Lu Lab

1. You can select a species: Human
2. You can select a RBP Gene Symbol: TP53

1. Piranha: Uren P.J. et al. Site identification in high-throughput RNA-protein interaction data. Bioinformatics 28, 3013-20 (2012).
2. PARalyzer (PAR-CLIP): Corcoran D.L. et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol 12, R79 (2011).
3. CIMS (HITS-CLIP): Moore M. et al. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc 9, 263-93 (2014).
4. CITS (iCLIP): Weyn-Vanhentenryck S.M. et al. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep 6, 1139-52 (2014).
5. ENCODE eCLIP: Van Nostrand E.L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods (2016).
6. PIP-seq: Silverman IM et al. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biol (2014).
7. GENCODE annotations: Harrow J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22, 1760-74 (2012).
8. Flybase: Drysdale R et al. FlyBase : a database for the Drosophila research community.. Methods Mol Biol. 420:45-59. (2008)
9. WormBase: Harris TW et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. (2010)
10. TAIR: Lamesch P et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. (2012)
21. SGD: Weng S et al. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. Jan 1;31(1):216-8 (2003).
12. PhastCons (Arabidopsis): Li F et al. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell. Nov;24(11):4346-59 (2012).
13. miRanda: Enright A.J. et al. MicroRNA targets in Drosophila. Genome Biol 5, R1 (2003).
14. RNAhybrid: Kruger J. & Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34, W451-4 (2006).
15. psRobot: Wu HJ et al. PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res. (2012).
16. psRNAtarget: Dai X et al. psRNATarget: a plant small RNA target analysis server Nucleic Acids Res. (2018).
17. RMBase2: Xuan JJ et al. RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. Nucleic Acids Res. (2018).
18. RADAR: Ramaswami G. & Li J.B. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res 42, D109-13 (2014).
19. DARNED: Kiran A. & Baranov P.V. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 26, 1772-6 (2010).
20. RNA editome (worm): Zhao HQ et al. Profiling the RNA editomes of wild-type C. elegans and ADAR mutants. Genome Res. (2015).
21. dbSNP: Smigielski E.M., Sirotkin K., Ward M. & Sherry S.T. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28, 352-5 (2000).
22. GWASdb: Li M.J. et al. GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res 44, D869-76 (2016).
23. ClinVar: Landrum M.J. et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 42, D980-5 (2014).
24. Cancer COSMIC SNVs: Forbes S.A. et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet Chapter 10, Unit 10.11 (2008).
25. Cancer TCGA whole-genome SNVs: Alexandrov L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-21 (2013).
26. TCGA whole-exome SNVs: Ellrott K et al. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 271-281(2018).