Tissue-specific gene and regulatory factor data storage method

A tissue-specific and regulatory factor technology, applied in the field of bioinformatics, can solve problems such as inconsistent labeling and expression standards, multiple biological information databases, and reduced research quality and efficiency, and achieve the effect of improving quality and efficiency

Inactive Publication Date: 2010-09-29
TIANJIN UNIV
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Problems solved by technology

However, at this stage, due to the scattered data of tissue-specific genes and their regulatory factors, multiple and complex biological information databases, many-to-many complex relationships between tissues and genes and genes and regulatory factors, and inconsistent labeling and expression s

Method used

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  • Tissue-specific gene and regulatory factor data storage method
  • Tissue-specific gene and regulatory factor data storage method

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Embodiment Construction

[0018] The tissue library tissue includes all the tissue information in the database, including tissue_id, tissue_name, category, and description. Among them, tissue_id is a self-increasing variable, which uniquely identifies an organization in the tissue database; tissue_name corresponds to the name of the organization; category corresponds to the category of the organization (consistent with the classification standard in EMBL); description corresponds to the description of the organization.

[0019] The gene bank gene includes all tissue-specific gene information in the database, including gene_id, gene_name, tr_factor_url, and sequence_link. Among them, gene_id is self-increasing and uniquely identifies a gene in the gene library; gene_name corresponds to the name of the gene (a gene may have multiple names, where gene_name corresponds to the gene name in EMBL); tr_factor_url points to this The regulatory factor xml file corresponding to the gene; sequence_link corresponds...

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Abstract

The invention discloses a tissue-specific gene and regulatory factor data storage method. In the method, data storage is realized by establishing a tissue-specific gene and regulatory factor database comprising a tissue bank, a gene bank, a gene reference name bank, a tissue-specific gene bank and the tissue bank of tissue-specific genes. The method comprises the following steps of: extracting the tissue-specific genes from a Pubmed bibliographic database in a literature mining form; adding extracted tissue information into the tissue bank; retrieving information about the genes in the European Molecular Biology Laboratory (EMBL), Genebank and NCBI by utilizing names of the genes, and adding the information into corresponding items of the gene bank; and generating regulatory factor XML files by utilizing the information of regulating the searching of the genes from Transfac, an Eukaryotic Promoter Database (EPD) and a compel database. Compared with the prior art, the method has the advantages of bringing convenience to researchers utilizing modern computing technology to detect gene expression and regulate an inherent mechanism of network tissue specificity to acquire data on sequences of the tissue-specific genes and corresponding regulatory factors, fully utilizing tissue-specific gene analysis tools and improving research quality and efficiency.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to the database technology of the relationship between the specific expression of tissue-specific genes and regulatory factors in this field. Background technique [0002] With the completion of the Human Genome Project and the development of computational biology, a large amount of data on gene expression and its regulatory relationship has been accumulated, providing a wealth of information resources for studying the tissue specificity of gene expression and its regulatory relationship. [0003] It is one of the most challenging tasks in current bioinformatics to mine the internal mechanisms of gene expression and regulatory network organization-specificity using modern computational techniques. However, at this stage, due to the scattered data of tissue-specific genes and their regulatory factors, the numerous and complex biological information databases, the complex many-to-many re...

Claims

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Application Information

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IPC IPC(8): G06F19/00G06F17/30
Inventor 赵菲菲宫秀军刘新觅
Owner TIANJIN UNIV
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