This repository provides annotation resources and tools for genome annotation, specifically focusing on three annotation methods: GenoCanyon, GenoSkyline, and GenoSkyline-Plus.
GenoCanyon is a statistical framework to predict functional non-coding regions in the human genome through integrated analysis of genomic conservation measures and biochemical annotations.
GenoSkyline is a principled framework to predict tissue-specific functional regions through integrating high-throughput epigenomic annotations.
GenoSkyline-Plus is a comprehensive update of GenoSkyline that incorporates more annotation data into the framework and extends to 127 integrated annotation tracks covering a spectrum of human tissue and cell types.
These methods are described in the following peer-reviewed publications:
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GenoCanyon:
- Lu, Q., Hu, Y., Sun, J., Cheng, Y., Cheung, K.-H., & Zhao, H. "A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data." Scientific Reports. https://doi.org/10.1038/srep10576 (*Equal Contribution)
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GenoSkyline:
- Lu, Q., Powles, R.L., Wang, Q., He, B., Zhao, H. (2016). "Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome-wide association studies." PLOS Genetics, 12(4), e1005947. https://doi.org/10.1371/journal.pgen.1005947
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GenoSkyline-Plus:
- Lu, Q., Powles, R., Abdallah, S., Ou, D., Wang, Q., Hu, Y., Lu, Y., Liu, W., Li, B., Mukherjee, S., Crane, P., Zhao, H. (2017). "Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease." PLOS Genetics, 13(7), e1006933. https://doi.org/10.1371/journal.pgen.1006933 (*Equal Contribution)
The annotation data for GenoCanyon, GenoSkyline, and GenoSkyline-Plus is available at GenomeAnnotation Releases.