Appendix II. Databases & Servers

1) Projects

2) Databases

(1) General

    1.
    NCBI
    contribute to the NIH mission of ‘uncovering new knowledge’. https://www.ncbi.nlm.nih.gov/
    2.
    UCSC
    genome browser for vertebrate. https://genome.ucsc.edu/
    3.
    Ensemble
    genome annotation. http://www.ensembl.org/index.html

(2) Expression Data

    1.
    GTEx
    gene expression in different tissues. https://www.gtexportal.org/home/
    2.
    Expression Atlas
    exploring gene expression results across species under different biological conditions. https://www.ebi.ac.uk/gxa/home
    3.
    GEPIA
    gene expression in different TCGA tumor types. http://gepia.cancer-pku.cn/index.html
    4.
    cBioPortal
    visualization, analysis and download of large-scale cancer genomics data sets. http://www.cbioportal.org/index.do

(3) Exosomal database

1.ExoCarta
A web-based compendium of exosomal cargo.http://www.exocarta.org/
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
A database of miRNA profiling in extracellular vesicles. http://bioinfo.life.hust.edu.cn/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/

3) Servers

(1) General

    1.
    BLAST
    finds regions of similarity between biological sequences. https://blast.ncbi.nlm.nih.gov/Blast.cgi

(2) Gene functional analysis

    1.
    David
    gene functional classification tool. https://david.ncifcrf.gov/
    2.
    KAAS
    KEGG Automatic Annotation Server. https://www.genome.jp/kegg/kaas/

(3) RNA secondary structure

    1.
    RNAfold
    predict secondary structures of single stranded RNA or DNA sequences. http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
    2.
    RNAstructure
    RNA secondary structure prediction and analysis. http://rna.urmc.rochester.edu/RNAstructureWeb/

(4) miRNA targets prediction

    1.
    TargetScan
    search for predicted microRNA targets in mammals http://www.targetscan.org/vert_72/
    2.
    psRNATarget
    plant small RNA target analysis https://plantgrn.noble.org/psRNATarget/

(5) Sequence motif analysis

    1.
    MEME motif based sequence analysis tools http://meme-suite.org/
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