阅读说明：本技术 一种长非编码rna的癌症相关可变剪接数据库系统 (Cancer-related alternative splicing database system of long non-coding RNA ) 是由 刘伦旭 邓雨岚 于 2020-05-22 设计创作，主要内容包括：本发明涉及生物医学领域,公开了一种长非编码RNA的癌症相关可变剪接数据库系统,以便于帮助研究人员更好理解癌症中lncRNA可变剪接的作用。本发明包括搜索模块、可视化模块以及文件交互模块：搜索模块用于根据用户输入的与长非编码RNA相关的搜索条件,从系统的数据区搜索出长非编码RNA在指定癌症中的剪接信息,并将搜索结果通过可视化模块展现给用户；当用户点击可视化模块展示中的搜索结果,可获得更详细的可视化信息和注释信息；其中,可视化信息包括剪接图、三文鱼图、箱式图和基因组浏览器；文件交互模块用于提供文件上传功能,以及搜索结果的下载和调用功能。本发明适用于癌症研究。(The invention relates to the field of biomedicine, and discloses a database system for long non-coding RNA (ribonucleic acid) related alternative splicing of cancer, which is used for helping researchers to better understand the alternative splicing effect of IncRNA in cancer. The invention comprises a searching module, a visualization module and a file interaction module: the search module is used for searching splicing information of the long non-coding RNA in the specified cancer from a data area of the system according to a search condition which is input by a user and is related to the long non-coding RNA, and displaying a search result to the user through the visualization module; when a user clicks a search result displayed by the visualization module, more detailed visualization information and annotation information can be obtained; wherein the visual information comprises a splice graph, a salmon graph, a box graph and a genome browser; the file interaction module is used for providing a file uploading function and a downloading and calling function of the search result. The invention is suitable for cancer research.)

1. The database system for the cancer-related alternative splicing of the long non-coding RNA is characterized by comprising a searching module, a visualization module and a file interaction module;

the search module is used for searching splicing signals of the long non-coding RNA in the specified cancer from a data area of the system according to search conditions which are input by a user and are related to the long non-coding RNA, and displaying the search result to the user through the visualization module; wherein the splicing signal in the data region is derived from the sequencing data of the tissue mass and the sequencing data of the single cell;

when a user clicks a search result displayed by the visualization module, more detailed visualization information and annotation information can be obtained; the visual information comprises a splicing map, a salmon map, a box map and a genome browser, wherein the splicing map is used for globally displaying exons of a single long non-coding RNA gene and the signal strength of connecting reads; salmon plots are used to show local signal differences between different components for a particular splicing event; boxplots are used to show the signal differences of specific splicing events in different diseases or tissues; the genome browser displays potential functional effects of spliced sequences from multiple angles, including protein binding site, RNA binding site and functional element information; the annotation information comprises basic annotation information of long non-coding RNA, basic annotation information of splicing events and related literature reports of splicing sequences;

the file interaction module is used for providing a file uploading function and a downloading and calling function of a search result.

2. The database system of claim 1, wherein the search criteria comprises one or more of lncRNA name, genomic locus, tissue type, cancer type, alternative splicing type, cancer cell line name, and splicing ID.

3. The database system of claim 1, wherein the splicing signals of the data region relate to splicing signals of long non-coding RNAs under a plurality of conditions, including cancer patients, cancer cell lines, and human tumor xenograft models.

Technical Field

The invention relates to the field of biomedicine, in particular to a cancer-related alternative splicing database system of long non-coding RNA (lncRNA).

