Gene-chip analysis of the effect of tripeptide tyroservatide (YSV) on gene-expression in human hepatocarcinoma BEL-7402 tumors transplanted to nude mice

2006 ◽  
Vol 45 (3) ◽  
pp. 197-203 ◽  
Author(s):  
Jing Jia ◽  
Rong Lu ◽  
Chunlei Zhou ◽  
Lan Zhao ◽  
Zheng Fu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nude Mice ◽  
Gene Chip ◽  
Chip Analysis

Gene chip analysis of gastric gene expression in gastrin-deficient mice

2001 ◽  
Vol 120 (5) ◽  
pp. A181-A181
Author(s):  
L FRIISHANSEN ◽  
P BENNETT ◽  
K BENDTZEN ◽  
K RIENECK
Keyword(s):  
Gene Expression ◽  
Gene Chip ◽  
Deficient Mice ◽  
Chip Analysis

Gene chip analysis of gastric gene expression in gastrin-deficient mice

2001 ◽  
Vol 120 (5) ◽  
pp. A181
Author(s):  
Lennart Friis-Hansen ◽  
Phillip Bennett ◽  
Klaus Bendtzen ◽  
Klaus Rieneck
Keyword(s):  
Gene Expression ◽  
Gene Chip ◽  
Deficient Mice ◽  
Chip Analysis

S5-8 Altered pattern of gene expression in heart failure-gene chip analysis

2002 ◽  
Vol 34 (10) ◽  
pp. A13
Author(s):  
Haruhiro Toko ◽  
Masaya Sakamoto ◽  
Masanori Sano ◽  
Mutsuo Harada ◽  
Issei Komuro
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Gene Chip ◽  
Chip Analysis

Local mechanisms for acupoint sensitization in gall bladder meridian of foot shaoyang-a gene chip study

2019 ◽  
Vol 44 (2) ◽  
pp. 77-87
Author(s):  
Koichi Ishida ◽  
Liyue Qin ◽  
Ting Wang ◽  
Ying Lei ◽  
Weiwei Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gall Bladder ◽  
Interleukin 1 ◽  
Gene Chip ◽  
Molecular Evidence ◽  
Sprague Dawley ◽  
Sprague Dawley Rats ◽  
Bladder Meridian ◽  
Integrin Linked Kinase ◽  
Necrosis Factor

Acupuncture manipulations are clinically important to traditional Chinese medicine, yet the biological mechanisms have not been fully understood. This study aimed to investigate continuous stimulation-induced gene expression changes at stimulated and non-stimulated adjacent acupoints in the same meridian. Catgut embedding into acupoint (CEP) was conducted at acupoint Yanglingquan (gall bladder meridian of foot-shaoyang 34, GB34) of Sprague Dawley rats once or continuously for eight weeks, and gene expression changes at GB34 were assessed by gene chip array analysis 72 h after the last CEP treatment. A total of 688 genes exhibited opposite changes in expression between the two treatments, and 1,336 genes were regulated only by the eight-week CEP treatment. Ingenuity Pathway Analysis revealed that among these differentially regulated genes by one-time and eight-week CEP treatment, insulin-like growth factor-1 pathway and integrin-linked kinase pathway, and Wnt/~ catenin signaling pathway match the observed gene changes to predicted up/down regulation patterns. Upstream analysis further predicted six molecules, namely, tumor necrosis factor, interleukin 1~, interleukin la, kallikrein-related peptidase 5, protein kinase Ca, and catenin ~1. On the other hand, continuous eight-week CEP stimulation at acupoint Xuanzhong (GB39) caused similar changes in the expression of 32 genes at acupoints GB34 and Fengshi (GB31) on the same meridian. Taken together, our results provide the first molecular evidence for the local acupoints' mechanisms for acupoint sensitization theory, and implicate the existence of signaling pathways, either direct or indirect, between acupoints within the meridian GB.

scholarly journals Research on Complex Classification Algorithm of Breast Cancer Chip Based on SVM-RFE Gene Feature Screening

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Guobin Chen ◽  
Xianzhong Xie ◽  
Shijin Li
Keyword(s):  
Gene Expression ◽  
Classification Problem ◽  
Classification Algorithm ◽  
Gene Chip ◽  
Classification Problems ◽  
Gene Chips ◽  
Gene Expression Matrix ◽  
Performance Indexes ◽  
Characteristic Sequences

Screening and classification of characteristic genes is a complex classification problem, and the characteristic sequences of gene expression show high-dimensional characteristics. How to select an effective gene screening algorithm is the main problem to be solved by analyzing gene chips. The combination of KNN, SVM, and SVM-RFE is selected to screen complex classification problems, and a new method to solve complex classification problems is provided. In the process of gene chip pretreatment, LogFC and P value equivalents in the gene expression matrix are screened, and different gene features are screened, and then SVM-RFE algorithm is used to sort and screen genes. Firstly, the characteristics of gene chips are analyzed and the number between probes and genes is counted. Clustering analysis among each sample and PCA classification analysis of different samples are carried out. Secondly, the basic algorithms of SVM and KNN are tested, and the important indexes such as error rate and accuracy rate of the algorithms are tested to obtain the optimal parameters. Finally, the performance indexes of accuracy, precision, recall, and F1 of several complex classification algorithms are compared through the complex classification of SVM, KNN, KNN-PCA, SVM-PCA, SVM-RFE-SVM, and SVM-RFE-KNN at P=0. 01,0.05,0.001. SVM-RFE-SVM has the best classification effect and can be used as a gene chip classification algorithm to analyze the characteristics of genes.

Development and Implementation of an Analysis Tool for Array-based Comparative Genomic Hybridization

2007 ◽  
Vol 46 (05) ◽  
pp. 608-613 ◽  
Author(s):  
M. Rosolowski ◽  
H. Berger ◽  
C. Schwaenen ◽  
S. Wessendorf ◽  
M. Loeffler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Comparative Genomic Hybridization ◽  
Gene Expression Data ◽  
Array Cgh ◽  
Comparative Genomic ◽  
Analysis Tool ◽  
Expression Data ◽  
Mrna Gene ◽  
Mrna Gene Expression ◽  
Chip Analysis

Summary Objectives: Array-comparative genomic hybridization (aCGH) is a high-throughput method to detect and map copy number aberrations in the genome. Multi-step analysis of high-dimensional data requires an integrated suite of bioinformatic tools. In this paperwe detail an analysis pipeline for array CGH data. Methods: We developed an analysis tool for array CGH data which supports single and multi-chip analyses as well as combined analyses with paired mRNA gene expression data. The functions supporting relevant steps of analysis were implemented using the open source software R and combined as package aCGHPipeline. Analysis methods were illustrated using 189 CGH arrays of aggressive B-cell lymphomas. Results: The package covers data input, quality control, normalization, segmentation and classification. For multi-chip analysis aCGHPipeline offers an algorithm for automatic delineation of recurrent regions. This task was performed manuallyup to now. The package also supports combined analysis with mRNA gene expression data. Outputs consist of HTML documents to facilitate communication with clinical partners. Conclusions: The R package aCGHPipeline supports basic tasks of single and multi-chip analysis of array CGH data.

Sign in / Sign up

Export Citation Format

Share Document