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Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues. First, a variation of the Relief algorithm, "RFE_Relief algorithm" was proposed to learn the relations between genes and tissue types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper. 相似文献
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Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods
to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues.
First, a variation of the Relief algorithm, “RFE_Relief algorithm” was proposed to learn the relations between genes and tissue
types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing
cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed
to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence
of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression
patterns of these genes in cancerous tissues are summarized at the end of this paper. 相似文献
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Roth CM 《Current issues in molecular biology》2002,4(3):93-100
Identifying those genes that are expressed and at what levels is an essential part of almost any biological inquiry at the cellular level. Techniques such as Northern blot have been in existence for decades to perform this task, but advances in molecular biology and bioinstrumentation have led to the development of a variety of new techniques with a range of sensitivities, throughputs and quantitative capabilities. This review focuses on the latter issue. For several commonly used gene expression techniques, the extent and range of quantitative applicability are reviewed, and approaches for maximizing the accuracy and precision of these measurements are discussed. 相似文献
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Post-meiotic gene expression 总被引:14,自引:0,他引:14
R P Erickson 《Trends in genetics : TIG》1990,6(8):264-269
Evolutionary arguments and well-designed experiments (based on false premises, however) had suggested that post-meiotic gene expression did not occur in animals. The techniques of molecular genetics have now clearly demonstrated such genetic activity in mammalian testes. The current problem is to understand why some classes of genes, such as Zfy and many oncogenes, are expressed in this manner. 相似文献
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Nodule-specific gene expression 总被引:2,自引:0,他引:2
Katharina Pawlowski 《Physiologia plantarum》1997,99(4):617-631
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Auxin-regulated gene expression 总被引:6,自引:0,他引:6
J L Key P Kroner J Walker J C Hong T H Ulrich W M Ainley J S Gantt R T Nagao 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》1986,314(1166):427-440
During the 1960s a wide range of studies provided an information base that led to the suggestion that auxin-regulated cell processes--especially cell elongation--may be mediated by auxin-regulated gene expression. Indirect evidence from our work, based on the influence of inhibitors of RNA synthesis (e.g. actinomycin D) and of protein synthesis (e.g. cycloheximide) on auxin-induced cell elongation, coupled with correlations of the influence of auxin on RNA synthesis and cell elongation, provided the basis for this suggestion. With the availability of techniques for DNA-DNA and DNA-RNA hybridization, mRNA isolation-translation, in vitro 2D gel analysis of the translation products, and ultimately the cloning by recombinant DNA technologies of genomic DNA and copy DNAs (cDNAs) made to poly(A)+ mRNAs, we and others have provided direct evidence for the influence of auxin on the expression of a few genes (i.e. poly(A)+ RNA levels). Our laboratory has provided evidence for auxin's both down-regulating and up-regulating the level of a few poly(A)+ mRNAs out of a population of about 4 X 10(4) sequences that are not significantly affected by auxin. In our studies on auxin-regulated cell elongation, two cDNA clones (pJCW1 and pJCW2) were isolated which corresponded to poly(A)+ mRNAs that responded during growth transitions in a way consistent with a potential role of their protein products in cell elongation. These mRNAs are most abundant in the elongating zone of the soybean hypocotyl. Upon excision and incubation in the absence of auxin, these mRNAs deplete in concert with a decreasing rate of cell elongation. Addition of auxin to the medium results in both increased levels of these mRNAs and enhanced rates of cell elongation. These mRNAs do not deplete if auxin is added to the medium at the onset of excised incubation, and cell elongation rates remain high. We have isolated and sequenced genomic clones that are homologous to these cDNAs. Of the two genes sequenced, both genes are members of small multigene families. There are regions of high amino acid homology even though the nucleotide sequences are sufficiently different in these regions for cross-hybridization of the clones not to be observed. More recently others, especially Guilfoyle's laboratory, have shown that auxin selectively and rapidly influences the level of certain mRNAs and proteins. We have worked on other gene systems such as ribosomal proteins and possible cell wall proteins that are responsive to auxin; again the nature of regulation of expression of these genes is not known.(ABSTRACT TRUNCATED AT 400 WORDS) 相似文献
