机器学习方法在CRISPR/Cas9系统中的应用

张桂珊,杨勇,张灵敏,戴宪华

Application of machine learning in the CRISPR/Cas9 system

Zhang Guishan,Yang Yong,Zhang Lingmin,Dai Xianhua

表1 优化CRISPR/Cas9系统的机器学习方法常用数据集

Table 1 Major datasets of machine learning methods for optimizing the CRISPR/Cas9 system

工具名	年份	Cas类型	数据集\|数据集来源	数据集URL	参考文献
Elevation	2018	Cas9	FC, “Sch?nig”, “Concordet”, “Eschstruth”, “Shkumatava”\| U2OS, HEK293	https://www.ncbi.nlm.nih.gov/sra?term=SRP117146%5BAccession%5D https://github.com/maximilianh/crisporWebsite	[13]
DeepCpf1	2018	Cpf1	HT 1-2, HT 2, HT 3, HEK-lenti, HEK-plasmid, HCT-plasmid\| HEK293T cells	http://www.rgenome.net/cpf1-database	[14]
CRISTA	2017	Cas9	GUIDE-seq data, BLESS data, HTGTS data\| HEK293, U2OS	http://crista.tau.ac.il/	[52]
CRISPRpred	2017	Cas9	FC, RES	http://research.microsoft.com/en-us/projects/azimuth/	[60]
sgRNA Designer (Rule Set 2)	2016	Cas9	FC, RES\| A375, HL60, KBM7, mouse ESC JM8	https://www.nature.com/articles/nbt.3437#supplementary-information	[22]
predictSGRNA	2017	Cas9	ribosomal genes, non-ribosomal genes, essential genes\| HL-60, KBM-7, mouse ESC JM8	http://genome.cshlp.org/content/25/8/1147/suppl/DC1 http://www.sciencemag.org/content/343/6166/80/suppl/DC1 http://www.nature.com/nbt/journal/v32/n3/full/nbt.2800.html#supplementary information	[23]
Big Papi	2017	Cas9	A375, 293T, MOLM13	https://github.com/mhegde	[16]
—	2017	Cas9	FC, RES, UniRef100	http://research.microsoft.com/en-us/projets/azimuth	[24]
sgRNA Scorer 2.0	2017	Cas9 Cpf1	293T	https://pubs.acs.org/doi/abs/%2010.1021%2Facssynbio.6b00343	[62]
工具名	年份	Cas类型	数据集\|数据集来源	数据集URL	参考文献
CRISPR-DO	2016	Cas9	full human (GRCh37/hg19, GRCh38/hg38) mouse (NCBI37/mm9 GRCm38/mm10) zebrafish (danRer7), fly (dm6), worm (ce10)\| HL60, 293T, KBM7	https://www.ncbi.nlm.nih.gov/pubmed/?term=CRISPR-DO+for+genome-wide+CRISPR+design+and+optimization	[63]
CRISPR multitargeter	2015	Cas9	BioMart, zebrafish ohnologs	https://github.com/SergeyPry/CRISPR_MultiTargeter	[64]
CRISPRscan	2015	Cas9	One-cell-stage zebrafish embryos, germ	https://www.nature.com/articles/nmeth.3543	[46]
WU-CRISPR	2015	Cas9	FC\| 293T, K562, A549, HepG2, SKNAS, U2OS, PGP1-iPS, HEK293	https://www.ncbi.nlm.nih.gov/sra/	[6]
CRISPR (SSC)	2015	Cas9	HL60, KBM7, ABL1, BCR, 293T, LNCaP- abl, mouse ESC JM8\| A promoter-level mammalian expression atlas; Determinants of nucleosome organization in primary human cells; An integrated encyclopedia of DNA elements in the human genome	http://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/TSS_classifier/ https://www.encodeproject.org/files/ENCFF000VNN https://www.encodepro ject.org/files/EN-CFF000TLU	[65]
CRISPRko	2014	Cas9	FC\| A375, EL4, AML, MOLM13, NB4, TF1	https://www.nature.com/articles/nbt.3026#supplementary-information	[45]
—	2014	Cas9	HL60, 293T, KBM7, DH5α	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3972032/#SD1	[47]
SgRNA Scorer 1.0	2015	Cas9	DNase-seq (GSM1008573), H3K4-trimethylation (GSM945288) \|293T, K562, A549, HepG2, SKNAS, U2OS, PGP1-iPS, HEK293	http://arep.med.harvard.edu/CasFinder/	[66]
CRoatan	2017	Cas9	FC\| A375, K562	http://dx.doi.org/10.1016/j.molcel.2017.06.030	[61]
TKOv3	2017	Cas9	essential genes, nonessential genes\| CEG2, KBM7, HL60, RPE1, DLD1, GBM, HAP1, HCT116, RPE1dTP53	http://tko.ccbr.utoronto.ca/	[18]
BAGEL	2016	Cas9	essential genes, nonessential genes\| GBM, HCT116, HeLa, RPE1	http://tko.ccbr.utoronto.ca/	[20]
CRISPRiaDesign	2016	Cas9	FANTOM Consortium、ENCODE; Consortium (accession no. ENCFF000VNN); ENCODE Consortium (accession no. ENCFF000TLU)\|; K562, HEK293T; A promoter-level mammalian expression atlas; Determinants of nucleosome, organization in primary human cells	http://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/TSS_classifier/ https://www.encodeproject.org/files/ENCFF000VNN https://www.encodeproject.org/files/ENCFF000TLU	[8]
CRISPRstrand	2014	Cas	REPEATS_Lange,; REPEATS_Kunin; REPEATS_Shah	http://www.ncbi.nlm.nih.gov/	[19]
H1/H2 library	2018	Cas9	K562, Raji, Jiyoye, KBM7	https://doi.org/10.1093/bioinformatics/bty450	[67]