Looking for breakthrough ideas for innovation challenges? Try Patsnap Eureka!

A method for joint analysis of multi-omics data

A technology of omics data and joint analysis, applied in the field of bioinformatics, can solve problems such as high method limitations, poor versatility, and difficulty in meeting scientific research needs

Active Publication Date: 2022-04-05
BGI TECH SOLUTIONS
View PDF10 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The existing analysis methods have poor versatility, and different projects may need to adjust the methods and parameters for analysis; the method has relatively high limitations, and it is difficult to meet the scientific research needs of more than two omics data

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • A method for joint analysis of multi-omics data
  • A method for joint analysis of multi-omics data
  • A method for joint analysis of multi-omics data

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0056] Embodiment 1, joint analysis of rat mRNA and small RNA data

[0057] 1. Experimental samples

[0058] Normal tissue samples from rats at 6 different developmental time stages.

[0059] 2. Data collection

[0060] Using conventional RNA-Seq and small RNA standard information analysis, the input data of mRNA and small RNA were obtained from normal tissue samples of 6 different developmental time stages of rats.

[0061] Finally, the mRNA data includes the expression levels of 25,289 genes, and the small RNA data includes the expression levels of 631 miRNAs. The targeting relationship between miRNA and mRNA is based on the prediction results of TargetScan and miRanda target gene prediction software, including 76069 pairs of targeting relationships.

[0062] 3. Data preprocessing

[0063] Delete data with a missing rate higher than the set threshold (the default threshold is 0.2, that is, the missing rate is 20%) (delete the corresponding rows).

[0064] 4. Co-expressi...

Embodiment 2

[0097] Example 2, joint analysis of apple methylation, mRNA and small RNA data

[0098] 1. Experimental samples

[0099] Samples of 4 different treatments of apples.

[0100] 2. Data collection

[0101] The input data of mRNA, methylation and small RNA were obtained from 4 different apple samples by routine RNA-Seq, genome-wide Bisulfite methylation and Small RNA standard information analysis.

[0102] Finally, the data of mRNA include the expression of 31,964 genes, the data of small RNA are the expression of 167 miRNAs, and the methylation is the result of the methylation rate of 34,889 methylated regions. The targeting relationship between miRNA and mRNA is based on the prediction results of psRobot and targetfinder target gene prediction software, including 9033 pairs of targeting relationships.

[0103] 3. Data preprocessing

[0104] Delete data with a missing rate higher than the set threshold (the default threshold is 0.2, that is, the missing rate is 20%) (delete t...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

The invention discloses a method for joint analysis of multi-omics data. The method for joint analysis of multi-omics data provided by the present invention includes the following steps: (A) performing co-expression network analysis on each single-omics index data in the multi-omics data to be analyzed, and finding respective expression modules; B) According to the overlapping relationship between the respective expression modules of different omics data, screen out the significantly correlated interaction modules among the multi-omics data to be analyzed. The multi-omics data joint analysis method provided by the present invention is not limited by the number of omics data, and theoretically can be any number of groups; at the same time, it does not depend on the source of the input data, as long as it is the index data that can measure the corresponding omics ( Such as gene expression value, apparent degree of methylation, SNP mutation rate, etc.), can be used as input data.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a method for joint analysis of multi-omics data. Background technique [0002] With the continuous advancement of science and technology, high-throughput omics data has become easy to obtain, and they provide a comprehensive description of almost all members and interactions in cells. Joyce et al. divided these data into 3 categories: membership, interaction and functional status data. Member data describes the properties of cell molecules; interaction data records the relationship between molecular members; functional state data refers to the overall cell phenotype, revealing the overall performance of all omics data. Existing genome data describe the flow of biological signals from the genome to the metabolome. First, DNA (genome) is transcribed into mRNA (transcriptome), which is then translated into proteins (proteome), which catalyze reactions to generate metabolites, glycopr...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Patents(China)
IPC IPC(8): G16B25/00G16B40/00G16B50/00
CPCG16B25/00G16B40/00G16B50/00
Inventor 朱欠华高强杨林峰唐冲刘赤川何长寿
Owner BGI TECH SOLUTIONS
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Patsnap Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Patsnap Eureka Blog
Learn More
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic, Popular Technical Reports.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com