Appendix II. Databases & Servers

0) Genome Browsers

1) Projects

  1. ENCODE

    Encyclopedia of DNA Elements: a comprehensive parts list of functional elements in the human genome. https://www.encodeproject.org/

  2. 1000 Genomes

    most genetic variants with frequencies of at least 1% in the populations studied. http://www.internationalgenome.org/

  3. TCGA

    The 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. ​https://portal.gdc.cancer.gov/

    http://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html

  4. CCLE (cancer cell lines)

    Cancer Cell Line Encyclopedia: https://portals.broadinstitute.org/ccle

2) Databases

2a) 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

2b) 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

2c) 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.http://www.ebi.ac.uk/GOA/exosome

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

3a) General

  1. BLAST

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

3b) 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. agriGO

    gene ontology (GO) enrichment analyses of plant and agricultural species. http://systemsbiology.cau.edu.cn/agriGOv2/

3c) 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/

3d) 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/

3e) motif analysis

sequence

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

  2. HOMER Software for motif discovery and next-gen sequencing analysis http://homer.ucsd.edu/homer/motif/

structure

  1. RNApromo Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes https://genie.weizmann.ac.il/pubs/rnamotifs08/

  2. GraphProt modeling binding preferences of RNA-binding proteins http://www.bioinf.uni-freiburg.de/Software/GraphProt/