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Method, system and application for discovering rectal cancer-related microRNA molecular markers using tcga database resources

A molecular marker and resource discovery technology, applied in medical data mining, biostatistics, bioinformatics, etc., can solve the problems of not being able to independently complete miRNA bioinformatics analysis, not good at integrating existing network resources, etc., to achieve The effect of clear thinking, reducing scientific research costs and improving analysis efficiency

Active Publication Date: 2019-04-09
SOUTHEAST UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0006] The purpose of the present invention is to provide a method for discovering rectal cancer-related miRNA using TCGA public data resources, so as to solve the problems of not being good at integrating existing network resources and not being able to independently complete miRNA-related bioinformatics analysis

Method used

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  • Method, system and application for discovering rectal cancer-related microRNA molecular markers using tcga database resources
  • Method, system and application for discovering rectal cancer-related microRNA molecular markers using tcga database resources
  • Method, system and application for discovering rectal cancer-related microRNA molecular markers using tcga database resources

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Embodiment

[0097] Firstly, the raw data is filtered, and then low-quality data are removed to obtain effective miRNA normalized expression values. Based on the results of miRNA differential analysis, target gene prediction can be performed based on its sequence characteristics. On the basis of the above analysis, a series of statistical and visual analysis can be carried out.

[0098] 1. The miRNA expression value file is shown in Table 1

[0099] Analysis platform: R platform

[0100] Analysis software: TCGAbiolinks

[0101] Table 1

[0102]

[0103] Explanation of column names:

[0104]

[0105] 2. The results of miRNA expression analysis are shown in Table 2

[0106] Analysis platform: R platform

[0107] Analysis software: TCGAbiolinks

[0108] Table 2

[0109]

[0110] Explanation of column names:

[0111]

[0112] 3. The results of differentially expressed miRNAs are shown in Table 3

[0113] Analysis platform: R platform

[0114] Analysis software: TCGAbioli...

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Abstract

The invention discloses a method and a system for detecting a rectal cancer related microRNA molecular marker by TCGA (the cancer genome atlas) database resources and application of the method and the system. On the basis of public data resources such as rectal cancer miRNA sequencing data of the TCGA database, open big data resources and versatile bioinformatics analysis means are reasonably used for analysis and processing of miRNA expression data to recognize miRNA related to complex diseases such as rectal cancers. The method includes: sample data downloading and sorting; differential expression analysis of the miRNA expression data; sequencing the miRNA according to variation amplitude; target gene selection; target gene function analysis. Problems of poor capability in integration of existing network resources, lack of familiarity in miRNA related most common databases and frontal analysis methods, failure in independent completion of miRNA expression profile related bioinformatics analysis and the like can be solved.

Description

technical field [0001] The invention relates to the fields of medical genomics and computational biology, in particular to a method for discovering rectal cancer-related miRNAs using TCGA public data resources. Background technique [0002] Bioinformatics is a subject combining life science and computer science, which studies the collection, processing, storage, analysis and interpretation of biological information, and reveals the complex biological data through the comprehensive use of biology, computer science and information technology. biological mysteries. Public databases are important tools for bioinformatics research. How to make full use of free resources, efficiently integrate data, and deeply mine and analyze has become an important topic in bioinformatics. [0003] The Cancer Genome Atlas (TCGA) project initiated by the U.S. government attempts to map out the genome variation maps of all human cancers by applying genome analysis techniques, especially large-sc...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16H50/70G16B40/00G16B50/00
CPCG16B40/00G16B50/00G16H50/70
Inventor 陈瑞高娜李晓波孟庆涛吴申申
Owner SOUTHEAST UNIV