 CA051008NCI NIH HHS R01 CA050633NCI NIH HHS R01 CA143420NCI NIH HHS U01 CA185188NCI NIH HHS U54 CA149147NIGMS NIH HHS R01 GM086746
6 · The paper itself

Abstract

In this paper, we introduce a novel computational method for constructing protein networks based on reverse phase protein array (RPPA) data to identify complex patterns in protein signaling. The method is applied to phosphoproteomic profiles of basal expression and activation/phosphorylation of 76 key signaling proteins in three breast cancer cell lines (MCF7, LCC1, and LCC9). Temporal RPPA data are acquired at 48h, 96h, and 144h after knocking down four genes in separate experiments. These genes are selected from a previous study as important determinants for breast cancer survival. Interaction networks are constructed by analyzing the expression levels of protein pairs using a multivariate analysis of variance model. A new scoring criterion is introduced to determine relevant protein pairs. Through a network topology based analysis, we search for wiring patterns to identify key proteins that are associated with significant changes in expression levels across various experimental conditions.

Indexed as

Gene Expression Regulation, NeoplasticGene Regulatory NetworksProtein Processing, Post-TranslationalATPases Associated with Diverse Cellular ActivitiesBreast NeoplasmsCell Line, TumorCysteine-Rich Protein 61FemaleHumansIntracellular Signaling Peptides and ProteinsMCF-7 CellsMultivariate AnalysisNeoplasm ProteinsPhosphorylationProteasome Endopeptidase ComplexProtein Array AnalysisATPases Associated with Diverse Cellular ActivitiesCCN1 protein, humanCysteine-Rich Protein 61Intracellular Signaling Peptides and ProteinsNeoplasm ProteinsPOLR2B protein, humanProteasome Endopeptidase ComplexPSMC5 protein, humanRNA Polymerase IIRNA, Small InterferingTOB1 protein, humanTumor Suppressor ProteinsBreast cancerMANOVANetwork constructionRPPATopology analysis

Identifiers

PMID28651964
PMCPMC5603262

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.