Figure 1

Setup of the AnnoMiner web-server. The user interacts with the web-server via the front-end for data upload and data mining. Genomic peak data (in BED format), annotation data, e.g. from transcriptomic analysis, or a list of co-regulated genes can be uploaded to the server. The user can either annotate peaks (peak annotation), integrate peaks (peak integration) or annotate and analyse nearby genes (nearby genes annotation, long-range interactions) of a peak. AnnoMiner’s fourth function allows searching for enriched transcription factor binding or histone modification events in the promoter regions of a list of co-regulated genes (TF & HM enrichment analysis). In the back-end, Java servlets are responsible for data upload, analysis, integration and ID conversion. User data, genome feature data from ENSEMBL, UCSC and NCBI, as well as ENCODE, modENCODE and modERN ChIP-seq data are stored in a MongoDB database. Currently, we host genome feature data from H. sapiens, M. musculus, D. melanogaster, C. elegans and S. cerevisiae. Data from ENCODE, modENCODE and modERN are available in AnnoMiner for human, mouse, Drosopihla and C. elegans.