Lab1 Database and resource

General database

KEGG            http://www.genome.jp/kegg/

Gene Ontology     http://www.geneontology.org/

SBML            http://sbml.org/

Transcriptome database

GEO             http://www.ncbi.nlm.nih.gov/geo/

TCGA            https://portal.gdc.cancer.gov/

Protein interaction database

STRING              https://string-db.org/cgi/input.pl

DIP              http://dip.doe-mbi.ucla.edu/dip/Main.cgi

HPRD            http://www.hprd.org/

Metabolic database

BioCyc           http://www.biocyc.org/

Reactome        https://www.reactome.org/

BIGG            http://bigg.ucsd.edu/

Yeast consensus metabolic network    https://github.com/SysBioChalmers/yeast-GEM/

Assignment:

1. Search the TCA pathway in human and convert it to the XML format file.

2. Browse Gene Ontology tree to understand the functional classification. Search one gene annotation as an example.

3. Search the gene expression information of liver cancer from TCGA Database, identify significantly differential expressed genes using DESeq2 in R(SEE GUIDE)
or Click here for script.
  And then do enrichment analysis using at least two of the following resources or tools:

Gene Ontology Consortium (GOC)

DAVID

GSEA

Enrichr

4. Get the metabolic network model from corresponding database:

E.coli from BIGG

Yeast from consensus list

Human from BIGG

Please send the report to molle_faust@hotmail.com before March.17th 23:59. (Label the file name with Lab1_Name_ID)