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Brassinosteroid-regulated gene expression 总被引:21,自引:0,他引:21
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Dimerizer-regulated gene expression 总被引:6,自引:0,他引:6
Control of gene expression using small molecules is a powerful research tool and has clinical utility in the context of regulated gene therapy. Use of chemical inducers of dimerization, or dimerizers, for this purpose has several advantages, including tight regulation, modularity to facilitate iterative improvements, and assembly from human proteins to minimize immune responses in clinical applications. Recent developments include the use of the rapamycin-based dimerizer system to regulate the expression of endogenous genes, the generation of new chemical dimerizers based on FK506, dexamethasone and methotrexate, and progress towards the clinical use of adeno-associated virus and adenovirus vectors regulated by rapamycin analogs. 相似文献
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转录后水平沉默与基因表达 总被引:8,自引:0,他引:8
基因沉默是1个非常复杂和普遍的现象。转录后水平的基因沉默是指转基因在细胞核里能稳定转录,细胞质里却无相应的稳定态mRNA存在的现象。它往往被称为共抑制、静息作用或RNA干预等。本文介绍了转录后水平的基因沉默现象的发现、分子机理和应用等方面的进展。提出了克服转录后水平基因沉默的一些对策。 相似文献
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Chen S Ni X Krinsky BH Zhang YE Vibranovski MD White KP Long M 《The EMBO journal》2012,31(12):2798-2809
New genes originate frequently across diverse taxa. Given that genetic networks are typically comprised of robust, co-evolved interactions, the emergence of new genes raises an intriguing question: how do new genes interact with pre-existing genes? Here, we show that a recently originated gene rapidly evolved new gene networks and impacted sex-biased gene expression in Drosophila. This 4–6 million-year-old factor, named Zeus for its role in male fecundity, originated through retroposition of a highly conserved housekeeping gene, Caf40. Zeus acquired male reproductive organ expression patterns and phenotypes. Comparative expression profiling of mutants and closely related species revealed that Zeus has recruited a new set of downstream genes, and shaped the evolution of gene expression in germline. Comparative ChIP-chip revealed that the genomic binding profile of Zeus diverged rapidly from Caf40. These data demonstrate, for the first time, how a new gene quickly evolved novel networks governing essential biological processes at the genomic level. 相似文献
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A recent publication has shown that a significant portion of gene expression levels are under genetic control in different organisms, that there are hotspot regions in the genome that control the expression of many other genes, and how gene expression data can be used to localize genes that affect clinical traits. 相似文献
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Human globin genes can be transferred into mouse and human erythroid cells in culture, and can be appropriately expressed at the mRNA level in these cells. A plasmid containing a human beta globin gene is expressed in mouse erythroleukemia cells (MELC), and another containing a human epsilon or gamma gene is expressed in human erythroleukemia (K562) cells. A neomycin resistance (neoR) gene on the plasmids has been used to select for those cells containing the transferred globin genes; this selection may favor the expression of the globin genes by providing chromosomal positions requiring neoR expression. Analyzing clones resistant to G418, a neomycin analogue, demonstrated globin mRNA expression and induction. Retroviral vectors have also been used to transfer and appropriately express human beta genes in MELC. In addition, a plasmid containing a dihydrofolate reductase (DHFR) gene as well as neoR and beta globin genes has been used to amplify and express beta globin mRNA in MELC. These experiments suggest that high level appropriate expression of human beta globin genes is feasible and provides potentially useful approaches to the long-range goal of gene therapy for sickle cell anemia and beta thalassemia. 相似文献
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Ilse M. Boudewijn Alen Faiz Katrina Steiling Erica van der Wiel Eef D. Telenga Susan J. M. Hoonhorst Nick H. T. ten Hacken Corry-Anke Brandsma Huib A. M. Kerstjens Wim Timens Irene H. Heijink Marnix R. Jonker Harold G. de Bruin J. Sebastiaan Vroegop Henk R. Pasma Wim G. Boersma Pascal Wielders Frank van den Elshout Khaled Mansour Avrum Spira Marc E. Lenburg Victor Guryev Dirkje S. Postma Maarten van den Berge 《Respiratory research》2017,18(1):213