Appendix II. Databases & Servers
- ENCODEEncyclopedia of DNA Elements: a comprehensive parts list of functional elements in the human genome. https://www.encodeproject.org/
- 1000 Genomesmost genetic variants with frequencies of at least 1% in the populations studied. http://www.internationalgenome.org/
- TCGAThe Cancer Genome Atlas: From the analysis of over 11,000 tumors from 33 of the most prevalent forms of cancer, the Pan-Cancer Atlas provides a uniquely comprehensive, in-depth, and interconnected understanding of how, where, and why tumors arise in humans. As a singular and unified point of reference, the Pan-Cancer Atlas is an essential resource for the development of new treatments in the pursuit of precision medicine.
- CCLE (cancer cell lines)Cancer Cell Line Encyclopedia
- Other Integrative Projects
- 1.NCBI
- 2.UCSC
- 3.Ensemble
- 1.GTEx
- 2.Expression Atlasexploring gene expression results across species under different biological conditions. https://www.ebi.ac.uk/gxa/home
- 3.GEPIA
- 4.cBioPortalvisualization, analysis and download of large-scale cancer genomics data sets. http://www.cbioportal.org/index.do
1.ExoCarta
2.exoRBase
A repository of circular RNA (circRNA), long non-coding RNA (lncRNA) and messenger RNA (mRNA) derived from RNA-seq data analyses of human blood exosomes. Experimental validations from published literature are also included.http://www.exorbase.org/
3.EVmiRNA
4.EV-TRACK
Transparent reporting and centralizing knowledge in extracellular vesicle research.http://www.evtrack.org/
5.EVpedia
An integrated database of high-throughput data for systemic analyses of extracellular vesicles. A community web portal for extracellular vesicles research. http://evpedia.info
6.Vesiclepedia
A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 12, e1001450. http://www.microvesicles.org/
7.EMBL-EBI
The EMBL-EBI exosomes database is a comprehensive annotated database of GO function analysis of human exosomal proteins. The database works closely with laboratory researchers (Dr S Mathivanan - La Trobe Institute, Dr A Kalea - UCL) and the exosomal database Exocarta (http://www.exocarta.org/) and Vesiclepedia to identify annotations for focus Annotation of the target protein as well as the experimental methodology of the exosomes.
8.Urinary Exosome Protein Database
This database of urinary exosome proteins is based on published protein mass spectrometry data from the NHLBI Epithelial Systems Biology Laboratory (ESBL). All data are from urinary exosomes isolated from healthy human volunteers.https://hpcwebapps.cit.nih.gov/ESBL/Database/Exosome/
- 1.BLAST
- 1.David
- 2.KAAS
- 1.RNAfoldpredict secondary structures of single stranded RNA or DNA sequences. http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
- 2.RNAstructure
- 1.TargetScan
- 2.psRNATarget
- 1.