-
ENCODE
Encyclopedia of DNA Elements: a comprehensive parts list of functional elements in the human genome. https://www.encodeproject.org/
-
Roadmap Epigenomics
A public resource of human epigenomic data. https://egg2.wustl.edu/roadmap/web_portal/
More recently, Kellis Lab developed EpiMap, a more comprehensive data resource of human epigenomic data by integrating ChIP-seq datasets from ENCODE, Roadmap and other public data resource. http://compbio.mit.edu/epimap/
-
1000 Genomes
Most genetic variants with frequencies of at least 1% in the populations studied. http://www.internationalgenome.org/
-
gnomAD
gnomAD is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects. https://gnomad.broadinstitute.org/
-
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 Line Encyclopedia)
- CCLE
- CCLE RNA-seq BAM files：[https://portal.gdc.cancer.gov/legacy-archive/search/f?filters={"op":"and","content":[{"op":"in","content":{"field":"cases.project.program.name","value":["CCLE"]}}]}](https://portal.gdc.cancer.gov/legacy-archive/search/f?filters={"op":"and","content":[{"op":"in","content":{"field":"cases.project.program.name","value":["CCLE"]}}]})
- CCLE Raw data
- CCLE Seven Bridges
-
ICGC
-
More Cancer Genomics Projects
-
NCBI
contribute to the NIH mission of ‘uncovering new knowledge’. https://www.ncbi.nlm.nih.gov/
-
UCSC
genome browser for vertebrate. https://genome.ucsc.edu/
-
Ensemble
genome annotation. http://www.ensembl.org/index.html
-
GENCODE
human and mouse genome annotation. https://www.gencodegenes.org/
-
GTEx
gene expression in different tissues. https://www.gtexportal.org/home/
-
Expression Atlas
exploring gene expression results across species under different biological conditions. https://www.ebi.ac.uk/gxa/home
-
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/
-
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/
-
GEPIA
gene expression in different TCGA tumor types. http://gepia.cancer-pku.cn/index.html
-
cBioPortal
visualization, analysis and download of large-scale cancer genomics data sets. http://www.cbioportal.org/index.do
-
TCGA ncRNA
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/
-
BLAST
finds regions of similarity between biological sequences. https://blast.ncbi.nlm.nih.gov/Blast.cgi
-
David
gene functional classification tool. https://david.ncifcrf.gov/
-
KAAS
KEGG Automatic Annotation Server. https://www.genome.jp/kegg/kaas/
-
RNAfold
predict secondary structures of single stranded RNA or DNA sequences. http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
-
RNAstructure
RNA secondary structure prediction and analysis. http://rna.urmc.rochester.edu/RNAstructureWeb/
-
TargetScan
search for predicted microRNA targets in mammals http://www.targetscan.org/vert_72/
-
psRNATarget
plant small RNA target analysis https://plantgrn.noble.org/psRNATarget/
- MEME motif based sequence analysis tools http://meme-suite.org/