Integrative topological analysis of mass spectrometry data reveals molecular features with clinical relevance in esophageal squamous cell carcinoma

Scientific Reports
She-Gan GaoYuan-Fang Ma

Abstract

Combining MS-based proteomic data with network and topological features of such network would identify more clinically relevant molecules and meaningfully expand the repertoire of proteins derived from MS analysis. The integrative topological indexes representing 95.96% information of seven individual topological measures of node proteins were calculated within a protein-protein interaction (PPI) network, built using 244 differentially expressed proteins (DEPs) identified by iTRAQ 2D-LC-MS/MS. Compared with DEPs, differentially expressed genes (DEGs) and comprehensive features (CFs), structurally dominant nodes (SDNs) based on integrative topological index distribution produced comparable classification performance in three different clinical settings using five independent gene expression data sets. The signature molecules of SDN-based classifier for distinction of early from late clinical TNM stages were enriched in biological traits of protein synthesis, intracellular localization and ribosome biogenesis, which suggests that ribosome biogenesis represents a promising therapeutic target for treating ESCC. In addition, ITGB1 expression selected exclusively by integrative topological measures correlated with clinical stages and...Continue Reading

References

Jun 1, 1994·The Journal of Pathology·D E HughesA al-Nafussi
May 3, 2001·Nature·H JeongZ N Oltvai
Apr 11, 2002·Nature Cell Biology·Cindy K Miranti, Joan S Brugge
May 18, 2004·Trends in Genetics : TIG·Haiyuan YuMark Gerstein
Jul 18, 2006·Bioinformatics·Pall F Jonsson, Paul A Bates
Feb 15, 2007·Molecular Systems Biology·Ayla ErgünJames J Collins
Mar 14, 2007·Molecular Systems Biology·Roded SharanRon Shamir
Jun 30, 2007·BMC Bioinformatics·Hon Nian ChuaLimsoon Wong
Jun 26, 2007·Proceedings of the National Academy of Sciences of the United States of America·Shai CarmiEran Shir
Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker
Dec 23, 2008·Molecular & Cellular Proteomics : MCP·Rod K NibbeMark R Chance
Feb 3, 2009·Nature Biotechnology·Ian W TaylorJeffrey L Wrana
Jul 2, 2009·International Journal of Cancer. Journal International Du Cancer·Wenjun ChangGuangwen Cao
Oct 13, 2009·NeuroImage·Mikail Rubinov, Olaf Sporns
Jul 14, 2010·Nature Biotechnology·Parag Mallick, Bernhard Kuster
Jan 5, 2011·Methods in Molecular Biology·Vivek KaimalAnil G Jegga
Feb 8, 2011·CA: a Cancer Journal for Clinicians·Ahmedin JemalDavid Forman
Mar 18, 2011·Journal of Proteome Research·Wilson Wen Bin GohLimsoon Wong
Jan 17, 2012·Proteomics·Wilson W B GohLimsoon Wong
Jan 11, 2013·BMC Systems Biology·Meeta P PradhanMathew J Palakal
Feb 5, 2013·Lancet·Arjun PennathurJames D Luketich
Feb 27, 2013·Molecular Cell·Matthias MannJürgen Cox
May 1, 2013·Journal of Epidemiology·Yingsong LinHideo Tanaka
Apr 1, 2014·IEEE Transactions on Biomedical Circuits and Systems·Pei WangJinhu Lü
Jun 3, 2014·Arthritis Research & Therapy·Adam StevensRachelle P Donn
Jun 8, 2014·Annals of Oncology : Official Journal of the European Society for Medical Oncology·J WenJ H Fu
Jan 7, 2015·Journal of Cellular and Molecular Medicine·Hao ChenYunfeng Cheng

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BETA
GSE
45670

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MASCOT
ArrayTools
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ClueGo
Cytoscape
LC
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