Background

Aberrant alternative splicing patterns in cancer are associated with a number of oncogenic processes, such as dedifferentiation and metastasis. Thus, Ryan et al developed a database of records of alternative splicing of protein-encoding genes in cancer, named TCGA SpliceSeq, under the http:// bioinformatics. mdanderson. org/TCGASpliceSeq. The database collected the tissue RNA sequencing data of 33 cancers in TCGA, and identified alternative splicing signals of protein-encoding genes therein using the software package splieseq, and expressed as Percent-insertion (PSI, Ψ). The user can search for alternatively spliced signals of the gene encoding the protein of interest, compare their differences in different cancers, and differences in cancer tissues and normal tissues. The database provides visualization of splicing patterns and provides statistical information supporting reads, PSI, and the like. The user can also download related data from the data for subsequent integration analysis. However, the database has the following disadvantages:

1. the database contains only information on alternative splicing of protein-encoding genes in cancer, and no information on alternative splicing of long non-coding RNAs in cancer.

2. This data may only provide tissue-based splicing signals, not single cell-based splicing signals, and thus may be affected by cancer heterogeneity.

Disclosure of Invention

The technical problem to be solved by the invention is as follows: a database system of long non-coding RNAs for cancer-associated alternative splicing is provided to help researchers better understand the role of IncRNA alternative splicing in cancer.

In order to solve the problems, the invention adopts the technical scheme that: a cancer-related alternative splicing database system of long non-coding RNA comprises a search module, a visualization module and a file interaction module;

the search module is used for searching splicing signals of the long non-coding RNA in the specified cancer from a data area of the system according to search conditions which are input by a user and are related to the long non-coding RNA, and displaying the search result to the user through the visualization module; wherein the splicing signal in the data region is derived from the sequencing data of the tissue mass and the sequencing data of the single cell;

when a user clicks a search result displayed by the visualization module, more detailed visualization information and annotation information can be obtained; the visual information comprises a splicing map, a salmon map, a box map and a genome browser, wherein the splicing map is used for globally displaying exons of a single long non-coding RNA gene and the signal strength of connecting reads; salmon plots are used to show local signal differences between different components for a particular splicing event; boxplots can be used to show the signal differences of specific splicing events in different diseases or tissues; the genome browser displays potential functional effects of spliced sequences from multiple angles, including protein binding site, RNA binding site and functional element information; the annotation information comprises basic annotation information of long non-coding RNA, basic annotation information of splicing events and related literature reports of splicing sequences;

the file interaction module is used for providing a file uploading function and a downloading and calling function of a search result.

Specifically, the search condition may include one or more of lncRNA name, genomic locus, tissue type, cancer type, alternative splicing type, cancer cell line name, splicing ID.

In particular, the splicing signals of the system data region relate to the splicing signals of long noncoding RNAs in various cases, including cancer patients, cancer cell lines, and human-Derived tumor Xenograft models (PDX).

The invention has the following beneficial effects: through the database system, a user can search for splicing signals of lncRNA of interest in a specific cancer from multiple angles such as lncRNA name, cancer type, alternative splicing type and gene locus, or perform batch search by using a logical connector. To allow the user to better understand the splicing signals, the database provides a splicing map visualization for all splicing events and a salmon map visualization for differential splicing events. To help users explore the functional impact of incrna alternative splicing in cancer, the database provides a genome browser that integrates protein binding sites, RNA binding sites and functional elements. The user can also compare the sequence of interest with the sequence regulated by lncRNA splicing by using blast, compare the difference of lncRNA alternative splicing in a plurality of cancers, or evaluate the influence of lncRNA splicing on the prognosis of cancer patients through survival analysis results. Finally, the user can download the result file of the database through the file interaction module, and call the content in the database in batch by using an Application Programming Interface (API) mode provided by the file interaction module, or upload the own data for comparative analysis. Therefore, the database system of the invention is a systematic database of cancer-related lncRNA alternative splicing, which can help researchers to better understand the role of lncRNA alternative splicing in cancer, and provides references for cancer mechanism research and development of related biomarkers.

Drawings

FIG. 1 is a diagram of the contents and functions of L ncAS2 cancer.

FIG. 2 is a database header diagram.

FIG. 3 is a query pattern diagram of L ncAS2 cancer.

FIG. 4 is an illustration of the results of a query of L ncAS2 cancer.

Detailed Description