About dbMCS
Lacking of database focusing on the mutation markers of anti-cancer drug sensitivity limited the investigation of patterns for mutation markers. We developed construct an infrastructure to highly operable and quick access to data of drug sensitivity mutation markers. The dbMCS mainly consists of five parts: Home, About, Submit, Download and Contact. Users can use keywords to quickly determine whether a cancer caused by a genetic mutation responds to an anticancer drug. Each association in the database contains information of gene, cancer type, mutation, drug response, etc., and relevant references are also provided for each independent item. The database will be of great importance for tackling the problem of drug sensitivity prediction and biomarker identification in cancers.
According to Human Genome Variation Society nomenclature, we standardized the variant descriptions for all three levels (gDNA, cDNA and protein) using TransVar (
https://bioinformatics.mdanderson.org/transvar). To acquire standard disease terminology, we mapped the related disease onto Disease Ontology (
https://disease-ontology.org). For the drugs involved in the database, we get the standard drug names in DrugBank (
https://go.drugbank.com). Users can query and browse the detailed information of each index, and also link to the above useful public resources.
Web Browser Requirements
The dbMCS requires a modern web browser with JavaScript and cookies enabled. To view the complex details, pop-ups must not be blocked. The following browsers have been thoroughly tested with dbMCS:
- Mozilla Firefox, version 7 or above
- Internet Explorer, versions 11 or above
- Chrome, version 8 or above
The latest version of Firefox and Chrome is recommended for visualization.
Evidence System
Levels of evidence for entries in dbMCS.
Level NO. |
Category |
Definition |
Level 1 |
Approved |
Items associated with FDA-approved and international guidelines. |
Level 2 |
Clinical |
Items associated with clinical trials such as Phase I, Phase II, Phase III, clinical study and so on. |
Level 3 |
Preclinical |
Items associated with in preclinical experiments such as preclinical-cell culture, preclinical-PDX, preclinical-cell line xenograft and so on. |
What can users do in dbMCS
- The users can browse the data about the mutation markers of anti-cancer drug sensitivity by key words, disease, gene, cDNA and drug.
- The users can easily apply the search function supporting fuzzy query to acquire what interested in the cancer research field.
- For the locations of mutation and protein domains, dbMCS provides direct visualization.
- The users can freely download the standardized data which are valuable for clinical treatment of cancer.
- The users can submit new data to us for expending the database.
Usage
In dbMCS, we tried to make it powerful and convenient to be used. This Usage is prepared for the online service.
Capitalised titles correspond to column headings in the web page tables:
- GENE: The official gene symbol
- DISEASE: disease terminology in Disease Ontology
- DOID: Disease Ontology identifier
- DRUG: The uniform drug names in DrugBank
- Type: missense, FS-indel, duplication or complex-indel (insertion occurs simultaneously with deletion)
1. Browse
You can select one or more of the four options listed in the browse area (Disease, Gene, cDNA and Drug). The cDNA option only can be available after a gene is selected.
2. Search
You can input one keyword to search in the dbMCS. The search fields include disease name, gene name, drug name or mutation (gDNA, cDNA or protein sequences). Only the GRCh37 genome assembly is supported.
3. Download
We provide the option to download the full database. If you'd like to download it, please select the menu "Download" and click the download button.
4. Contact
If you have some suggestion or questions which are not listed above, please contact us for details.
(Email: zhenyuyue@ahau.edu.cn)
Database Summary (current version)
(A) Statistics in dbMCS
Gene |
Mutation |
Disease |
Reference |
Drug |
Sensitivity Entry |
Resistance Entry |
146 |
1271 |
185 |
1306 |
486 |
3151 |
1276 |
Note: Sensitivity Entry, number of entries recording a mutation-disease-drug relationship with sensitivity. Resistance Entry, number of entries recording a mutation-disease-drug relationship with resistance.
(B) Type distribution
Type |
Number |
Type |
Number |
Missencse |
978 |
Copy number gain |
46 |
IF-deletion |
61 |
Copy number loss |
1 |
IF-insertion |
35 |
Nonsense |
31 |
FS-deletion |
6 |
Synonymous |
16 |
FS-insertion |
7 |
Noncoding |
4 |
Duplication |
19 |
Other |
27 |
Complex-indel |
40 |
Total |
1271 |
Note: FS, frameshift; IF, inframe; Complex-indel, insertion occurs simultaneously with deletion.
Version
The current version number is 1.0 - January, 2021. The most recent update to data was on January 6th, 2021.