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特征选择；高维；学习技术；微阵列数据集 1

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Characterization of the genes involved in nitrogen cycling in wastewater treatment plants using DNA microarray

Junqin PANG, Masami MATSUDA, Masashi KURODA, Daisuke INOUE, Kazunari SEI, Kei NISHIDA, Michihiko IKE

《环境科学与工程前沿（英文）》 2016年 第10卷 第4期 doi: 10.1007/s11783-016-0846-x

摘要： Nitrogen-cycling microbial communities in municipal WWTPs were characterized. Numbers of , and genes were quantified by MPN-PCR. Diversity of whole nitrogen-cycling communities was analyzed with DNA microarray. CAS process retained diverse nitrogen cycling populations. Specific, limited populations may be dominated in nitrogen removal processes. To improve nitrogen removal performance of wastewater treatment plants (WWTPs), it is essential to understand the behavior of nitrogen cycling communities, which comprise various microorganisms. This study characterized the quantity and diversity of nitrogen cycling genes in various processes of municipal WWTPs by employing two molecular-based methods:most probable number-polymerase chain reaction (MPN-PCR) and DNA microarray. MPN-PCR analysis revealed that gene quantities were not statistically different among processes, suggesting that conventional activated sludge processes (CAS) are similar to nitrogen removal processes in their ability to retain an adequate population of nitrogen cycling microorganisms. Furthermore, most processes in the WWTPs that were researched shared a pattern:the and the bacterial genes were more abundant than the and archaeal genes, respectively. DNA microarray analysis revealed that several kinds of nitrification and denitrification genes were detected in both CAS and anaerobic-oxic processes (AO), whereas limited genes were detected in nitrogen removal processes. Results of this study suggest that CAS maintains a diverse community of nitrogen cycling microorganisms; moreover, the microbial communities in nitrogen removal processes may be specific.

关键词： DNA microarray analysis     Nitrogen cycling functional genes     Most probable number-polymerase chain reaction (MPN-PCR)     Wastewater treatment plants (WWTPs)    

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A microarray study of altered gene expression during melanoblasts migration in normal pigmented White

Yulin LI,Deping HAN,Junying LI,Dawn KOLTES,Xuemei DENG

《农业科学与工程前沿（英文）》 2014年 第1卷 第4期   页码 299-306 doi: 10.15302/J-FASE-2014040

摘要： Melanoblasts originating from neural crest cells can migrate through the mesenchyme of the developed embryo and give rise to melanocytes. Unlike the melanocytes that are confined to the integument in other vertebrates, melanocytes in Silky Fowl can reach the ventral regions of the embryos owing to differences in gene expression in the process of melanoblasts migration. In this study, we used microarray profiling to identify differences in gene expression between White Leghorn and Silky Fowl. Differential expression of 2517 microarray probes ( <0.01, Fold Change>2) was observed in Silky Fowl compared to White Leghorn. After filtration by cluster analysis, functional annotation and pathway analysis, eight differentially expressed genes were identified to be closely related to the development of melanocytes. Moreover, differences in expression of immune genes were also detected between Silky Fowl and White Leghorn. The differentially expressed genes associated with melanocyte development were verified by q-PCR, and results were highly consistent with the microarray data. The genes with significantly altered expression involved in melanoblast migration and development suggested that different microenvironments resulted in the abnormal melanoblast migration in Silky Fowl, although there were no big differences in melanoblast development between these two breeds. The candidate genes discovered in this study are beneficial to understand the molecular mechanism of hyperpigmentation in Silky Fowl.

关键词： Silky Fowl     White Leghorn     melanoblast migration     gene expression    

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微阵列数据集的特征选择技术：综合评述、分类和未来方向 Review

Kulanthaivel BALAKRISHNAN, Ramasamy DHANALAKSHMI

《信息与电子工程前沿（英文）》 2022年 第23卷 第10期   页码 1451-1478 doi: 10.1631/FITEE.2100569

摘要：

为获得最佳结果，从微阵列数据集中检索相关特征已成为特征选择（FS）技术的研究热点。本综述旨在全面阐述各种最新特征选择技术，同时介绍了基于微阵列数据集的处理多类分类问题的技术以及提高学习算法性能的不同方法。我们试图理解和解决数据集不平衡问题，以证实研究人员在微阵列数据集上的工作。对文献的分析为理解和强调在通过各种特征选择技术寻找最佳特征子集时存在的众多挑战和问题铺平了道路。同时提供了一个案例说明该方法的实施过程，该方法使用3个微阵列癌症数据集评估一些包装方法和混合方法的分类精度和收敛能力，以确认最优特征子集。

