DBTSS

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 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 […]

[…] 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. […]