MGDB Document

Data collection of melanoma gene and how to use melanoma gene database (MGDB)

1. Data collection of melanoma genes database

 

2. Annotation for melanoma genes

     2.1 General information

     2.2 Gene expression information

     2.3 Methylation information

     2.4 Mutation information

     2.5 Interaction information

     2.6 Pathway information

     2.7 Drug information

 

3. Search

    3.1 General Search

    3.2 Literature Search

    3.3 Quick search

    3.4 BLAST

 

4. Browse

 

5. Data download and feedback to us

 


1. Data collection of melanoma genes database

 

To obtain a complete list of publications for melanoma genes, we made a comprehensive search for melanoma-related genetic studies in NCBI PubMed, and a total of 980 publications were collected. After carefully checking manually, we finally obtained 527 human melanoma genes (422 protein-coding genes, 95 microRNAs and 10 long noncoding RNAs)

 

Data sources for melanoma genes

Source
Data category Related entries Annotated Melanoma genes Contents/sources
Human melanoma genes 527 527 Gene names, full name, genomics position, synonym, definition from Entrez gene database
Literature 9788 997 Literature evidence for human melanoma genes
Expression of protein-coding genes 420 420 Expression in 470 SKCM samples and 80 UVM from TCGA database
Expression of non-coding genes 89 89 Expression in 452 SKCM samples and 80 UVM from TCGA database
Methylation 1926 396 Methylation in melanoma-related samples from GSE44661
Genomic variation 2418 300 COSMIC database
Protein-Protein Interaction 10667 352 PINA database
Pathway 1833 185 KEGG database
Drug 1236 133 DGIdb database and ClinicalTrials.gov

 

2. Annotation for melanoma genes


Information is represented on seven different types of pages, including general information, gene expression information, methylation information, mutation information, interaction, pathway information 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

 

2.2 Gene expression information


In this page, users can find gene expression profiles from TCGA. Output in MGDB is a box plot which shows the two melanoma subtypes (Skin Cutaneous Melanoma (SKCM) and Uveal Melanoma (UVM)) expression levels.

2.3 Methylation information

The methylation in promoter regions was annotated based on data from the GEO database(GEO accession: GSE44661).

2.4 Mutation information


In the 'mutation' page, full mutation details have been curated from the COSMIC (v73) database. Genomic variants in a specific gene were described for its genomic information and the corresponding histology of melanoma.

 

2.5 Interaction information


In the 'interaction' page, the interaction table for storing gene corresponding UniProt accession number and its interacting partner, which extracted from PINA (v2.0) database.

2.6 Pathway information


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

 

2.7 Drug information


In the 'Drug' page, we extracted the gene targeted drug information through integrating the DGIdb (v1.72) database. If a drug is carried out a clinical trail for melanoma, there is recorded for melanoma, otherwise there is no information. The identifier stands for the ID of ClinicalTrials. For example, we search the 'NCT00466687' in the ClinicalTrials websites. More detailed information will be obtained.

 

3. Search

 

3.1 Gene General Information Search:

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


3.2 Literature Search

3.3 Quick search

Please input gene id or gene names.

 

3.4 Blast


In the BLAST menu, users can search the Melanoma gene database based on their input sequences. The high similarity melanoma genes with input sequences will be listed in the BLAST result page. In the input page, users can choose various sequence alignment options such as E-value and identity. The matched sequence signatures are visualized on the query sequence with colored bars containing the alignment score.




4. Browse


Browse all melanoma genes by genomic position. Allow users to browse all melanoma genes by their chromosome. Result shows a list of genes.


5. 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 MGDB or to revise wrong information in current MGDB, please send us email jfxia@ahu.edu.cn directly.