Appendix II. Databases & Servers

1) Projects

1. ENCODE

   Encyclopedia of DNA Elements: a comprehensive parts list of functional elements in the human genome. https://www.encodeproject.org/

2. 1000 Genomes

   most genetic variants with frequencies of at least 1% in the populations studied. http://www.internationalgenome.org/

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. ​https://portal.gdc.cancer.gov/​

   ​http://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html​

4. CCLE (cancer cell lines)

   Cancer Cell Line Encyclopedia: https://portals.broadinstitute.org/ccle

2) Databases

2a) General

1. NCBI

   contribute to the NIH mission of ‘uncovering new knowledge’. https://www.ncbi.nlm.nih.gov/

2. UCSC

   genome browser for vertebrate. https://genome.ucsc.edu/

3. Ensemble

   genome annotation. http://www.ensembl.org/index.html

2b) Expression Data

1. GTEx

   gene expression in different tissues. https://www.gtexportal.org/home/

2. Expression Atlas

   exploring gene expression results across species under different biological conditions. https://www.ebi.ac.uk/gxa/home

3. GEPIA

   gene expression in different TCGA tumor types. http://gepia.cancer-pku.cn/index.html

4. cBioPortal

   visualization, analysis and download of large-scale cancer genomics data sets. http://www.cbioportal.org/index.do

5. TCGA ncRNA

   ​http://ibl.mdanderson.org/tanric/_design/basic/index.html​

3) Servers

3a) General

1. BLAST

   finds regions of similarity between biological sequences. https://blast.ncbi.nlm.nih.gov/Blast.cgi

3b) Gene functional analysis

1. David

   gene functional classification tool. https://david.ncifcrf.gov/

2. KAAS

   KEGG Automatic Annotation Server. https://www.genome.jp/kegg/kaas/

3. agriGO

   gene ontology (GO) enrichment analyses of plant and agricultural species. http://systemsbiology.cau.edu.cn/agriGOv2/

3c) RNA secondary structure

1. RNAfold

   predict secondary structures of single stranded RNA or DNA sequences. http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi

2. RNAstructure

   RNA secondary structure prediction and analysis. http://rna.urmc.rochester.edu/RNAstructureWeb/

3d) miRNA targets prediction

1. TargetScan

   search for predicted microRNA targets in mammals http://www.targetscan.org/vert_72/

2. psRNATarget

   plant small RNA target analysis https://plantgrn.noble.org/psRNATarget/