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 displays activities of cis-regulatory elements (CREs) provided by fanta.bio.
We quantify the CRE activities by measuring their transcription outputs per cell or tissue type. RNA 5'-ends obtained by a dedicated protocol (e.g. CAGE) within each of the the CRE regions are counted, normalized as CPM (counts per million) to adjust sequence depth, and scaled by the RLE method (Anders et al. 2013) to make sample-wise comparison sensible.
The CRE activities measured as CPM (Counts Per Million) are further transformed into BED scores using the following formula:
BED score = 0 (if CPM = 0)
BED score = 1 (if CPM > 0 and log2CPM ≤ -0.5)
BED score = ⌊((log2CPM + 0.5)/10.5)*999⌋ + 1 (if CPM > 0 and -0.5 < log2CPM < 10)
BED score = 1000 (if CPM > 0 and log2CPM ≥ 10)
ChIP-seq peaks (TF and Others) are obtained from ChIP-Atlas, where peaks of multiple factors are included. The ChIP-seq peaks can be filtered based on Qscore and the factors' names throguh clicking 'Configure'
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)