fanta.bio (Functional genome ANnotations with Transcriptional Activities) is a database that collects functional annotations of genomes for studying gene regulation, with a primary focus on cis-regulatory elements (CREs) such as promoters and enhancers. This track display the CREs identified in fanta.bio.
Identification of potential CREs in fanta.bio is based on transcription signatures. Both promoters and enhancers produce specific sets of RNAs, including mRNA, lncRNA, uaRNA (upstream antisense RNA), and eRNA (enhancer RNA). These transcription signatures are effectively used in the course of the identification. The pioneering work of transcriptome-based CRE identification was carried out in the FANTOM5 project.
CRE peaks are identified based on the experimental measures of transcription starting sites in a broad range of samples. CAGE (Cap Analysis of Gene Expression) is a method to sequence capped RNA 5'-ends, and publicly available data produced by CAGE are utilized in our pipeline for identification, including the ones produced by FANTOM5, FANTOM6, and others deposited in SRA / ENA / DRA. Our pipeline utilizes a newly developed method based on transcription divergence (Kawaji et al. in prep.).
The CRE peaks are categorized into two groups: promoter level activity (PLA) and enhancer level activity (ELA), based on the levels of transcription (that is, CRE activity). Genomic coordinates of the CREs are provided in BED9+ format, where thickStart/thickEnd represent the core region of the CRE peak bounded by the highest signals in forward and reverse strands.
The color of CRE peaks with PLA ranges from red to blue, indicating the direction of transcription. Red is used for the forward direction (+1), blue for the reverse direction (-1), and intermediate colors for directionalities in-between, where directionality is defined as . The CRE peaks with ELA are indicated by yellow.
| CRE peaks (PLA) | |||||||||||
| directionality | -1 | +1 |
| CRE peaks (ELA) |
Please refer the download archive for further details, including the release notes, data source, etc.
All data produced by fanta.bio is distributed under the CC-BY 4.0 license. When you use the data and/or the website, please attribute fanta.bio as the source.
fanta.bio: a database of functional genome annotations with transcriptional activities, https://fanta.bio/, 2024.
If you have any questions or need assistance, please feel free to contact us at help [at] fanta.bio.
The construction and maintenance of fanta.bio is a collaborative effort of the following three labs:
fanta.bio is supported by JST NBDC Grant Number JPMJND2202 in Database Integration Coordination Program (DICP)