关键词： 特征选择；高维；学习技术；微阵列数据集    

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Data mining of microarray for differentially expressed genes in liver metastasis from gastric cancer

Ling XU MM, Feng WANG MM, Xuan-Fu XU MD, Wen-Hui MO BM, Rong WAN MD, Chuan-Yong GUO MD, Xing-Peng WANG MD,

《医学前沿（英文）》 2010年 第4卷 第2期   页码 247-253 doi: 10.1007/s11684-010-0027-4

摘要： Tumor metastasis is the leading cause of death for gastric cancer. Metastasis is the main reason for the failure of clinical treatment for gastric cancer. In order to find metastasis-related genes and abnormal signal transduction pathway of high-invasive gastric cancer, samples of gastric cancer with liver metastasis were collected for microarray detection; up-regulated or down-regulated genes in all three cases were simultaneously screened out. Subsequently, from the preliminary screened genes, molecular pathways possibly impacting liver metastasis from gastric cancer were investigated by the Gene Cluster with Literature Profiles (GenCLip) analysis software. Many biological effects including apoptosis have been validated. Functional analysis of differentially expressed genes revealed that a variety of biological pathways, such as blood circulation and gas exchange, vasodilation and vasoconstriction regulation, and immune defense, could be significantly activated. Besides, gene sequences, specific keywords or gene regulatory networks were further searched by GenCLiP. We conclude that data mining allows to quickly identify a series of special signal transduction pathways involving abnormally expressed genes.

关键词： gastric carcinoma     metastasis     signal transduction     gene chips    

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Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome

null

《医学前沿（英文）》 2013年 第7卷 第3期   页码 280-289 doi: 10.1007/s11684-013-0265-3

摘要：

Many gene fusions have been recognized as important diagnostic and/or prognostic markers in human malignancies. In recent years, novel gene fusions have been identified in cases without prior knowledge of the genetic background. Accompanied by a powerful computational data analysis method, new genome-wide screening approaches were used to detect cryptic genomic aberrations. This review focused on advanced genome-wide screening approaches in fusion gene identification, such as microarray-based approaches, next-generation sequencing, and NanoString nCounter gene expression system. The fundamental rationale and strategy for fusion gene identification using each biotech platform are also discussed.

关键词： gene fusion     cancer     microarray     next-generation sequencing     NanoString nCounter system    

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MiRNA-451 is a potential biomarker for estrogenicity in mouse uterus

Lingyan HOU, Yun LU, Ying LI, Li LI

《环境科学与工程前沿（英文）》 2014年 第8卷 第1期   页码 99-105 doi: 10.1007/s11783-013-0490-7

摘要： The uterotrophic assay has been commonly used to test environmental estrogens in vivo, however, it is often not sensitive enough sometimes. An alternative way is to evaluate estrogenicity through biomarker genes. MicroRNA (miRNA) is a class of regulatory gene, which has been shown to be a good biomarker for many diseases and toxicological effects in recent years, and some evidences showed that estrogen induced response was partially mediated by miRNAs. In this study, two types of microarrays were used to test the 17β-estradiol (E2) induced miRNA expression profile at different time points in the immature mouse uterus. Statistical analysis showed the aldehyde slide based array had less variation than the amino slide based array, and 11 dysregulated miRNAs were screened out for significant fold change. Real-time PCR was performed to further confirm that 4 out of 7 selected miRNAs, namely miR-451, miR-155, miR-335-5p, and miR-365, are E2 regulated miRNAs in the uterus. The function of the predicted targets of these miRNAs is involved in cell grow control, which is consistent with the main E2 function in the uterus. MiR-451 had similar strong responses to E2 in the uterus of both immature and overiectomized mice, and could be a potential biomarker for estrogenicity in the uterus.

