An updated omic space with emerging omics layers: epigenome, interactome and hormonome added to each of the closely related layers with illustrative resources for Arabidopsis available on the web. ¹http://www.arabidopsis.org/, ²http://ricefox.psc.riken.jp/, ³http://rarge.gsc.riken.jp/dsmutant/index.pl, ⁴http://signal.salk.edu/tabout.html, ⁵http://tilling.fhcrc.org/, ⁶http://arabidopsis.org.uk/home.html, ⁷http://abrc.osu.edu/, ⁸http://plantcyc.org/, ⁹http://www.reactome.org/ReactomeGWT/entrypoint.html, ¹⁰http://prime.psc.riken.jp/, ¹¹http://gmd.mpimp-golm.mpg.de/, ¹²http://phosphoproteome.psc.database.riken.jp/, ¹³http://ppdb.tc.cornell.edu/, ¹⁴http://phosphat.mpimp-golm.mpg.de/, ¹⁵http://podb.nibb.ac.jp/Organellome/, ¹⁶http://suba.plantenergy.uwa.edu.au/, ¹⁷http://proteomics.arabidopsis.info/, ¹⁸http://www.megabionet.org/atpid/webfile/, ¹⁹http://interactome.dfci.harvard.edu/A_thaliana/, ²⁰http://www.brc.riken.jp/lab/epd/catalog/cdnaclone.html, ²¹http://rarge.psc.riken.jp/, ²²http://www.arabidopsis.org/portals/expression/microarray/ATGenExpress.jsp, ²³https://www.genevestigator.com/gv/, ²⁴http://mpss.udel.edu/at/, ²⁵http://atted.jp/, ²⁶http://1001genomes.org/index.html, ²⁷http://rarge.psc.riken.jp/rartf/, ²⁸http://arabidopsis.med.ohio-state.edu/, ²⁹http://datf.cbi.pku.edu.cn/, ³⁰http://signal.salk.edu/cgi-bin/methylome, ³¹https://www.plant-epigenome.org/links.

An example of integrated biological instances in a genome sequence. A gene annotation and related data, phosphorylation site, cDNA/EST, homology-based mapping, mutants and polymorphisms were retrieved from TAIR. Methylome data sets were retrieved from the Arabidopsis Epigenetics & Epigenomics group's web site. Each data set has been allocated onto the genomic region defined as a TAIR8 annotation.

An example of the schematic relationship between biological instances gained from omics analysis that are associated with a gene. Each instance is roughly classified into four data set types: sequence/structure, profile, molecular network and bioresource. Shaded nodes are sequence-oriented instances in similarity searches. Each instance is inter-related based on experimental and/or computational identification, genetic association and sequence mapping.