Evidence map›Paper›PMID 24911777›Full record

ReviewJournal of theoretical biology2014

Pathway and network analysis in proteomics.

Xiaogang Wu, Mohammad Al Hasan, Jake Yue Chen

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Journal of theoretical biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
66citing papers in PubMed, 1 pooled it
–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

66 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  11. Heterogeneous network approaches to protein pathway prediction.Computational and structural biotechnology journal · 2024
    Review
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6 more citing papers are in PubMed but not listed here.

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

3 authors.

Xiaogang WuInstitute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, Wenzhou, Zhejiang Province, China; School of Informatics and Computing, Indiana University-Purdue University, Indianapolis, IN 46202, USA; Institute for Systems Biology, Seattle, WA 98109, USA.
Mohammad Al HasanDepartment of Computer Science and Information Science Purdue University, Indianapolis, IN 46202, USA.
Jake Yue ChenInstitute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, Wenzhou, Zhejiang Province, China; School of Informatics and Computing, Indiana University-Purdue University, Indianapolis, IN 46202, USA; Department of Computer Science and Information Science Purdue University, Indianapolis, IN 46202, USA; Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA. Electronic address: jakechen@iupui.edu.

Funding

Use of Micro-RNA Arrays to Identify MDSC Functional Pathways and MarkersR21CA173918 · NCI · PURDUE UNIVERSITY · PI RATLIFF, TIMOTHY L. · 2013 to 2014
$369k
NCI NIH HHS R21 CA173918
6 · The paper itself

Abstract

Proteomics is inherently a systems science that studies not only measured protein and their expressions in a cell, but also the interplay of proteins, protein complexes, signaling pathways, and network modules. There is a rapid accumulation of Proteomics data in recent years. However, Proteomics data are highly variable, with results sensitive to data preparation methods, sample condition, instrument types, and analytical methods. To address the challenge in Proteomics data analysis, we review current tools being developed to incorporate biological function and network topological information. We categorize these tools into four types: tools with basic functional information and little topological features (e.g., GO category analysis), tools with rich functional information and little topological features (e.g., GSEA), tools with basic functional information and rich topological features (e.g., Cytoscape), and tools with rich functional information and rich topological features (e.g., PathwayExpress). We first review the potential application of these tools to Proteomics; then we review tools that can achieve automated learning of pathway modules and features, and tools that help perform integrated network visual analytics.

Indexed as

AlgorithmsAnimalsColorectal NeoplasmsComputational BiologyDatabases, ProteinFemaleGene Expression RegulationHumansMaleMultigene FamilyOvarian NeoplasmsPattern Recognition, AutomatedProstatic NeoplasmsProtein Array AnalysisProtein Interaction MappingProteinsProteinsComplex networksFunctional analysisHybrid strategyNetwork modulesPathway analysis

Identifiers

PMID24911777
PMCPMC4253643

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

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.