共查询到20条相似文献，搜索用时 15 毫秒
1.
2.
3.
4.
运用复杂网络理论,对TCGA胃癌数据进行了筛选与降维,筛选出275个胃癌相关的基因,获得样本容量为40的胃癌ⅡB期样本组和样本容量为36的胃癌ⅢA期样本组。通过分析胃癌ⅡB期样本组与胃癌ⅢA期样本组的基因变化率,建立节点（基因）间的连边关系,从而构建了胃癌恶化过程的基因表达网络。引入综合中心性指标对网络进行分析,筛选出17个综合中心指数较高的基因。应用复杂网络的相关理论对胃癌基因网络进行社区划分,发现17个综合中心指数较高的基因全部落在一个规模较大的连通的子网络中,此拓扑结构与胃癌基因表达网络的关键节点一致。通过综合分析获取了胃癌恶化过程中的关键基因,提供了良好的胃癌恶化早期的预警信号。 相似文献
5.
6.
微卫星是遍布于人类基因组中的短串重复序列,肿瘤组织的微卫星由于重复单位的插入或缺失而导致微卫星长度的改变的现象叫做微卫星不稳定性（Microsatellite Instability,MSI）。MSI型胃癌往往拥有独特的分子表型以及临床病理特征,且微卫星的不稳定性决定了胃癌患者对免疫疗法的反应是否良好,因此MSI状态的术前检测对于胃癌患者治疗方案的制定具有重要意义。传统的MSI检测方法需要进行免疫组化及基因分析,不仅需要增加额外的成本,而且在临床实践中难以推广至每一个患者。应用图像特征提取技术和机器学习算法对胃癌患者的高分辨组织病理图像进行定量分析,实现对胃癌患者MSI状态的预测。从TCGA数据库获取279例原始数据,经预处理和上采样后得到442个样本,从每例样本的组织病理图像中提取出445个定量图像特征,包括图像的一阶统计量,纹理特征以及小波特征。应用Lasso回归进行特征筛选并构造胃癌MSI状态的预测标签（Risk-score）,并通过logistics分类模型对预测标签分类性能进行验证,进而结合每例患者的临床特征进行多变量分析,构建个性化的列线图进行MSI状态预测。实验结果显示,基于组织病理图像纹理特征的预测标签的预测性能AUC值为0.74,现有的基于组织病理图像纹理特征的MSI预测模型AUC值为0.73;基于全部样本,结合临床特征与Risk-score构建的MSI预测模型AUC值为0.802,而现有的结合临床特征和图像特征的MSI预测模型的AUC值仅为0.752,相较于现有方法,提出的MSI预测模型具有更优的预测性能,可以为胃癌患者的临床决策提供更有价值的参考信息。 相似文献
7.
8.
9.
10.
11.
12.
马斌 《计算机科学技术学报》2010,25(1):107-123
Mass spectrometry is an analytical technique for determining the composition of a sample. Recently it has become a primary tool for protein identification and quantification, and post translational modification characterization in proteomics research. Both the size and the complexity of the data produced by this experimental technique impose great computational challenges in the data analysis. This article reviews some of these challenges and serves as an entry point for those who want to study the area in ... 相似文献
13.
《Proteomics. Clinical applications》2018,12(3)
Background
Optimized blood collection tubes (BCT) have been developed to expand the utility of plasma cell‐free DNA (cfDNA) and are in clinical use. The appropriateness of plasma collected and stored in these tubes for proteomic analysis is unknown.Methods
Paired blood samples were collected in BCT and traditional K3EDTA (EDTA) tubes from healthy controls and from colorectal cancer (CRC) patients before and after surgery, and stored for between 45 min and 48 h at room temperature. Plasma proteins were analyzed following high‐abundant plasma protein depletion in quantitative discovery and targeted proteomics by liquid chromatography tandem‐mass spectrometry (LC‐MS/MS).Results
BCT reduced cellular protein contamination in healthy controls over time, and increased the number of high confident low‐abundant protein identifications in CRC blood samples compared to matched samples collected in EDTA tubes. The known CRC plasma protein biomarker, carcinoembryonic antigen (CEA), showed elevated levels across patients pre‐operatively when collected and stored in BCT compared to EDTA tubes. Emerging CRC biomarkers, Dickkopf‐3 (DKK3) and Gelsolin (GSN), showed elevated levels pre‐operatively when collected in BCT.Conclusions
Optimized BCT are appropriate for low‐abundant plasma protein analysis and can be used with confidence for clinical proteomics.14.
