Eucaryon alternative splicing analysis method and system based on RNA-seq data

A variable and data technology, applied in the field of bioinformatics

Inactive Publication Date: 2018-03-06
武汉生命之美科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Study and analysis of alternative splicing events remains challenging

Method used

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  • Eucaryon alternative splicing analysis method and system based on RNA-seq data
  • Eucaryon alternative splicing analysis method and system based on RNA-seq data
  • Eucaryon alternative splicing analysis method and system based on RNA-seq data

Examples

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Embodiment 1

[0050] [Example 1] Basic Analysis

[0051] The present invention uses the illumina Nextseq500 sequencing platform to perform transcriptome sequencing process schematically as follows figure 1 . After obtaining the transcriptome sequencing data of the sample based on the NextSeq500 platform, search for the reference database of the sample and the corresponding annotation files (genes and genomes of the species itself), and then use such as figure 2 The comparative analysis workflow shown provides a detailed analysis of the data. Since all the following processes are based on reference sequences, it is very important to select an appropriate reference database (such as genome sequences and cDNA sequences of public databases such as NCBI and UCSC).

[0052] Data filtering, since some original sequencing sequences have adapter sequences or contain a small amount of low-quality sequences, a series of data filtering is first required to remove impurity data. The data obtained aft...

Embodiment 2

[0068] [Example 2] Alternative splicing analysis

[0069] Algorithms for identification of various alternative splicing events (e.g. image 3 ):

[0070] 1. Gene model:

[0071] Alternative splicing is a relative event. An alternative splicing event contains at least two splicing types, and one splicing type is variable relative to the other. Since a gene has more than one transcript in many annotation files, in order to facilitate the study of the relativity of alternative splicing, we will select a transcript from each gene as a reference model, that is, the gene model for our alternative splicing research. This model is considered to have occurred, and if evidence supporting other splicing patterns, such as new splice sites, is detected, it is considered that an alternative splicing event may have occurred here.

[0072] 2. Exon skipping event (ES):

[0073] There are N exons in the gene model, N>=3, if there is a splice junction between exon [0] and exon [N-1], exon [1...

Embodiment 3

[0106] Figure 8 It is a block diagram of an embodiment of an alternative splicing analysis system based on RNA-seq data of the present invention. Such as Figure 8 As shown, the analysis system includes a data processing module 11, which is used to filter unqualified sequences in the raw sequencing data of each sample, and obtains clean reads of each transcriptome; a comparison module 12, connected to the data processing module 11, used to combine each The transcriptome data is compared to the reference genome, and the unique comparison sequence is extracted; the expression analysis module 13 is connected to the comparison module 12, and is used to calculate the expression RPKM value of the gene; the differential gene analysis module 14, and the expression analysis module Module 13 is connected to screen genes with significant expression differences; functional annotation analysis module 15 is connected to differential gene analysis module 14 and alternative splicing event d...

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Abstract

The invention provides a eucaryon alternative splicing analysis method and system based on RNA-seq data. The method comprises the steps that transcriptome original sequencing data of one or more samples of a certain eucaryon with a reference genome and annotation is acquired through an illumina next-generation sequencing platform; unqualified data is filtered out, and the remaining data serves asto-be-analyzed data; next, basic analysis is performed, wherein the to-be-analyzed data of all the transcriptome samples is compared to the reference genome of the species, and a unique comparison result is screened out; expression quantities of all sample genes are calculated; the genes with significant difference expression are screened out; functional annotation and analysis are performed on the differential genes; then alternative splicing analysis is performed, wherein a known alternative splicing event is identified; a new alternative splicing event is identified; the difference betweenalternative splicing events of samples (sample groups) is analyzed; the correlation between alternative splicing and gene expression is analyzed; the alternative splicing analysis result is subjectedto statistical analysis, and a report is generated; and an alternative splicing visual graph is generated.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a eukaryotic alternative splicing analysis method and system based on RNA-seq data. Background technique [0002] In eukaryotes, one mRNA precursor of some genes produces different mRNA splicing isoforms through different splicing methods (selecting different splicing sites). This process is called alternative splicing (or alternative splicing, alternativesplicing ). Alternative splicing is an important mechanism for regulating gene expression and generating proteome diversity, and is an important reason for the large differences in the number of genes and proteins in eukaryotes. [0003] High-throughput sequencing technology (High-throughput sequencing), also known as "next-generation" sequencing technology ("Next-generation" sequencing technology), can perform sequence determination and general reading on hundreds of thousands to several million DNA molecules in...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/20G06F19/28
CPCG16B25/00G16B50/00
Inventor 张翼程超
Owner 武汉生命之美科技有限公司
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