Case study: Exploratory ACE2 analysis using multi-omic web tools
Table of contents
Introduction
This website is connected to the article “Fantastic databases and where to find them” (Genetics and Molecular Biology) and shows how the tools covered in the above mentioned manuscript work, using ACE2 as a case study. ACE2, the Angiotensin I Converting Enzyme 2 has been shown to modulate SARS-Cov2 infection. In this example, we show how to use the top tools provided in our study to explore ACE2 information. Cite us: https://doi.org/10.1590/1678-4685-gmb-2020-0203
Databases used in this Case Study
Alternative splicing:
- ASPicDB - http://srv00.recas.ba.infn.it/ASPicDB/
- TassDB2 - http://tassdb2.leibniz-fli.de/
Cancer databases:
- CCLE - https://portals.broadinstitute.org/ccle
- TCGA data Portal - https://portal.gdc.cancer.gov/
Comparative databases:
- TISSUES - https://tissues.jensenlab.org/Search
- ToppCluster - https://toppcluster.cchmc.org/
Disease-specific and variant-disease association:
- MARRVEL - http://marrvel.org/
- Varsome - https://varsome.com/
Methylation databases:
- BECon - https://redgar598.shinyapps.io/BECon/
- DiseaseMeth - http://bio-bigdata.hrbmu.edu.cn/diseasemeth/
Gene expression databases:
- ESCAPE - http://www.maayanlab.net/ESCAPE/
- GTEX - https://gtexportal.org/home/
Genomic and sequence databases
- DisGeNET - https://www.disgenet.org/home/
- Harmonizome - http://amp.pharm.mssm.edu/Harmonizome/
LncRNA and miRNA databases
- exoRBase - http://www.exoRBase.org
- miRDB - http://mirdb.org/index.html
- BONUS: Viral miRNA - http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/miRNA.cgi
Metabolic databases:
- CIDeR - http://mips.helmholtz-muenchen.de/cider/
- Human Metabolome Database - https://hmdb.ca/
Proteome and protein-protein interaction databases:
- PDID: Protein-Drug Interaction Database - http://biomine.cs.vcu.edu/servers/PDID/index.php
- The Proteome Browser - http://proteomebrowser.org/tpb/home.jspx
Regulatory Databases:
- Interferome - http://interferome.its.monash.edu.au/interferome/home.jspx
- TTSMI - http://ttsmi.bii.a-star.edu.sg/
Other databases:
- Semantic Body Browser - http://sbb.cellfinder.org/
- VDJdb (COVID-19) - https://vdjdb.cdr3.net/