1.2 生物信息學(xué)相關(guān)數據庫

生物信息學(xué)數據庫可以分為4大類(lèi):即基因組數據庫、核酸和蛋白質(zhì)一級結構數據庫、生物大分子三維空間結構數據庫，當前研究比較熱點(diǎn)的集中于基因組、miRNA、LncRNA、circRNA等分子的查詢(xún)，以及蛋白或蛋白修飾變化（甲基化、乙?；龋┡cDNA啟動(dòng)子、miRNA、LncRNA、circRNA的互作，LncRNA與miRNA、mRNA、circRNA等相互的結合調控，目前各種數據庫大概有上百種，沒(méi)有系統性針對性的數據庫，以下是我們對數據的整理，通過(guò)數據庫查詢(xún)分類(lèi)、數據庫功能及用途、示例結合分析、數據庫優(yōu)化等這四大項，進(jìn)行闡述和演示數據庫的查詢(xún)和使用，希望對您的實(shí)驗項目有所幫助

1. 基因查詢(xún)數據庫：

查詢(xún)獲取你的基因信息及相關(guān)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查詢(xún)數據庫：

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查詢(xún)數據庫：

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查詢(xún)數據庫：

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

常用數據庫功能用途介紹：

基因數據庫功能：

1. NCBI：

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

數據庫功能：

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.

數據庫功能：

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數據庫：

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.

數據庫功能：

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數據庫：

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

數據庫功能：

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數據庫：

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

數據庫功能（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

基因查詢(xún)：以H19為例

UCSC數據庫

1. 打開(kāi)主頁(yè)面

2. 點(diǎn)擊Genome Browser，選擇種屬，

3. 對話(huà)框中輸入基因，點(diǎn)擊“GO”

4. 即可查詢(xún)到基因的相關(guān)信息

數據庫優(yōu)化：

UCSC數據庫可查詢(xún)到基因的信息，以及該基因在不同物種中，序列的保守性等數據

2. miRNA查詢(xún)：

miRBase使用：以has-mir-9為例

1. 輸入網(wǎng)址，打開(kāi)主頁(yè)面

2. “search by miRNA name or keyword’對話(huà)框中輸入miRNA名稱(chēng)

3. 點(diǎn)擊“GO”查詢(xún)

4. 根據您的物種需要，點(diǎn)擊即可獲取該miRNA的相關(guān)信息

5. 點(diǎn)擊“Get sequence”，即可獲取序列信息

數據庫優(yōu)化：

MiRbase是一款非常強大的miRNA查詢(xún)數據庫，可查詢(xún)miRNA相關(guān)信息外，還可以做與mRNA的結合預測分析，詳細請您進(jìn)一步探知

 LncRNA查詢(xún)：以L(fǎng)ncRNA H19為例

Ensembl genome browser數據庫：

1. 打開(kāi)主頁(yè)面

2. 選取種屬，對話(huà)框輸入查詢(xún)LncRNA

3. 點(diǎn)擊進(jìn)入，即可獲取LncRNAH19的相關(guān)信息

數據庫優(yōu)化：Ensembl數據庫是一款可查詢(xún)LncRNA不同剪接變體及詳細信息的數據庫，對于LncRNA有多種剪接變體來(lái)說(shuō)，可查詢(xún)獲取得到確切的研究變體序列

CircRNA查詢(xún)：

CircRNA數據庫：以CDR1（小腦變性相關(guān)蛋白1）為例，查詢(xún)環(huán)狀RNA信息

數據庫優(yōu)化：circbase可查詢(xún)基因轉錄對應的環(huán)狀RNA信息外，還可以直接通過(guò)輸入環(huán)狀RNA的ID或是名稱(chēng)進(jìn)行查詢(xún)，可得到詳細的環(huán)狀RNA的信息

• 1 . 生物信息學(xué)概述
• 2 . 生物信息學(xué)相關(guān)數據庫
• 3 . 轉錄因子相關(guān)數據庫
• 4 . miRNA與mRNA結合預測
• 5 . LncRNA與miRNA結合預測
• 6 . LncRNA與蛋白RNP結合預測