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Protocols
DBTSS specifications
Information
Unique identifier | OMICS_01860 |
---|---|
Name | DBTSS |
Alternative name | DataBase of Transcriptional Start Sites |
Restrictions to use | None |
Community driven | No |
Data access | Browse |
User data submission | Not allowed |
Version | 10.1 |
Maintained | Yes |
Taxon
-
Primates
- Homo sapiens
-
Rodents
- Mus musculus
- Rattus norvegicus
Subtool
- DBKERO
Maintainer
- person_outline Yutaka Suzuki
Additional information
Publications for DataBase of Transcriptional Start Sites
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data
DBTSS citations
(51)Rotating night work, lifestyle factors, obesity and promoter methylation in BRCA1 and BRCA2 genes among nurses and midwives
[…] hole blood samples using QIAamp DNA Blood Mini Kit (Qiagen), according to the manufacturer’s instructions.The promoter region with the transcriptional start site of BRCA1 and BRCA2 was analyzed using DBTSS database (http://dbtss.hgc.jp) for further CpG island identification. Chemical modification of 500 ng of genomic DNA isolated from whole blood was performed with the use of Cells-to-CpG™ Bisulfi […]
Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks
[…] et []. We also observed apparent better quality of a promoter identification program when using EPDnew data. For example, for CNN predictor computed on 1083 mouse TATA promoter regions extracted from DBTSS [], we also reached a pretty good performance on a test set of 271 promoters: Sn = 0.94, Sp = 0.94 and CC = 0.86. However, CNN model trained using mouse TATA promoters regions from EPDnew demons […]
Identification of Epigenetic Biomarkers of Lung Adenocarcinoma through Multi Omics Data Analysis
[…] We used ChIP-seq data of 26 lung adenocarcinoma cell lines and SAEC from the DBTSS database () []. To identify the regions of histone modifications, “peaks” of ChIP-Seq tags were called by MACS2 for the six types of histone modifications (H3K27ac, H3K4me3, H3K4me1, H3K9me3, H3 […]
Building the Frequency Profile of the Core Promoter Element Patterns in the Three ChromHMM Promoter States at 200bp Intervals: A Statistical Perspective
[…] e the ChromHMM annotation of 9 cell lines (K562, GM12878, H1HESC, HEPG2, HMEC, HSMM, HUVEC, NHEK, and NHLF). The last two fields indicate the existence of DataBase of Human Transcription Start Sites (dbTSS) data [], and the GC ratio, respectively, where the hg19promoter file for dbTSS data was used for indexing (ftp://ftp.hgc.jp/pub/hgc/db/dbtss/dbtss_ver8/Sanger_data/). shows the summary of our p […]
The impact of sequence length and number of sequences on promoter prediction performance
[…] the studies conducted in this work, promoter and non-promoter sequences derived from human genome were used for datasets construction.Promoters were obtained from a set of sequences available in the DBTSS database [] (version 8.0), which has already been used in several other works [,,,], and is a set of approximately 98,000 experimentally validated promoter sequences with active TSS, where each […]
The Retinoblastoma Tumor Suppressor Transcriptionally Represses Pak1 in Osteoblasts
[…] t site. The TRED accession numbers for the human and mouse Pak1 promoters are 114750 and 76974, respectively. Sequence alignment and identification of transcriptional start sites were performed using DBTSS (http://dbtss.hgc.jp). Genomatrix (www.genomatix.de/en/index.html) was used to identify transcription factor binding sites within the human and mouse Pak1 promoters. […]
Citations
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