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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

SOURCE

link/access

Type of tool/repository

Type of available data

Elixir Core Data Resource

Ensembl

www.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

Rfam

rfam.xfam.org/;

Database of non-coding RNA families

Vertebrates organisms

free access

RNAcentral

rnacentral.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 TCGA

The 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 TCGA

Human cancer data

free access

Broad Institute

http://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

OncoLnc

http://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 Viewer

http://bioinformatics.mdanderson.org/tcgambatch/

Webtool designed to to help assess, diagnose and correct for any batch effects in TCGA data.

Human cancer data

cBioPortal

http://www.cbioportal.org; Open source license via GitHub

Software allowing integrative analysis of cancer genomics

Human cancer data