October 30, 2020
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.

Several recent studies have described DNA methylation as a new player in the recruitment of transcription factor (TF) in chromatin, highlighting the need to connect the TF binding site (TFBS) in DNA methylation profiles of each. However, while limited TFBS databases for sequence DNA binding motif.

Here, we present MethMotif, TFBS two-dimensional database that records the position weight matrix TFBS together with a certain cell type CpG methylation information is calculated from a combination of CHIP-seq and whole genome bisulfite sequencing datasets. Integrating TFBS motif with DNA methylation TFBS better illustrate the features recognized by TF DNA loci. Specifically, we found that DNA methylation patterns in TFBS can be specific cells (eg MAFF).

Furthermore, for the TF is given, the DNA methylation profile associated with a different distinct DNA binding motifs (eg REST). To date, the database record of more than 500 TFBSs MethMotif count of more than 2000 CHIP-Seq datasets in 11 different cell types.

TADB 2.0: updated database of bacterial type II toxin-antitoxin loci.

Compared with the previous version, smooth database and new data schema is used. With the help of text mining and manual curation, it recorded 6193 TA type II loci in bacteria and archaea replicons 870, including 105 experimentally validated TA loci. In addition, the newly developed TAfinder tool combines search and detection of homologous operon structure, allowing the prediction for type II TA pairs in the bacterial genome sequence. It also helps to investigate the genomic context predicted TA loci for suspected virulence factors, antimicrobial resistance determinants and mobile genetic elements via specific alignments to the public database.

In addition, the module enables TAfinder-Compare compares the presence of TA given locus in the whole genome close relatives. With the latest update, TADB2.0 may provide better support to understand the important role of type II TA systems in prokaryotic life activities.

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.

Alea: a toolbox for epigenomics allele-specific analysis.

Assessment of expression and epigenomic Status using sequencing-based methods provide unprecedented opportunity to identify and differences in allele correlated with the status epigenomic. We present Alea, box computing equipment for epigenomics allele-specific analysis, combining data allelic variation within the existing resources, allowing for the identification of a significant relationship between epigenetic modifications and a specific allele variants in human and mouse cells.

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Alea provide customized pipes command-line tool for allele-specific generation sequencing data analysis (CHIP-Seq, RNA-Seq, etc.) that take the raw sequencing data and generate separate alleles tracks ready to be viewed on a genome browser. pipe has been validated using hybrid human and rat CHIP-seq and RNA-seq Data.

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