Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
BioData Min. 2012 Aug 28;5(1):11. doi: 10.1186/1756-0381-5-11.
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.
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.
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.
大多数当前的蛋白质组学研究都集中在由于病理紊乱（例如：结直肠癌）而导致的蛋白质组改变，而不是提到结肠时的正常健康状态。因此，关于正常的整个组织-结肠蛋白质组的信息很少。
我们在这里报告了一个详细的鼠（鼠）整个组织-结肠蛋白质参考数据集，该数据集由 1237 个置信蛋白（FDR<2）组成，对其肽性质、细胞和亚细胞定位、功能网络 GO 注释分析及其相对丰度有全面的了解。所提供的数据集包括广泛的 pI 和 Mw 范围，分别为 3-12 和 4-600 kDa。Gravy 指数评分预测 19.5%的膜蛋白和 80.5%的球状蛋白。GO 层次结构和功能网络分析说明了蛋白质与其相关性一起发挥功能，以及它们在几种恶性肿瘤中的相关性和意义，如结直肠癌中的丝裂原激活蛋白激酶（Mapk8、9）、成纤维细胞生长因子受体（Fgfr2）、前列腺癌中的谷胱甘肽 S-转移酶（Gstp1）和胰腺癌中的细胞分裂控制蛋白（Cdc42）、Ras 相关蛋白（Rac1、2）。使用 3 种不同算法（NSAF、PAF 和 emPAI）计算的蛋白质丰度提供了正常条件下的相对定量作为指导。
这个高度置信的结肠蛋白质组目录不仅将作为进一步实验的有用参考，以表征从疾病状态诱导的差异表达蛋白，而且还将有助于更好地理解结肠的本体论和功能吸收机制。
