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
| 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 | |