关键词： estrogen     microRNA (miRNA)     microarray     biomarker    

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Transcriptional modules related to hepatocellular carcinoma survival: coexpression network analysis

null

《医学前沿（英文）》 2016年 第10卷 第2期   页码 183-190 doi: 10.1007/s11684-016-0440-4

摘要：

We performed weighted gene coexpression network analysis (WGCNA) to gain insights into the molecular aspects of hepatocellular carcinoma (HCC). Raw microarray datasets (including 488 samples) were downloaded from the Gene Expression Omnibus (GEO) website. Data were normalized using the RMA algorithm. We utilized the WGCNA to identify the coexpressed genes (modules) after non-specific filtering. Correlation and survival analyses were conducted using the modules, and gene ontology (GO) enrichment was applied to explore the possible mechanisms. Eight distinct modules were identified by the WGCNA. Pink and red modules were associated with liver function, whereas turquoise and black modules were inversely correlated with tumor staging. Poor outcomes were found in the low expression group in the turquoise module and in the high expression group in the red module. In addition, GO enrichment analysis suggested that inflammation, immune, virus-related, and interferon-mediated pathways were enriched in the turquoise module. Several potential biomarkers, such as cyclin-dependent kinase 1 (CDK1), topoisomerase 2α (TOP2A), and serpin peptidase inhibitor clade C (antithrombin) member 1 (SERPINC1), were also identified. In conclusion, gene signatures identified from the genome-based assays could contribute to HCC stratification. WGCNA was able to identify significant groups of genes associated with cancer prognosis.

关键词： hepatocellular carcinoma     coexpression     module     microarray     prognosis    

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Gene expression disparity in giant cell tumor of bone

Xiaohua PAN, Shuhua YANG, Deming XIAO, Yong DAI, Lili REN

《医学前沿（英文）》 2009年 第3卷 第1期   页码 49-56 doi: 10.1007/s11684-009-0012-y

摘要： The aim of this paper was to study the differential gene expression of giant cell tumor of bone (GCTB) by gene chip technology. Total RNA of 8 fresh GCTB specimens (Jaffe I∶6 cases, II∶1 case, III∶1 case; Campanacci I∶6 cases, II∶1 case, III∶1 case; Enneking Staging G T M : 5 cases, G T M : 2 cases, G T M : 1 case) and 4 normal bony callus specimens (the control group) were extracted and purified to get mRNA and then reverse transcribed to complementary DNA, respectively. Microarray screening with a set of 8064 human cDNA genes was conducted to analyze the difference among the samples and the control. The hybridization signals were scanned. The gene expression disparity between the GCTB samples and normal bony callus was significantly different ( <0.01), and the disparity of over 5-fold was found in 47 genes in the GCTB specimens, with 25 genes up-regulated and 22 down-regulated including the extracellular matrix and transforming-related genes, oncogene and its homolog genes, cytokine and its receptor genes. Specific gene spectrum associated with GCTB can be identified by cDNA microarray, which will be the foundation of progressive etiology elucidation, diagnosis and treatment of GCTB.

关键词： giant cell tumor of bone     gene     microarray     cDNA    

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Expression and bioinformatic analysis of lymphoma-associated novel gene KIAA0372

BAI Xiangyang, TANG Duozhuang, ZHU Tao, SUN Lishi, YAN Lingling, LU Yunping, ZHOU Jianfeng, MA Ding

《医学前沿（英文）》 2007年 第1卷 第1期   页码 93-98 doi: 10.1007/s11684-007-0018-2

摘要： The purpose of this study was to explore the differentially expressed genes in lymph-node cells (LNC) of lymphomas and reactive lymph node hyperplasia, and to perform an initial bioinformatic analysis on a novel gene, KIAA0372, which is highly expressed in the LNC of lymphomas. mRNA extracted from LNC of lymphomas and reactive lymph node hyperplasia were respectively marked with biotin and hybridized with Gene Expression Chips, resulting in differentially expressed genes. Initial bioinformatic analysis was then performed on a novel gene named KIAA0372, whose function has not yet been explored. Its structure and genomic location, its product s physical and chemical properties, subcellular localization and functional domains, were also predicted. Further, a systematic evolution analysis was performed on similar proteins from among several species. Using Gene Expression Chips, many differentially expressed genes were uncovered. Efficient bioinformatic analysis has fundamentally determined that KIAA0372 is an extracellular protein which may be involved in TGF-β signaling. Microarray is an efficient and high throughput strategy for detection of differentially expressed genes. And KIAA0372 is thought to be a potential target for tumor research using bioinformatic analysis.

