Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bullets030.gifCancer Cell Metabolism Gene Search
1. Data collection of ccmGDB database

2. Understanding of ccmGDB's annotation category
     
search page, example: PTEN
     
cmGene search result page
     
cmGene annotation result page
     
1) Gene Summary Category
     
2) Mutation Category
     
3) Gene Expression Category
     
4) Gene-Gene Network Category
     
5) Pharmacological Information Category
     
6) Phenotypic Information Category
     
7) Cross Reference Table

3. Search
     
Gene Accession Search
     
Cell Metabolism Pathway Searh
     
Copy Number Varied Gene Search
     
Cancer Gene Set Search
     
Significantly Mutated Genes per Cancer Type Search
     
Related Drug's Status Search
     
EXAMPLE - Cell Metabolism Pathway Searh

4. Download and contact us
 

1. Data collection of ccmGDB database
We gathered cell metabolism genes from KEGG and REACTOME pathway databases. Among all 2071 cell metabolism genes, 922 genes were from KEGG and 1597 were from REACTOME. There were 477 genes that were common between the two pathway data sets. For all genes, we checked cancer genes using well-characterized cancer gene databases. These databases are Cancer Gene Census, CancerGenes, Network of Cancer Genes, Oncogenes, TSGene
and Significantly Mutated Genes in Cancer. Detailed description about cancer gene annotation can be found in The Catalogue of Cancer Genes in our previous study. We also supply information on whether or not the gene is involved in therapeutic vulnerabilities in cancers.

Data collection
 

2. Understanding of ccmGDB's annotation category

annotation category 

search page, example: PTEN
PTEN search page example
 
Insert query
 - official HUGO gene symbol, Entrez Gene ID, Ensembl ID, Iniprot Accession

 

cmGene search result page

search page result page
 Select your gene among the gene list

 

cmGene annotation result page

annotation result page
 These are ccmGDB's annotation categories for your query. Each has been linked to each annotation part.

 

1) Gene Summary Category

This category shows the gene's overall information from basic information such as symbol, alias, and locations to expression, pathway, regulation, and context. Blue letters are linked to each the respective database.

gene summary category

 

2) Mutation Category

ccmGDB offers various mutation annotations. The first image shows the structural variations in a circos plot.

This is for chromosomal rearrangement variations. ccmGDB shows inter-chromosomal rearrangements and intra-chromosomal rearrangements seperately. For PTEN gene, in prostate cancer type, inter-chromosomal variations is high. However, for the intra-chromosomal variations, ovary cancer type is high.

 inter-chromosomal rearrangement variations

intra-chromosomal rearrangement variations

From the ChiTars2.0's human 1,400 break point information, ccmGDB shows the chimeric transcripts including PTEN as shown below. We also supply links for structural variants of other databases.chimeric transcripts

From COSMIC's CNV data, ccmGDB shows the GAIN (red) or LOSS (green) information per each tissue. information per each tissue

From COSMIC SNV data, ccmGDB shows the lollipop plot for PTEN with the non-synonymous (red circles) and synonymous (blue circles) mutations. Circle size indicateds mutaiton counts for that loci such that a larger circle indicates more mutation counts.lollipop plot for PTEN

These piecharts show the SNV ratio per tissue and mutation type of COSMIC data. mutation type of COSMIC data

This table shows the top 10 SNVs for PTEN. Sorting is based on number of recurrent samples.top 10 SNVs

This lollipop image is for SNV data from TCGA.lollipop for SNV

This table shows the top 10 SNVs for TCGA data. And ccmGDB offers other database links.top 10 SNVs for TCGA data

This copy number plot shows the differential copy number for 15 TCGA cancer types. 15 TCGA cancer types

 

 

3) Gene Expression Category

The gene expression category covers various expression from 3 different databases. The image below shows gene expression for 20 CCLE cancer types. 20 CCLE cancer types

ccmGDB provides protein expression plots. Only 24 genes were included among over 2,00 cmGenes.protein expression plot

From 8 TCGA cancer types' RNA-seq expression values, ccmGDB provide differential gene expression between tumor and matched normal samples. differential gene expression

From 15 TCGA cancer types, we drew the correlation plots between CNV and gene expression. In the LAML cancer type, there's no copy number variation. However, in the LUSC cancer type, we can see the positive correlation.positive correlation
positive correlation 
positive correlation 

 

4) Gene-Gene Network Category

To compare the active genes between tumor and matched normal samples, we analyzed expression using the top 20 co-expressed genes' expression with PPI and we made a network. Using gene elements under the network, we can do the pathway enrichment test.pathway enrichment testGene Network Category
 

From all interacting genes, ccmGDB shows the most related KEGG pathway using DAVID web site links.most related KEGG pathway

This table shows all interacting genes which are from PathwayCommons database. interacting genes

 

 

5) Pharmacological Information Category

Pharmarcological information category shows drug related cross references. Drug-Gene Interaction Network image shows gene-centered network and drug-centered netwrok
Pharmarcological information

Under network is for drug-centered network. And user also can see the drug structure.drug structure

 

 

6) Phenotypic Information Category

This cagegory shows information related phenotypes of this gene. The major phenotype is cancer. The second is OMIM's supporting disease information. And Orphanet also supports related syndromes. Lastly mouse phenotype link is provided to see the phenotype.Phenotypic Information

 

 

7) Cross Reference Table

This table shows cross reference information from parsing Uniprot data.cross reference information

 

 

3. Search

Gene Accession Search

This search system suports input as an official HUTO gene symbol including wildcard character, Entrez Gene ID, Ensembl ID, and Uniprot Accession.official HUTO gene symbol

Cell Metabolism Pathway Search

This search system supports input as a cell metabolism pathway from KEGG and REACTOME pathway databases.Cell Metabolism Pathway Search

Copy Number Variation Related Gene Search

This search system suports input as a copy number variation type per each tissue from COSMIC data sets.Copy Number Variation Related Gene┬áSearch

Cancer Gene Set Search

This search system suports input as a cancer gene set from 5 cancer gene databases.5 cancer gene databases

Significantly Mutated Genes per Cancer Type Search

This search system suports input as a significantly mutated gene set for each cancer type.Significantly Mutated Genes

Related Drug's Status Search

This search system suports input as a status of the drug related with cmGenes.

Related Drug Status Search

 

EXAMPLE - Cell Metabolism Pathway Search

Let's search using 'Cell Metabolism Pathway Searh' system with 'KEGG_GALACTOSE_METABOLISM' pathway. Cell Metabolism Pathway Search

Then, the gene search result page will show all gene list of 'GALACTOSE METABOLISM' of KEGG database. You can go to each gene's annotation page when you click the blue colored gene symbol.blue colored gene symbol

 

4. Download and contact us