I have tried using ENCODE. But I would like to refer to other available data. I do not know where to find it.
Raghad Mouhamad
ChIP-Atlas ChIP-Atlas aggregates ChIP-Seq data from multiple sources, including ENCODE, GEO, and ArrayExpress. You can input your gene of interest and specify parameters like the tissue type or organism, and it will display transcription factors with evidence of binding in proximity to your gene. It’s a robust tool for obtaining ChIP-Seq data across various experimental conditions.Website: ChIP-Atlas ReMap ReMap is a curated database of transcription factor binding sites derived from ChIP-Seq experiments. It has an extensive dataset with information on a variety of organisms, and it can provide insights into potential binding regions on your gene. ReMap is frequently updated and is especially helpful if you're interested in human or model organisms like mouse.Website: ReMap GTRD (Gene Transcription Regulation Database) GTRD is another valuable source for ChIP-Seq data on transcription factor binding sites. It integrates data from multiple sources and focuses on high-confidence binding sites, which makes it reliable for identifying TF binding regions. GTRD is particularly useful for human and mouse genes.Website: GTRD Cistrome Data Browser The Cistrome Data Browser provides ChIP-Seq data mainly for human and mouse samples, with a focus on transcription factors and chromatin regulators. This platform allows you to browse through cell type- and tissue-specific binding data, which can help in understanding context-specific binding patterns.Website: Cistrome Data Browser JASPAR Although primarily a motif database, JASPAR includes tools for predicting transcription factor binding sites based on DNA motifs from ChIP-Seq data. If you have a promoter or enhancer sequence, JASPAR’s TFBS prediction tool can complement ChIP-Seq databases by identifying potential TF binding motifs.Website: JASPAR GEO (Gene Expression Omnibus) GEO has a substantial amount of ChIP-Seq data, which you can filter for transcription factors. While not as user-friendly as dedicated ChIP-Seq databases, GEO often has studies that may not yet be incorporated into centralized resources like ENCODE.Website: GEO
To find transcription factors that might bind to your gene of interest using ChIP-Seq data, there are several well-established databases beyond ENCODE that you can explore:
These databases should provide a comprehensive overview of potential transcription factor binding sites around your gene of interest based on existing ChIP-Seq data. Each has its strengths, so it may be useful to compare results across several to confirm potential interactions.
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