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ENdb: a manually curated database of experimentally supported enhancers for human and mouse

2019 Nucleic Acids Research  
Here, we established a comprehensive manually-curated enhancer database for human and mouse, which provides a resource for experimentally supported enhancers, and to annotate the detailed information of  ...  The current release of ENdb documents 737 experimentally validated enhancers and their related information, including 384 target genes, 263 TFs, 110 diseases and 153 functions in human and mouse.  ...  Here, we established a comprehensive, manually curated enhancer database for human and mouse (ENdb, http:// www.licpathway.net/ENdb), which aimed to provide a resource for experimentally-supported enhancers  ... 
doi:10.1093/nar/gkz973 pmid:31665430 pmcid:PMC7145688 fatcat:7mvdzd5v2fe5bkuzlazujivamq

Experiment level curation identifies high confidence transcriptional regulatory interactions in neurodevelopment [article]

Eric Ching-Pan Chu, Alexander Morin, Tak Hou Calvin Chang, Tue Nguyen, Yi-Cheng Tsai, Aman Sharma, Chun Chao Liu, Paul Pavlidis
2021 bioRxiv   pre-print
In our survey of previous curation efforts, we identified the lack of details about the quantity and the types of experimental evidence to be a major gap, despite the importance of such details for the  ...  The majority of DTRIs (965, 64%) were supported by two or more types of experimental evidence and 27% were supported by all three.  ...  A small fraction (204; 14%) of all DTRIs were supported by evidence in 185 both humans and mice ( Fig 3A) .  ... 
doi:10.1101/2021.04.11.439248 fatcat:sbxh5pkuxvcwdknp2jicwl6y3i

TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse

Yuexin Zhang, Chao Song, Yimeng Zhang, Yuezhu Wang, Chenchen Feng, Jiaxin Chen, Ling Wei, Qi Pan, Desi Shang, Yanbing Zhu, Jiang Zhu, Shuangsang Fang (+7 others)
2021 Nucleic Acids Research  
TcoFBase curated 2322 TcoFs and 6759 TcoFs associated ChIP-seq data from over 500 tissues/cell types in human and mouse.  ...  Here, we developed the TcoFBase database (http://tcof.liclab.net/TcoFbase), which aimed to document a large number of available resources for mammalian TcoFs and provided annotations and enrichment analyses  ...  Moreover, experimentally validated enhancers were downloaded from ENdb, which were manually curated based on low-throughput experimental data.  ... 
doi:10.1093/nar/gkab950 pmid:34718747 pmcid:PMC8728270 fatcat:7yh7b4lsubgfranuxyu2a62sdm

Experiment level curation of transcriptional regulatory interactions in neurodevelopment

Eric Ching-Pan Chu, Alexander Morin, Tak Hou Calvin Chang, Tue Nguyen, Yi-Cheng Tsai, Aman Sharma, Chao Chun Liu, Paul Pavlidis
2021
The majority of DTRIs (965; 64%) were supported by two or more types of experimental evidence and 27% were supported by all three.  ...  In our survey of previous curation efforts, we identified the lack of details about the quantity and the types of experimental evidence to be a major gap, despite the theoretical importance of such details  ...  Shamsuddin Bhuiyan for providing advice on setting up the initial curation protocol. We thank Nathaniel Lim for providing the formatted ontology hierarchy files for tissue and cell type analyses.  ... 
doi:10.1371/journal.pcbi.1009484 pmid:34665801 pmcid:PMC8565786 fatcat:ficuropvyzgslono3x5efotc4u