Research

BioData Mining

, 5:11

Open Access This content is freely available online to anyone, anywhere at any time.

Murine colon proteome and characterization of the protein pathways

  • Sameh MagdeldinAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata UniversityDepartment of Physiology, Faculty of Veterinary Medicine, Suez Canal University Email author 
  • , Yutaka YoshidaAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University
  • , Huiping LiAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata UniversityDepartment of Intensive Care Unit, West-China Hospital, Sichuan University
  • , Yoshitaka MaedaAffiliated withAnimal resource branch, Center of Bio-based researches, Brain research Institute, Niigata University
  • , Munesuke YokoyamaAffiliated withAnimal resource branch, Center of Bio-based researches, Brain research Institute, Niigata University
  • , Shymaa EnanyAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata UniversityDepartment of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University
  • , Ying ZhangAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University
  • , Bo XuAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University
  • , Hidehiko FujinakaAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University
    • , Eishin YaoitaAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University
    • , Sei SasakiAffiliated withDepartment of Nephrology, Tokyo Medical and Dental University
    • , Tadashi YamamotoAffiliated withDepartment of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University

Abstract

Background

Most of the current proteomic researches focus on proteome alteration due to pathological disorders (i.e.: colorectal cancer) rather than normal healthy state when mentioning colon. As a result, there are lacks of information regarding normal whole tissue- colon proteome.

Results

We report here a detailed murine (mouse) whole tissue- colon protein reference dataset composed of 1237 confident protein (FDR < 2) with comprehensive insight on its peptide properties, cellular and subcellular localization, functional network GO annotation analysis, and its relative abundances. The presented dataset includes wide spectra of pI and Mw ranged from 3–12 and 4–600 KDa, respectively. Gravy index scoring predicted 19.5% membranous and 80.5% globularly located proteins. GO hierarchies and functional network analysis illustrated proteins function together with their relevance and implication of several candidates in malignancy such as Mitogen- activated protein kinase (Mapk8, 9) in colorectal cancer, Fibroblast growth factor receptor (Fgfr 2), Glutathione S-transferase (Gstp1) in prostate cancer, and Cell division control protein (Cdc42), Ras-related protein (Rac1,2) in pancreatic cancer. Protein abundances calculated with 3 different algorithms (NSAF, PAF and emPAI) provide a relative quantification under normal condition as guidance.

Conclusions

This highly confidence colon proteome catalogue will not only serve as a useful reference for further experiments characterizing differentially expressed proteins induced from diseased conditions, but also will aid in better understanding the ontology and functional absorptive mechanism of the colon as well.

Keywords

Colon Proteome Mass spectrometry HPLC