Appendix II. Databases & Servers
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ENCODE
Encyclopedia of DNA Elements: a comprehensive parts list of functional elements in the human genome.
1000 Genomes
most genetic variants with frequencies of at least 1% in the populations studied.
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.
CCLE (cancer cell lines)
Cancer Cell Line Encyclopedia
CCLE RNA-seq BAM files：[[)
ICGC
Other Integrative Projects
NCBI
UCSC
Ensemble
GTEx
Expression Atlas
GEPIA
cBioPortal
TCGA ncRNA
1.ExoCarta
2.exoRBase
3.EVmiRNA
4.EV-TRACK
5.EVpedia
6.Vesiclepedia
7.EMBL-EBI
8.Urinary Exosome Protein Database
BLAST
David
KAAS
RNAfold
RNAstructure
TargetScan
psRNATarget
contribute to the NIH mission of ‘uncovering new knowledge’.
genome browser for vertebrate.
genome annotation.
gene expression in different tissues.
exploring gene expression results across species under different biological conditions.
gene expression in different TCGA tumor types.
visualization, analysis and download of large-scale cancer genomics data sets.
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A web-based compendium of exosomal cargo.
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.
A database of miRNA profiling in extracellular vesicles.
Transparent reporting and centralizing knowledge in extracellular vesicle research.
An integrated database of high-throughput data for systemic analyses of extracellular vesicles. A community web portal for extracellular vesicles research.
A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 12, e1001450.
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 () and Vesiclepedia to identify annotations for focus Annotation of the target protein as well as the experimental methodology of the exosomes.
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.
finds regions of similarity between biological sequences.
gene functional classification tool.
KEGG Automatic Annotation Server.
predict secondary structures of single stranded RNA or DNA sequences.
RNA secondary structure prediction and analysis.
search for predicted microRNA targets in mammals
plant small RNA target analysis
MEME motif based sequence analysis tools