ArticleJournal of proteome research2011
Network-based pipeline for analyzing MS data: an application toward liver cancer.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed, 55 citations in OpenAlex.
- SNORD88B-mediated WRN nucleolar trafficking drives self-renewal in liver cancer initiating cells and hepatocarcinogenesis.Nature communications · 2024Article
- Anti-liver fibrosis effects of the total flavonoids of litchi semen on CClPharmaceutical biology · 2022Article
- Radiochemotherapy-induced DNA repair promotes the biogenesis of gastric cancer stem cells.Stem cell research & therapy · 2022Article
- Potential Biomarkers for Liver Cancer Diagnosis Based on Multi-Omics Strategy.Frontiers in oncology · 2022Review
- Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics.Frontiers in oncology · 2021Review
- Differential proteomics analysis of liver failure in peripheral blood mononuclear cells using isobaric tags for relative and absolute quantitation.Biomedical reports · 2017Article
- Fuzzy-FishNET: a highly reproducible protein complex-based approach for feature selection in comparative proteomics.BMC medical genomics · 2016Article
- Integrative topological analysis of mass spectrometry data reveals molecular features with clinical relevance in esophageal squamous cell carcinoma.Scientific reports · 2016Article
- Quantitative proteomics signature profiling based on network contextualization.Biology direct · 2015Article
- iTRAQ-based proteomic analysis of hepatic tissues from patients with hepatitis B virus-induced acute-on-chronic liver failure.Experimental and therapeutic medicine · 2015Article
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- Contemporary network proteomics and its requirements.Biology · 2013Article
- Serum proteomics analysis and comparisons using iTRAQ in the progression of hepatitis B.Experimental and therapeutic medicine · 2013Article
- Integrative toxicoproteomics implicates impaired mitochondrial glutathione import as an off-target effect of troglitazone.Journal of proteome research · 2013Article
- Comparative network-based recovery analysis and proteomic profiling of neurological changes in valproic acid-treated mice.Journal of proteome research · 2013Article
- Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies.BMC genomics · 2013Article
- Proteomics signature profiling (PSP): a novel contextualization approach for cancer proteomics.Journal of proteome research · 2012Article
- IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.BMC systems biology · 2012Article
- A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression.International journal of bioinformatics research and applications · 2012Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
Current limitations in proteome analysis by high-throughput mass spectrometry (MS) approaches have sometimes led to incomplete (or inconclusive) data sets being published or unpublished. In this work, we used an iTRAQ reference data on hepatocellular carcinoma (HCC) to design a two-stage functional analysis pipeline to widen and improve the proteome coverage and, subsequently, to unveil the molecular changes that occur during HCC progression in human tumorous tissue. The first involved functional cluster analysis by incorporating an expansion step on a cleaned integrated network. The second used an in-house developed pathway database where recovery of shared neighbors was followed by pathway enrichment analysis. In the original MS data set, over 500 proteins were detected from the tumors of 12 male patients, but in this paper we reported an additional 1000 proteins after application of our bioinformatics pipeline. Through an integrative effort of network cleaning, community finding methods, and network analysis, we also uncovered several biologically interesting clusters implicated in HCC. We established that HCC transition from a moderate to poor stage involved densely connected clusters that comprised of PCNA, XRCC5, XRCC6, PARP1, PRKDC, and WRN. From our pathway enrichment analyses, it appeared that the HCC moderate stage, unlike the poor stage, is enriched in proteins involved in immune responses, thus suggesting the acquisition of immuno-evasion. Our strategy illustrates how an original oncoproteome could be expanded to one of a larger dynamic range where current technology limitations prevent/limit comprehensive proteome characterization.
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Registered trials
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.