A database for associated traditional Chinese medicine, gene and disease infomation using text mining

Tutorial

1. TCM Herbs and Genes
2. Diseases
3. TCM effects


Search interface

The search interface of TCMGeneDIT is composed of three parts including (1)TCM Herbs and Genes, (2)Diseases and (3)TCM effects.


Search for association information about TCMs and Genes

1. Search with TCM Herb
2. Search with Gene Symbol
3. Search with Gene Keyword
4. TCM Herb Navigation

Search with TCM Herb

Step 1

Step 2

Associations with 99.5%, 99% and 97.5% confidences are highlighted with red, green and blue colors, respectively.

Step 3

Associations between TCM and Genes

Step 3

Transitive inference of the associations between TCM and Genes (step 1)

Step 4

Transitive inference of the associations between TCM and Genes (step 2)

The inference results are sorted by relation scores.

Step 5

Associations between TCM and Diseases

Please refer to the specification for TCM and gene associations.

Step 6

Please refer to the specification for TCM and gene associations.

Step 7


Search with gene symbol

Step 1

Step 2

The first part of the returned page contains general gene information, links to associations and gene ontology annotations. The gene function is collected from the NCBI Entrez Gene, if available.

The second part of the returned page contains information about protein-protein interactions and pathways.

Step 3

Associations between Gene and TCMs

Please refer the specification for TCM and gene associations.

Step 4

Associations between Gene, TCMs and Diseases

By following the Gene Symbol-TCMs-Diseases link, users can retrieve the associations among gene, TCMs and diseases. Information integration is also available.

Step 5

Integrated associations between Gene, TCMs and Diseases


Search with keyword

Step 1

If users do not know the exact gene symbol of interested gene, please search TCMGeneDIT with related keyword. For example, if you would like to access methylation information about TNF-alpha gene but forget or not know it's gene symbol, you can input keyword such as 'tumor necrosis factor' to search TCMGeneDIT.

Step 2

The returned page contains multiple entries with keyword 'tumor necrosis factor' in Description field. Please follow the link of Gene ID of interested gene for more information. The following search steps are similar to the search with gene symbol. Please refer to above examples.


TCM Herb Navigation

Step 1

For example, users can follow the link of 'G' to examine 'Ginkgo biloba'.

Step 2


Search for association information about Diseases

Step 1

Users can select a disease name to find general disease information.

Step 2

Step 3

Step 4

Step 5

Step 6

Trasitive association network about disease, TCM and genes


Search for association information about TCM effects

Step 1

Users can examine which TCMs have common effects.

Step 2

Please refer to the specification for TCM and gene associations.


© 2008 Systems Biology Lab, National Taiwan Univerisity, Taipei, Taiwan