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Table 3 Details of the largest and most utilized web-tools for omics analyses and a list of free access repositories to retrieve useful information related to mRNA, microRNA and other non coding-RNA

From: Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures

SOURCElink/accessType of tool/repositoryType of available data
Elixir Core Data ResourceEnsemblwww.ensembl.org/index;Genome browser that: annotates genes, computes multiple alignments, predicts regulatory function and collects disease data.Vertebrates organisms data
free access
European Genome-phenome Archive (EGA)www.ebi.ac.uk/ega/;Database containing all types of sequence and genotype experiments, including case-control, population, and family studies.Human, normal and disease associated
login requested
Rfamrfam.xfam.org/;Database of non-coding RNA familiesVertebrates organisms
free access
RNAcentralrnacentral.org/;Web tool with access to a set of non-coding RNA sequences, allowing: sequence search, public Postgres database and genome browser.
It enables integrated text search, sequence similarity search, bulk downloads, and programmatic data access.
Vertebrates and other organisms
free access  
Tools for querying TCGAThe cancer omics atlas (TCOA)www.tcoa.cpu.edu.cn;This tool provides useful functions complementary to other existing tools, for fast and straightforward querying of TCGAHuman cancer data
free access
Broad Institutehttp://gdac.broadinstitute.org/;Web tool to systematize analysis from TCGA, with the following functionalities: gene expression Viewer, data analysis (overview, results, methods and data), and data download.Human cancer data
Required TCGA controlled-access data
OncoLnchttp://www.oncolnc.org/;Web tool analyzes TCGA in terms of survival by selecting the target genes.Human cancer data
free access to survival data (raw data not accessible)
TCGA Batch Effects Viewerhttp://bioinformatics.mdanderson.org/tcgambatch/Webtool designed to to help assess, diagnose and correct for any batch effects in TCGA data.Human cancer data
cBioPortalhttp://www.cbioportal.org; Open source license via GitHubSoftware allowing integrative analysis of cancer genomicsHuman cancer data