Appendix II. Databases & Servers

1) Projects


    Encyclopedia of DNA Elements: a comprehensive parts list of functional elements in the human genome.

  2. 1000 Genomes

    most genetic variants with frequencies of at least 1% in the populations studied.

  3. 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. ​

  4. CCLE (cancer cell lines)

    Cancer Cell Line Encyclopedia:

2) Databases

2a) General

  1. NCBI

    contribute to the NIH mission of ‘uncovering new knowledge’.

  2. UCSC

    genome browser for vertebrate.

  3. Ensemble

    genome annotation.

2b) Expression Data

  1. GTEx

    gene expression in different tissues.

  2. Expression Atlas

    exploring gene expression results across species under different biological conditions.

  3. GEPIA

    gene expression in different TCGA tumor types.

  4. cBioPortal

    visualization, analysis and download of large-scale cancer genomics data sets.

  5. TCGA ncRNA

3) Servers

3a) General

  1. BLAST

    finds regions of similarity between biological sequences.

3b) Gene functional analysis

  1. David

    gene functional classification tool.

  2. KAAS

    KEGG Automatic Annotation Server.

  3. agriGO

    gene ontology (GO) enrichment analyses of plant and agricultural species.

3c) RNA secondary structure

  1. RNAfold

    predict secondary structures of single stranded RNA or DNA sequences.

  2. RNAstructure

    RNA secondary structure prediction and analysis.

3d) miRNA targets prediction

  1. TargetScan

    search for predicted microRNA targets in mammals

  2. psRNATarget

    plant small RNA target analysis

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