关键词： bioinformatic analysis     functional     KIAA0372     detection     Microarray    

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Nucleic acid-based diagnostics for infectious diseases in public health affairs

null

《医学前沿（英文）》 2012年 第6卷 第2期   页码 173-186 doi: 10.1007/s11684-012-0195-5

摘要：

Infectious diseases, mostly caused by bacteria and viruses but also a result of fungal and parasitic infection, have been one of the most important public health concerns throughout human history. The first step in combating these pathogens is to get a timely and accurate diagnosis at an affordable cost. Many kinds of diagnostics have been developed, such as pathogen culture, biochemical tests and serological tests, to help detect and fight against the causative agents of diseases. However, these diagnostic tests are generally unsatisfactory because they are not particularly sensitive and specific and are unable to deliver speedy results. Nucleic acid-based diagnostics, detecting pathogens through the identification of their genomic sequences, have shown promise to overcome the above limitations and become more widely adopted in clinical tests. Here we review some of the most popular nucleic acid-based diagnostics and focus on their adaptability and applicability to routine clinical usage. We also compare and contrast the characteristics of different types of nucleic acid-based diagnostics.

关键词： nucleic acid-based diagnostics     infectious disease     PCR     NASBA     LAMP     microarray     LOAC     public health affairs    

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Analysis of differential expression of genes induced by ethephon in elongating internodes of maize plants

Xiaoyi WEI,Weiqiang ZHANG,Qian ZHANG,Pei SUN,Zhaohu LI,Mingcai ZHANG,Jianmin LI,Liusheng DUAN

《农业科学与工程前沿（英文）》 2016年 第3卷 第3期   页码 263-282 doi: 10.15302/J-FASE-2016103

摘要： Plant growth regulators (PGRs) are commonly used in cereal cropping systems to restrict plant height and control lodging. Ethephon has been reported to shorten internodes and increase grain yield of maize. To analyze the transcriptomic profiles of maize internode elongation following ethephon treatment, differentially expressed genes were compared between the treatment and control samples of inbred line Zong 31 using the Affymetrix Maize Genome Array. According to the microarray data, 326 probe sets showed significant change in expression. Further research revealed that the most remarkable effects of ethephon on maize internodes elongation occurred during a 48 h period, when 89 differentially expressed genes were detected. There were dramatic change in transcript levels at 24 h and six Auxin transport genes and four gibberellin biosynthesis pathway genes were differentially expressed in Zong 31 in response to ethephon treatment. In summary, we showed that gaseous ethylene release is involved in internode meristem cell elongation through the regulation of plant hormone signaling in maize. This work provides a platform for studies in which candidate genes will be functionally tested for involvement in internode elongation.

关键词： maize     ethephon     internode elongation     microarray     qPCR    

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标题 作者 时间 类型 操作

Characterization of the genes involved in nitrogen cycling in wastewater treatment plants using DNA microarray

Junqin PANG, Masami MATSUDA, Masashi KURODA, Daisuke INOUE, Kazunari SEI, Kei NISHIDA, Michihiko IKE

期刊论文

A microarray study of altered gene expression during melanoblasts migration in normal pigmented White

Yulin LI,Deping HAN,Junying LI,Dawn KOLTES,Xuemei DENG

期刊论文

微阵列数据集的特征选择技术：综合评述、分类和未来方向

Kulanthaivel BALAKRISHNAN, Ramasamy DHANALAKSHMI

期刊论文

Data mining of microarray for differentially expressed genes in liver metastasis from gastric cancer

Ling XU MM, Feng WANG MM, Xuan-Fu XU MD, Wen-Hui MO BM, Rong WAN MD, Chuan-Yong GUO MD, Xing-Peng WANG MD,

期刊论文

Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome

null

期刊论文

MiRNA-451 is a potential biomarker for estrogenicity in mouse uterus

Lingyan HOU, Yun LU, Ying LI, Li LI

期刊论文

Transcriptional modules related to hepatocellular carcinoma survival: coexpression network analysis

null

期刊论文

Gene expression disparity in giant cell tumor of bone

Xiaohua PAN, Shuhua YANG, Deming XIAO, Yong DAI, Lili REN

期刊论文

Expression and bioinformatic analysis of lymphoma-associated novel gene KIAA0372

BAI Xiangyang, TANG Duozhuang, ZHU Tao, SUN Lishi, YAN Lingling, LU Yunping, ZHOU Jianfeng, MA Ding

期刊论文

Nucleic acid-based diagnostics for infectious diseases in public health affairs

null

期刊论文

Analysis of differential expression of genes induced by ethephon in elongating internodes of maize plants

Xiaoyi WEI,Weiqiang ZHANG,Qian ZHANG,Pei SUN,Zhaohu LI,Mingcai ZHANG,Jianmin LI,Liusheng DUAN

期刊论文