1.2 生物信息学相关数据库

生物信息学数据库可以分为4大类:即基因组数据库、核酸和蛋白质一级结构数据库、生物大分子三维空间结构数据库，当前研究比较热点的集中于基因组、miRNA、LncRNA、circRNA等分子的查询，以及蛋白或蛋白修饰变化（甲基化、乙酰化等）与DNA启动子、miRNA、LncRNA、circRNA的互作，LncRNA与miRNA、mRNA、circRNA等相互的结合调控，目前各种数据库大概有上百种，没有系统性针对性的数据库，以下是我们对数据的整理，通过数据库查询分类、数据库功能及用途、示例结合分析、数据库优化等这四大项，进行阐述和演示数据库的查询和使用，希望对您的实验项目有所帮助

1. 基因查询数据库：

查询获取你的基因信息及相关序列信息

①NCBI：https://www.ncbi.nlm.nih.gov/ 

②UCSC：http://genome.ucsc.edu/

③Ensembl：http://www.ensembl.org/index.html

④EBI：http ： //www.ebi.ac.uk/

⑤NIG：http： //www.nig.ac.jp/

MiRNA查询数据库：

①miRBase: http://www.mirbase.org

②microRNA.org:http://www.microrna.org/

③deepBase： http://deepbase.sysu.edu.cn/

④starBase： http://starbase.sysu.edu.cn/

⑤targetScan：http://www.targetscan.org/vert_70/

⑥TarBase: http://www.tarbase.com/

⑦miRanda： http://www.microrna.org/microrna/home.do

⑧RNAhybrid：https://bibiserv.cebitec.uni-bielefeld.de/

⑨CoGeMiR：http://cogemir.tigem.it/

⑩miRNApath：http://lgmb.fmrp.usp.br/mirnapath/tools.php

LncRNA查询数据库：

①Ensembl：http://www.ensembl.org/index.html

②LncRNAdb: http://www.lncrnadb.org/

③LNCipedia: https://lncipedia.org/

④CHIPbase: http://rna.sysu.edu.cn/chipbase/

⑤starBase： http://starbase.sysu.edu.cn/

circRNA查询数据库：

①circBase：http://www.circbase.org/

②CIRCpedia：http://www.picb.ac.cn/rnomics/circpedia/

③deepbase：http://rna.sysu.edu.cn/deepBase/

④starbase：http://starbase.sysu.edu.cn/index.php

常用数据库功能用途介绍：

基因数据库功能：

1. NCBI：

The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information

数据库功能：

Submit：NCBI collects submissions of data for the world's largest public repository of biological and scientific information

Download：The majority of NCBI data are available for downloading, either directly from the NCBI FTP site or by using software tools to download custom datasets

Learn：NCBI creates a variety of educational products including courses, workshops, webinars, training materials and documentation. NCBI educational events are free and open to everyone. All NCBI educational materials are available for anyone to re-use and distribute.

Develop：NCBI provides a variety of resources that allow developers to access and manipulate NCBI data in their applications.

Analyze：NCBI provides a wide variety of data analysis tools that allow users to manipulate, align, visualize and evaluate biological data.

2. UCSC Genome Browser：

The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the UCSC Genomics Institute. the website has grown to include a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data.

数据库功能：

Genome Browser：interactively visualize genomic data

BLAT：rapidly align sequences to the genome

Table Browser：download data from the Genome Browser database

Variant Annotation Integrator：get functional effect predictions for variant calls

Data Integrator：combine data sources from the Genome Browser database

Gene Sorter：find genes that are similar by expression and other metrics

Genome Browser in a Box (GBiB)：run the Genome Browser on your laptop or server

In-Silico PCR：rapidly align PCR primer pairs to the genome

LiftOver：convert genome coordinates between assemblies

VisiGene：interactively view in situ images of mouse and frog

MiRNA数据库：

1. miRBase

the microRNA database

•  The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.

2. microRNA.org ：

Targets and Expression，Predicted microRNA targets & target downregulation scores. Experimentally observed expression patterns.

数据库功能：

1. mirSVR predicted target site scoring method: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

2. microRNA target predictions: The microRNA.org resource: targets and expression.

3. miRanda application: Human MicroRNA targets.

4. miRanda algorithm: MicroRNA targets in Drosophila.

LncRNA数据库：

1. Ensembl genome browser

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species

数据库功能：

Variant Effect Predictor

Gene expression in Ensembl

Retrieving sequences

Compare genes across species

SNPs and other variants for my gene

Use my own data in Ensembl

2. LncRNAab :

Long Noncoding RNA Database v2.0- The Reference Database For Functional Long Noncoding RNAs

circRNA数据库：

1. circBase：

Circular RNA ( circ RNA) is a recent addition to the growing list of types of noncoding RNA．Here you can explore public circ RNA datasets and download the custom python scripts needed to dis cover cicRNAs in your own RNA-seq data

数据库功能（Database function）

•   Sequence-based search

•   Search the database by identifier, gene description, genomic position, or their lists.

•   Retrieve dataset slices by defining a set of conditions (table browser).

•   Export tables in a variety of formats.

•   Export FASTA files containing genomic sequence.

2. CIRCpedia：

CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines. Through employing an upgraded circRNA characterization pipeline (CIRCexplorer2), thousands of alternative back-splicing and alternative splicing events in circRNAs were identified. All these identified alternative back-splicing and alternative splicing in circRNAs, together with novel exons, are formatted and classified for being easily searched, browsed and downloaded from CIRCpedia

基因查询：以H19为例

UCSC数据库

1. 打开主页面

2. 点击Genome Browser，选择种属，

3. 对话框中输入基因，点击“GO”

4. 即可查询到基因的相关信息

数据库优化：

UCSC数据库可查询到基因的信息，以及该基因在不同物种中，序列的保守性等数据

2. miRNA查询：

miRBase使用：以has-mir-9为例

1. 输入网址，打开主页面

2. “search by miRNA name or keyword’对话框中输入miRNA名称

3. 点击“GO”查询

4. 根据您的物种需要，点击即可获取该miRNA的相关信息

5. 点击“Get sequence”，即可获取序列信息

数据库优化：

MiRbase是一款非常强大的miRNA查询数据库，可查询miRNA相关信息外，还可以做与mRNA的结合预测分析，详细请您进一步探知

 LncRNA查询：以LncRNA H19为例

Ensembl genome browser数据库：

1. 打开主页面

2. 选取种属，对话框输入查询LncRNA

3. 点击进入，即可获取LncRNAH19的相关信息

数据库优化：Ensembl数据库是一款可查询LncRNA不同剪接变体及详细信息的数据库，对于LncRNA有多种剪接变体来说，可查询获取得到确切的研究变体序列

CircRNA查询：

CircRNA数据库：以CDR1（小脑变性相关蛋白1）为例，查询环状RNA信息

数据库优化：circbase可查询基因转录对应的环状RNA信息外，还可以直接通过输入环状RNA的ID或是名称进行查询，可得到详细的环状RNA的信息

• 1 . 生物信息学概述
• 2 . 生物信息学相关数据库
• 3 . 转录因子相关数据库
• 4 . miRNA与mRNA结合预测
• 5 . LncRNA与miRNA结合预测
• 6 . LncRNA与蛋白RNP结合预测