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Omics Technology: Novel Approach for Screening of Plant-Based Traditional Medicines
Published in Megh R. Goyal, Hafiz Ansar Rasul Suleria, Ademola Olabode Ayeleso, T. Jesse Joel, Sujogya Kumar Panda, The Therapeutic Properties of Medicinal Plants, 2019
Rojita Mishra, Satpal Singh Bisht, Mahendra Rana
In 1995, Serial Analysis of Gene Expression (SAGE) was developed, which is based on the sequencing. The basic working principle is an analysis of concatenated random transcripts by Sanger‘s method. Briefly, in SAGE analysis, cDNA is produced from mRNA then is digested into 11bp tag fragments with the help of restriction endonucleases. The cDNA tags are concatenated head to tail into about 500 bp long strands and sequenced using Sanger sequencing. The sequences are deconvoluted into original 11bp tags. Two approaches are there: (1) If a reference genome is available then tags can be aligned to identify the corresponding genes; (2) In other approaches where a reference genome is not available, and tags are used as diagnostic markers if the tag is expressed differentially in the disease state. The Cap Analysis of Gene Expression (CAGE) is a slight variation of SAGE, where sequence tags are from the 5‘-end of the mRNA transcript. If the reference genome is available, then transcriptional starting site of the gene is identified in other words, promoter analysis, and cloning of full-length cDNAs become possible [4].
Animal Models of Down Syndrome and Other Genetic Diseases Associated with Mental Retardation
Published in Merlin G. Butler, F. John Meaney, Genetics of Developmental Disabilities, 2019
Angela J. Villar, Charles J. Epstein
The serial analysis of gene expression (SAGE) technique has been applied to study the differences in the global gene expression profiles induced by the aneuploidy in brains of normal and Ts65Dn adult male mice (41). The vast majority of transcripts are expressed at the same or similar levels between Ts65Dn and controls. However, 330 RNA TAGs demonstrated statistically significant differences in expression. Interestingly, approximately half of the differentially expressed TAGs were underexpressed and half were overexpressed in Ts65Dn male brains. Among the differentially expressed TAGs matching known genes, several candidate genes with a potential pathogenic role in both the developmental and neurodegenerative aspects of DS have been identified (41). Microarray experiments to assess gene expression differences in both human DS and mouse models of DS (Ts65Dn) are currently underway.
Precision medicine in asthma and chronic obstructive pulmonary disease
Published in Debmalya Barh, Precision Medicine in Cancers and Non-Communicable Diseases, 2018
Currently none of the available therapies can help in restricting the progression of COPD. Therefore, an urgent need exists for the development of new and effective treatments for COPD. There is an urgency to identify molecular targets for COPD treatment. Here, techniques such as gene expression profiling, serial analysis of gene expression, or microarrays may be utilized. Several research teams have mapped comparative gene expression in lung tissues of COPD patients, and it has been found that differentially regulated genes are associated with disease progression. Such studies have identified molecular mechanisms of COPD and also suggested new targets for COPD treatments (Chen et al., 2008).
Emerging drug targets for triple-negative breast cancer: a guided tour of the preclinical landscape
Published in Expert Opinion on Therapeutic Targets, 2022
Xuemei Xie, Jangsoon Lee, Toshiaki Iwase, Megumi Kai, Naoto T Ueno
One of the key challenges is the intratumoral heterogenicity of TNBC, whose TME is a complex entity composed of different stromal and immune cells and soluble factors. In the past decades, next-generation technology platforms and transcriptomic and computational screening methods have become a new standard for discovering novel targets for cancer treatment. However, most transcriptome analysis techniques, including the use of gene expression microarrays, serial analysis of gene expression, massively parallel signature sequencing, RNA sequencing (RNA-seq), and the detection flux of RNA seq, are based on data from the bulk cell population of a given tissue. Thus, these analyses may overlook genes that are differentially expressed by individual cells in the tissue. Indeed, different responses to treatment have been observed in clinics due to the extensive intratumoral heterogenicity of TNBC, namely, the existence of different gene expression patterns in different clusters of the same tumor [189–191]. Ideally, then, efforts to identify promising therapeutic targets in TNBC should produce results at the single-cell or single-tumor-component level.
The potential of circulating cell free RNA as a biomarker in cancer
Published in Expert Review of Molecular Diagnostics, 2019
Ka Wan Emily Cheung, Sin-yu Rachel Choi, Lok Ting Claire Lee, Nga Lam Ella Lee, Hin Fung Tsang, Yin Tung Cheng, William Chi Shing Cho, Elaine Yue Ling Wong, Sze Chuen Cesar Wong
Gene expression analysis is generally performed by various methods, for instance, northern blotting, RNase protection assay, serial analysis of gene expression (SAGE), RT-PCR, qRT-PCR and microarray assay [168,169]. Although northern blot analysis and RNase protection assays are ideal for the measurement of gene expression and mRNA levels, they both require the input of intact RNA, which is rare for extracellular RNA. For SAGE analysis, it is a highly complicated and labor-demanding technique that also requires high-quality RNA. Hence, the methods of choice for RNA species detection in plasma or serum are most commonly by RT-PCR or microarray analysis.
Transcriptomic profiling in Cutaneous Leishmaniasis patients
Published in Expert Review of Proteomics, 2020
Nasrin Masoudzadeh, Amir Mizbani, Sima Rafati
Gene expression profiling is generally performed using techniques including EST (Expressed Sequence Tags), SAGE (Serial Analysis of Gene Expression), microarrays, and RNA-Seq [38,39], each of which is briefly described here.