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1. Data collection of TissGDB
To obtain reliable TissGenes, we used three representative tissue-specific gene expression resources such as the Human Protein Atlas (HPA), tissue-specific gene expression and regulation (TiGER), and Genotype-Tissue Expression (GTEx). Two resources like HPA and TiGER selected TissGenes based on the fold change of protein or gene expression value across multiple tissues; here, we adopted their gene list for each corresponding tissue and obtained 2,543 and 4,899 genes, respectively. On the other hand, to select TissGenes from GTEx data, we used the standard z-score method. Through the empirical result for selecting proper z-score from 1.0 to 4.0, we set the threshold of the z-score value as over 3.0 in each tissue-type from GTEx expression data. The application of this method to GTEx data resulted in 11,223 genes across 32 tissues. For each tissue type from the three resources, we mapped to the cancer type of TCGA and obtained 22 tissue types matched with 28 cancer types. As a result, 2,050, 3,090, and 6,039 TissGenes were left for these 28 cancer types for each of HPA, TiGER, and GTEx, respectively. Among these genes, we only selected 2,461 TissGenes retrieved from at least two tissue-specific gene expression resources to ensure tissue specificity of the genes. (Go to the statistics page.)

2. Understanding TissGDB's annotation categories

Search page, example: TMPRSS2

TissGene search result page

 Select your gene from the gene list

TissGene annotation result page

 These are TissGeneDB's annotation categories for your query with links to their corresponding annotation parts.

1) TissGeneSummary category

This category shows the gene's overall information from basic information such as symbol, alias, and locations to expression, pathway, regulation, and context. Words in blue are linked to their respective databases. TissGeneSummary table also shows the tissue and cancer type information including manually curated PubMed article information.

2) TissGeneExp category

This category provides various annotations using gene expression values.

--- This image shows the gene expression across 28 cancer types.

--- This image shows the gene isoform expression across 28 cancer types. User can see the unique or different usage of the specific gene isoform.

--- This image shows the gene expression across 14 tissues from GTEx data.

--- This image shows the differentially expressed genes (DEGs) across 14 cancer types with comparison to their matched normal samples.

--- This table shows the significant DEG results.

3) TissGene-miRNA category

--- This table shows the significant anti-correlated miRNAs.

4) TissGeneMut category

--- This image shows the nsSNVs of TissGene on the amino acid sequence with a lollipop plot.

--- This figure and table show the frequency of nsSNVs across 28 cancer types.

--- This image shows the copy number variation frequency across 28 cancer types.

5) TissGeneNet category

--- To compare the active genes between ligand binding site mutation samples and the other samples, we analyzed their expressions using co-expressed genes with protein-protein interaction network (PPI network).

--- Using these co-expressed genes between each cancer type and the matched normal samples, users can infer the different module activity surrounding specific TissGene.

6) TissGeneProg category

--- These plots show the overall survival difference between high- and low-expressed TissGene samples across 28 cancer types.

--- These plots show the relapse free survival difference between high- and low-expressed TissGene samples across 28 cancer types.

--- This plots show the hazard ratio distribution using overall survival information across 28 cancer types.

--- This plots show the hazard ratio distribution using relapse free survival information across 28 cancer types.

7) TissGeneClin category

--- This table shows the related drug information for the TissGene from DrugBank.

--- This table shows the associated disease information for the TissGene.

3. Download data and contact us

Please go to download page and contact page.