Appendix II. Databases & Servers

1) Consortium 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

  4. GENCODE

    human and mouse genome annotation. https://www.gencodegenes.org/

(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. FANTOM

    generate maps of functional regulatory elements (i.e. promoters and emhancers) using CAGE (Cap Analysis of Gene Expression) sequencing on RNA samples from human cell and tissue types. http://fantom.gsc.riken.jp/5/data/

  4. Human Protein Atlas

    aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. https://www.proteinatlas.org/

  5. GEPIA

    gene expression in different TCGA tumor types. http://gepia.cancer-pku.cn/index.html

  6. 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.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

(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/