dbCPG Document


Data collection of cancer predisposition gene and how to use cancer predisposition gene database (dbCPG)

1. Data collection

 

2. Annotation

     2.1 General information and literature evidence

     2.2 Gene expression information

     2.3 Methylation information

     2.4 Post transcriptional modification information

     2.5 Mutation information

     2.6 Interaction information

     2.7 Pathway information

     2.8 Drug information

 

3. Search

    3.1 General Search

    3.2 Literature Search

    3.3 Quick Search

 

4. Browser

 

5. Data upload

 

6. Data download and feedback to us

 


1. Data collection

 


To provide a comprehensive resource for investigation of CPGs and their molecular mechanisms in cancer, we performed a collection and review of peer-reviewed literature from databases including Rahman's data, PubMed abstract, GeneReview, Online Mendelian Inheritance in Man (OMIM) and Gene Reference Into Function (GeneRIF). After carefully checking manually, we finally obtained 918 human CPGs, including 800 protein-coding genes. The gene contents from the two databases and three literature sources were summarized in the figure below.

 

 

2. Annotation


Information is represented on seven different types of pages, including General information and literature evidence, Gene expression information, Methylation information, Post transcriptional modification, Mutation information, Protein-protein interaction, and Drug information. It is easy to switch to other annotations by clicking the hyperlink at the top of the page.


2.1 General information and literature evidence

 

2.2 Gene expression information


In this page,users can find gene expression information from Expression Atlas.

2.3 Methylation information

In this page, users can find methylation information from DiseaseMeth.

2.4 Post transcriptional modification information


In PTM page, we extracted the gene PTM type information from dbPTM.

 

2.5 Mutation information


In the 'mutation' page, all the related germline mutations were curated from the ClinVar database.

 

2.6 Interaction information


In the 'interaction' page, the interaction table for storing gene corresponding UniProt accession number and its interacting partner, which were extracted from PINA database.

2.7 Pathway information


In the 'pathway' page, genes within its involved pathways were described. Through the hyperlink, we can link to the corresponding
pathway in MSigDB.

 

2.8 Drug information


In the 'Drug' page, we extracted the gene targeted drug information from DGIdb database.


 

3. Search

 

3.1 Gene General Information Search:

This gene information search retrieves lists of CPGs based on their general information such as gene name and its synonyms.


3.2 Literature Search

3.3 Quick search

 


4. Browser


Browse all CPGs by genomic position

Allow users to browse all CPGs by their chromosome. Result shows a list of genes.


Browse all CPGs by data source

Allows users to browse all CPGs by data source.

Rahman: 114 CPGs

PubMed search and curation: 245 CPGs

OMIM: 362 CPGs

GeneRIF curation: 469 CPGs

Rahman: 114 CPGs

Browse all CPGs by gene type

Allows users to browse all CPGs by coding, non-coding or unknown type genes.

All the human protein coding CPGs

All the human non-coding CPGs

All the human unknown type CPGs

Browse all CPGs by cancer type

From cancer type list, users can easily browser all the cancer type in our database


5. Upload


In the upload page, users can deposit an article to dbCPG database


6. Data download and feedback to us


You can freely download our data for academic researchers, but not for profit purposes. Please access Download page.


We also hope you can help us to improve our database. If you have any suggestion to add new comment to records in current dbCPG or to revise wrong information in current dbCPG, please send us email directly.