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NcRNA collaborative competition network identification method and device

A technology for network identification and expression profiling, applied in instruments, for analyzing two-dimensional or three-dimensional molecular structures, hybridization, etc.

Active Publication Date: 2020-04-17
UNIV OF ELECTRONICS SCI & TECH OF CHINA +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The study of the cooperative competition relationship in the ncRNA cooperative competition network can help to understand the cooperative competition mechanism of ncRNAs in complex human diseases, but there is no feasible solution in the prior art for identifying the ncRNA cooperative competition network

Method used

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  • NcRNA collaborative competition network identification method and device
  • NcRNA collaborative competition network identification method and device
  • NcRNA collaborative competition network identification method and device

Examples

Experimental program
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Effect test

Embodiment 1

[0129] Taking the corresponding lncRNA-lncRNA cooperative competition in glioblastoma multiforme as an example, the method for identifying the lncRNA-lncRNA cooperative competition network in this embodiment is realized by the following steps:

[0130] Step 1: Data source acquisition

[0131] lncRNA and mRNA expression profile data of matched samples of glioblastoma multiforme (GBM) were collected from the internationally renowned cancer gene expression profile database TCGA (the cancer genome atlas, https: / / cancergenome.nih.gov / ) . Through preprocessing (removing duplicates and lncRNAs and mRNAs without gene names), the expression profile data of 9704 lncRNAs and 18282 mRNAs of 451 breast cancer matched samples, as well as the clinical information of the samples were finally obtained. In this embodiment, ncRNA is lncRNA,

[0132] The prior lncRNA-mRNA competition network data was obtained by fusing multiple different databases. Specifically, by integrating miRSponge, L...

Embodiment 2

[0162] Taking the corresponding lncRNA-lncRNA cooperative competition in lung squamous cell carcinoma as an example, the method for identifying the lncRNA-lncRNA cooperative competition network in this embodiment is realized by the following steps:

[0163] In step 1 of this embodiment, the lncRNA of the matched sample of lung squamous cell carcinoma (Lung Squamous Cell Carcinoma, LSCC) was collected from the internationally renowned cancer gene expression profile database TCGA (the cancergenomeatlas, https: / / cancergenome.nih.gov / ) and mRNA expression profile data. After preprocessing (removing duplicates and lncRNAs and mRNAs without gene names), the expression profile data of 9704 lncRNAs and 18282 mRNAs of 113 breast cancer matched samples, as well as the clinical information of the samples were finally obtained. In this embodiment, ncRNA is lncRNA,

[0164] The prior lncRNA-mRNA competition network data is the same as in Example 1, and finally 10099 lncRNA-mRNA compet...

Embodiment 3

[0167] Taking the corresponding lncRNA-lncRNA cooperative competition in ovarian cancer as an example, the method for identifying lncRNA-lncRNA cooperative competition network in this embodiment is realized by the following steps:

[0168] In step 1 of this example, lncRNA and mRNA expressions of ovarian cancer (Ovarian Cancer, OvCa) matched samples were collected from the internationally renowned cancer gene expression profile database TCGA (the cancergenome atlas, https: / / cancergenome.nih.gov / ) spectral data. Through preprocessing (removing duplicates and lncRNAs and mRNAs without gene names), the expression profile data of 9704 lncRNAs and 18282 mRNAs of 585 ovarian cancer matched samples, as well as the clinical information of the samples were finally obtained. In this embodiment, ncRNA is lncRNA,

[0169] The prior lncRNA-mRNA competition network data is the same as in Example 1, and 10099 lncRNA-mRNA competition relationship pairs associated with ovarian cancer expr...

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Abstract

The invention provides an ncRNA collaborative competition network identification method and device, and relates to the technical field of gene identification. According to the method, ncRNA and mRNA expression profile data of a target disease type matching sample are obtained; and according to the ncRNA and mRNA expression profile data and preset ncRNA-mRNA competition relation data, an ncRNA-ncRNA pair consisting of two ncRNAs meeting a preset condition in the ncRNA and mRNA expression profile data is determined to be a cooperative competitive relationship pair. Thus, the ncRNA-ncRNA cooperative competition relation pair can be recognized an ncRNA cooperative competition network formed by competition of multiple ncRNAs and target gene mRNA can be recognized, and then reference can be provided for clinical diagnosis and targeted therapy of cancer and other human complex diseases.

Description

technical field [0001] The invention relates to the technical field of gene identification, in particular to an ncRNA cooperative competition network identification method and device. Background technique [0002] MicroRNA (miRNA) is a class of non-coding small RNA regulatory molecules with an endogenous length of about 22 nucleotides, which can regulate the expression level of protein-coding gene messenger RNA (messenger RNA, mRNA). Existing studies have shown that miRNAs play an important regulatory role in biological processes such as cell differentiation, cell proliferation, cell growth, cell migration, cell apoptosis, and cancer. According to the endogenous competing RNA (competing endogenous RNAs, ceRNA) hypothesis, different gene transcripts of miRNA response elements (miRNA response elements, MREs) compete with each other to regulate gene expression. These competing transcripts are collectively called ceRNA, including protein-coding mRNA, long non-coding RNA (long n...

Claims

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Application Information

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IPC IPC(8): G16B25/10G16B40/00G16B50/00G16B15/00
CPCG16B15/00G16B25/10G16B40/00G16B50/00
Inventor 张俊鹏饶妮妮王光斌
Owner UNIV OF ELECTRONICS SCI & TECH OF CHINA
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