index.md

Case study: Exploratory ACE2 analysis using multi-omic web tools

Table of contents

• Step 1 Searching basic information on ACE2

• Step 2 Genomic and sequence databases

• Step 3 Searching of ACE2 Gene expression

• Step 4 Searching in Cancer databases

• Step 5 Comparative databases

• Step 6 Alternative splicing databases

• Step 7 Methylation databases

• Step 8 Regulatory Databases

• Step 9 miRNA, lncRNA and circRNA Databases

• Step 10 Metabolic databases

• Step 11 Disease-specific and variant-disease association

• Step 12 Proteome databases

• Step 13 Other databases

• Complete list of databases

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/

Next - Step 1