15.
16.
上皮-间质转化(Epithelial-Mesenchymal Transition,EMT)是上皮细胞通过特定程序转变为间充质细胞的形态学过程,在癌症侵袭-转移级联过程中发挥着重要的作用。在癌症进程中,肿瘤细胞会经过一系列动态和可逆的细胞表型变化。EMT 程序的这种可塑性提示表观遗传调控在这一过程中发挥着重要的作用。EMT 相关的转录因子能够通过调控关键靶基因的表达,从而调节 EMT 程序。这些主要的 EMT 诱导因子依赖于表观遗传调控机制,从而调节 EMT 过程中基因表达变化。因此理解 EMT 调控的表观遗传机制有助于我们更好地了解肿瘤转移的分子机制,为恶性肿瘤的治疗提供新的靶点和思路。 相似文献
17.
The non‐surgical diagnosis of endometriosis is still challenging for the clinician. Ultrasonography and magnetic resonance imaging can be used to diagnose ovarian endometriotic cysts and deep infiltrating endometriosis; but their performance is poor in the diagnosis of initial stages of endometriosis. CA‐125 and other serum markers (such as CA 19‐9, serum protein PP14, interleukins, and angiogenetic factors) have been measured in women with endometriosis but they are not reliable for the diagnosis of the disease. Although several studies used proteomics technologies to identify plasmatic markers of endometriosis, the non‐invasive diagnosis of endometriosis is far from being achieved. In this issue, Manousopoulou et al. compare the integrated quantitative proteomic profile of eutopic endometrium and serum of women with endometriosis and controls. 1214 proteins are differentially expressed in the eutopic endometrium and 404 proteins in the serum of the two study groups. 21 proteins are aberrantly expressed in both eutopic endometrium and serum of women with endometriosis. More work is needed to assess if the differentially expressed proteins identified in this study can be used as clinical markers of endometriosis. 相似文献
18.
《Proteomics. Clinical applications》2018,12(3)
Purpose
The aim of this study was to screen for novel host proteins that play a role in HBx augmenting Hepatitis B virus (HBV) replication.Experimental design
Three HepG2 cell lines stably harboring different functional domains of HBx (HBx, HBx‐Cm6, and HBx‐Cm16) were cultured. ITRAQ technology integrated with LC‐MS/MS analysis was applied to identify the proteome differences among these three cell lines.Results
In brief, a total of 70 different proteins were identified among HepG2‐HBx, HepG2‐HBx‐Cm6, and HepG2‐HBx‐Cm16 by double repetition. Several differentially expressed proteins, including p90 ribosomal S6 kinase 2 (RSK2), were further validated. RSK2 was expressed at higher levels in HepG2‐HBx and HepG2‐HBx‐Cm6 compared with HepG2‐HBx‐Cm16. Furthermore, levels of HBV replication intermediates were decreased after silencing RSK2 in HepG2.2.15. An HBx‐minus HBV mutant genome led to decreased levels of HBV replication intermediates and these decreases were restored to levels similar to wild‐type HBV by transient ectopic expression of HBx. After silencing RSK2 expression, the levels of HBV replication intermediates synthesized from the HBx‐minus HBV mutant genome were not restored to levels that were observed with wild‐type HBV by transient HBx expression.Conclusion and clinical Relevance
Based on iTRAQ quantitative comparative proteomics, RSK2 was identified as a novel host protein that plays a role in HBx augmenting HBV replication.19.