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. Author manuscript; available in PMC: 2016 Jul 1.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2015 Apr 17;7(4):141–161. doi: 10.1002/wsbm.1297

Table 1.

A list of high-throughput technologies and the data they generated, with representative databases

Biotechnologies Experimental data Representative databases
DNA-seq, NGS DNA sequences, exome sequences, genomes, genes GenBank109, DDBJ110, Ensembl111
Microarray, RNA-seq Gene expression levels, microRNA levels, transcripts GEO112, Expression Atlas113
MS, iTRAQ Protein concentration, phosphorylations GPMdb, PRIDE, Human Protein Atlas22
C-MS, GC-MS, NMR Metabolite levels HMDB, GMD
ChIP-chip, ChIP-seq Protein-DNA interactions, transcript factor binding sites GEO112, TRANSFAC, JASPAR, ENCODE, modENCODE
CLIP-seq, PAR-CLIP, iCLIP MicroRNA-mRNA regulations StarBase114, miRTarBase
Y2H, AP/MS, MaMTH, maPPIT Protein-protein interactions HPRD115, BioGRID116, DIP, IntAct, and MINT, CCSB interactome database
Protein microarray Kinase–substrate interactions RegPhos, PhosphoPOINT
SGA, E-MAP, RNAi Genetic interactions HPRD115, BioGRID116
SNP genotyping array GWAS loci, eQTL, aberrant SNPs GWAS Catalog, GWASdb, GTEx, dbGAP, dbSNP HGMD
LUMIER, data integration Signaling pathways, metabolic pathways, molecular signatures KEGG, ConsensusPathDB, BioCart, Pathway Commons, MSigDB, Reactome, BiGG