Gene excavating method based on EST database and UniGene database

A database and gene technology, applied in the field of applied bioinformatics, can solve problems such as counting false positives of EST expression levels, inability to correctly mine induced genes, etc., and achieve the effects of avoiding errors, accurate analysis, and accurate results

Inactive Publication Date: 2010-03-03
NORTHEAST AGRICULTURAL UNIVERSITY
View PDF0 Cites 1 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] In order to overcome the problem of false positives in the counting of EST expression in the existing gene mining methods, which leads to the inability to correctly mine the induced genes related to traits, the present invention provides a gene mining method based on EST database and UniGene database

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
  • Gene excavating method based on EST database and UniGene database
  • Gene excavating method based on EST database and UniGene database
  • Gene excavating method based on EST database and UniGene database

Examples

Experimental program
Comparison scheme
Effect test

specific Embodiment approach 1

[0014] Specific embodiment one: see figure 1 The specific process of a gene mining method based on EST database and UniGene database described in this specific embodiment is:

[0015] Step A: Download the EST database and the UniGene database, and classify the EST sequence information in the UniGene database according to species type, and then perform step B;

[0016] Step B: Perform information retrieval on the annotation information of the EST library, and then classify the annotation information of the EST library, and then perform step C;

[0017] Step C: Calculate the EST expression level of the expressed gene UniGene transcriptome according to the classification information of the EST library annotation information, and then perform step D;

[0018] Step D: Perform hypergeometric distribution test on the EST expression of the obtained UniGene transcriptome of the expressed gene, calculate the hypergeometric distribution test value P-value of the differential expression of the exp...

specific Embodiment approach 2

[0033] Specific embodiment two: The gene mining method based on EST database and UniGene database described in this embodiment is different from specific embodiment one in that it is the mining of human cancer response genes:

[0034] In step A, download the human EST database and the human UniGene database;

[0035] In step B, the annotation information of the human EST library is directly extracted. First, the human abnormal state EST library is extracted, and the ID of the human abnormal state EST library is extracted, and then the human normal state EST library is extracted, and the human ID of the normal EST library;

[0036] In step C, according to the classification information of the annotation information of the human EST library, the health status of the human expression gene UniGene transcriptome is extracted from the human UniGene transcriptome file Hs.profiles in the human UniGene database. Breast tumor, leukemia under HealthState Leukemia, ovarian tumor, primitive neur...

specific Embodiment approach 3

[0244] Specific embodiment three: The gene mining method based on EST database and UniGene database described in this embodiment is different from specific embodiment one in that it is the mining of soybean stress response genes:

[0245] In step A, download the soybean EST database and soybean UniGene database;

[0246] In step B, "cold", "salt" and "drought" are used as keywords of abnormal states related to soybean adversity stress, and the keywords are information in the soybean EST library annotation information file Gma.lib.info Search, screen the soybean abnormal state EST library, and extract the ID of the soybean abnormal state EST library, then use other EST libraries in the soybean EST library as the soybean normal state EST library, and extract the ID of the soybean normal state EST library. The search items for information retrieval in the soybean EST library annotation information file Gma.lib.info include three items: TITLE, DEVELOPMENTAL_STAGE and VERBATIM_TISSUE;

...

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 provides a gene excavating method based on EST database and UniGene database, relating to the field of applied bioinformatics. The method overcomes the problem that characters-correlative induce gene can not be exactly excavated in the existing gene excavating method. The method comprises the steps: digitizing the EST expression quantity of expression gene UniGene transcriptome in the UniGene database with an EST sequence in the EST database; building hypergeometric distribution test; adjusting a hypergeometric distribution test value P-value of the differential expression of theexpression gene UniGene transcriptome by combining with an FDR method; screening error state response gene; and verifying the response gene is the characters-correlative induce gene with a RT-PCR technology. The method can be used for excavating the characters-correlative induce gene in the process of the disease occurrence of human beings, the growing development regulation of animals and plants, the disease regulation of the animals and plants, the adversity stress of the animals and plants, etc.

Description

Technical field [0001] The invention relates to the field of applied bioinformatics, in particular to a method for excavating specifically expressed genes in the UniGene database. Background technique [0002] EST (Expressed Sequence Tag) sequencing is one of the methods for high-throughput detection of gene expression information. In recent years, due to the long length of EST sequences, better specificity, and lower noise than gene chips, EST sequencing has been widely used. application. However, due to the high cost of EST sequencing, when a single researcher establishes EST sequence information, the mining of EST sequences is mainly focused on the discovery of EST sequence information, for example, EST sequence splicing, annotation of splicing results, and SSR With regard to the discovery of SNPs and other aspects, the number of EST sequences sequenced by ESTs is often small, that is, there are few quantitative studies on EST sequences, and only the qualitative analysis of t...

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 Applications(China)
IPC IPC(8): G06F19/00G06F17/30C12Q1/68G06F19/24G06F19/28
CPCY02A90/10
Inventor 朱延明李勇束永俊柏锡才华纪巍季佐军
Owner NORTHEAST AGRICULTURAL UNIVERSITY
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

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

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap