GENE
stringlengths 3
8
| Occurences
int64 2
7
| Present In
stringlengths 14
63
|
---|---|---|
TYMS | 7 | LKB1 KO, NF1 KO, NF2 KO, PBRM1 KO, PTEN KO, TP53 KO, TP53BP1 KO |
UBE2T | 6 | CDH1 KO, LKB1 KO, NF1 KO, NF2 KO, PBRM1 KO, TP53BP1 KO |
BRIP1 | 5 | LKB1 KO, NF1 KO, NF2 KO, PBRM1 KO, VHL KO |
DDX19A | 5 | ARID1A KD, CDH1 KO, NF2 KO, PBRM1 KO, RB1 KO |
PPP2R3C | 5 | CDH1 KO, LKB1 KO, NF2 KO, RB1 KO, VHL KO |
RPRD1B | 5 | LKB1 KO, NF1 KO, PTEN KO, TP53 KO, VHL KO |
BPTF | 4 | ARID1A KD, KEAP1 KO, PBRM1 KO, TP53 KO |
FANCA | 4 | LKB1 KO, NF2 KO, PBRM1 KO, VHL KO |
FANCD2 | 4 | CDH1 KO, NF2 KO, PBRM1 KO, TP53BP1 KO |
FANCF | 4 | CDH1 KO, LKB1 KO, NF2 KO, PBRM1 KO |
MCM9 | 4 | LKB1 KO, NF2 KO, VHL KO, TP53BP1 KO |
SDHB | 4 | BAP1 KO, LKB1 KO, PBRM1 KO, VHL KO |
USPL1 | 4 | BAP1 KO, NF2 KO, PTEN KO, TP53BP1 KO |
ATG9A | 3 | LKB1 KO, NF1 KO, VHL KO |
C16orf72 | 3 | ARID1A KD, BAP1 KO, NF1 KO |
COQ2 | 3 | BAP1 KO, KEAP1 KO, RB1 KO |
FAM106A | 3 | LKB1 KO, NF1 KO, PTEN KO |
FBXW11 | 3 | LKB1 KO, NF1 KO, VHL KO |
NDUFC1 | 3 | NF1 KO, PBRM1 KO, PTEN KO |
PMVK | 3 | BAP1 KO, NF1 KO, NF2 KO |
PRDX1 | 3 | NF1 KO, NF2 KO, PBRM1 KO |
PRKRA | 3 | LKB1 KO, NF1 KO, VHL KO |
SLC25A33 | 3 | LKB1 KO, VHL KO, TP53BP1 KO |
UIMC1 | 3 | CDH1 KO, KEAP1 KO, NF1 KO |
UMPS | 3 | PBRM1 KO, RB1 KO, VHL KO |
ARID2 | 2 | LKB1 KO, NF2 KO |
BIRC6 | 2 | LKB1 KO, VHL KO |
BUB1 | 2 | ARID1A KD, CDH1 KO |
BZW1 | 2 | BAP1 KO, NF2 KO |
C12orf44 | 2 | LKB1 KO, VHL KO |
C1orf228 | 2 | CDH1 KO, VHL KO |
CAB39 | 2 | TP53 KO, VHL KO |
CAPRIN1 | 2 | CDH1 KO, VHL KO |
CHMP6 | 2 | ARID1A KD, TP53BP1 KO |
CNKSR2 | 2 | NF1 KO, TP53 KO |
CNOT4 | 2 | PTEN KO, VHL KO |
CTBP2 | 2 | KEAP1 KO, RB1 KO |
DHODH | 2 | BAP1 KO, VHL KO |
DHX35 | 2 | LKB1 KO, VHL KO |
EBNA1BP2 | 2 | NF1 KO, RB1 KO |
ELMO2 | 2 | KEAP1 KO, RB1 KO |
FBXO42 | 2 | LKB1 KO, VHL KO |
G6PC | 2 | KEAP1 KO, NF1 KO |
GAK | 2 | RB1 KO, VHL KO |
GART | 2 | PBRM1 KO, RB1 KO |
GTPBP2 | 2 | LKB1 KO, VHL KO |
IGFALS | 2 | ARID1A KD, VHL KO |
IKBKG | 2 | LKB1 KO, TP53BP1 KO |
JTB | 2 | LKB1 KO, NF1 KO |
KIAA1524 | 2 | NF1 KO, VHL KO |
KPNA4 | 2 | LKB1 KO, VHL KO |
MAPKAP1 | 2 | PBRM1 KO, TP53BP1 KO |
MED13 | 2 | KEAP1 KO, RB1 KO |
MPV17 | 2 | LKB1 KO, VHL KO |
MTFMT | 2 | LKB1 KO, VHL KO |
NDUFB6 | 2 | LKB1 KO, NF1 KO |
NUP160 | 2 | ARID1A KD, PBRM1 KO |
PARD6B | 2 | PBRM1 KO, PTEN KO |
PDIA3 | 2 | PBRM1 KO, VHL KO |
PDS5A | 2 | LKB1 KO, VHL KO |
PIN1 | 2 | KEAP1 KO, RB1 KO |
PSMF1 | 2 | LKB1 KO, VHL KO |
RAD54L | 2 | PTEN KO, VHL KO |
RMI2 | 2 | CDH1 KO, TP53BP1 KO |
RRAS2 | 2 | BAP1 KO, KEAP1 KO |
SDHD | 2 | BAP1 KO, VHL KO |
SHBG | 2 | KEAP1 KO, NF1 KO |
STAC2 | 2 | KEAP1 KO, RB1 KO |
STUB1 | 2 | BAP1 KO, NF1 KO |
TADA1 | 2 | RB1 KO, TP53 KO |
TMCO6 | 2 | KEAP1 KO, PTEN KO |
DMAC1 | 2 | BAP1 KO, NF1 KO |
TOR4A | 2 | NF1 KO, VHL KO |
TUSC2 | 2 | CDH1 KO, KEAP1 KO |
UNC13D | 2 | RB1 KO, TP53 KO |
USH1G | 2 | KEAP1 KO, NF1 KO |
USP1 | 2 | PTEN KO, TP53BP1 KO |
USP48 | 2 | NF1 KO, NF2 KO |
VGLL3 | 2 | KEAP1 KO, RB1 KO |
WRAP53 | 2 | NF1 KO, TP53 KO |
YPEL5 | 2 | LKB1 KO, PBRM1 KO |
Dataset Card for PMC_35559673_table_s datasets
Dataset Details
Dataset Description
This dataset contains the results of genome-wide CRISPR screens using isogenic knockout cells to uncover vulnerabilities in tumor suppressor-deficient cancer cells. The data were originally published by Feng et al., Sci. Adv. 8, eabm6638 (2022), and are available via PubMed Central (PMC). The supplementary tables included in this dataset provide detailed data on raw counts, essentiality calls, Bayes factors, and synthetic lethality (SL) hits. The dataset supports research into genetic dependencies and potential therapeutic targets.
- Curated by: Feng et al., Sci. Adv. 8, eabm6638 (2022)
- Funded by: Likely supported by institutions affiliated with the authors.
- Shared by: Feng et al.
- Language(s): Not applicable (biomedical dataset).
- License: CC BY 4.0
Dataset Sources
- Repository: PubMed Central
- Paper: Sci. Adv. 8, eabm6638 (2022)
- Supplementary Materials: Tables S1-S7
Dataset Structure
This dataset consists of seven tables (S1-S7), each representing a different aspect of the CRISPR screen results:
Table S1: Raw counts for all CRISPR screens in this study.
- File Mapping:
sciadv.abm6638_table_s1.xlsx
- File Mapping:
Table S2: Binary essentiality calls matrix.
- File Mapping:
sciadv.abm6638_table_s2.xlsx
- File Mapping:
Table S3: Quantile-normalized Bayes factor (QBF) matrix.
- File Mapping:
sciadv.abm6638_table_s3.xlsx
- File Mapping:
Table S5: Total SL hits identified for each TSG KO screen.
- File Mapping:
sciadv.abm6638_table_s5.xlsx
- File Mapping:
Table S6: Shared SL hits across each TSG KO screen.
- File Mapping:
sciadv.abm6638_table_s6.xlsx
- File Mapping:
Table S7: Unique SL hits for each TSG KO screen.
- File Mapping:
sciadv.abm6638_table_s7.xlsx
- File Mapping:
Dataset Creation
Curation Rationale
This dataset was curated to facilitate research into the vulnerabilities of cancer cells deficient in tumor suppressor genes. The binary essentiality calls, synthetic lethality (SL) hits, and other data allow researchers to explore genetic interactions that could serve as potential therapeutic targets. The methodology behind the CRISPR screens and SL hit identification was detailed by Feng et al. in their 2022 study.
Data Collection and Processing
Data were collected from genome-wide CRISPR screens performed on isogenic knockout cells. The data were processed to produce raw counts, binary essentiality calls, and genetic interaction matrices, including shared and unique synthetic lethal hits.
Relevant references describing the data processing and methods can be found in the following sources:
- Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens (PMID: 28655737)
- High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities (PMID: 26627737)
- Identifying chemogenetic interactions from CRISPR screens with drugZ (PMID: 31439014)
Who are the source data producers?
The data were produced by Feng et al., as part of their research published in Science Advances. The researchers were affiliated with academic institutions engaged in cancer genomics and CRISPR screening methodologies.
Annotations
Annotation Process
Annotations were primarily focused on identifying shared and unique synthetic lethality hits across tumor suppressor knockout screens. Automated processing tools like CRISPR analysis pipelines were employed for initial hit identification, followed by manual validation based on genetic interactions.
Who are the annotators?
The original authors, including experts in CRISPR screening and cancer genomics, performed the annotations. No third-party annotations were added.
Bias, Risks, and Limitations
The dataset is limited to specific cancer cell lines and tumor suppressor gene knockouts. As a result, the findings may not be generalizable across all cancer types. Users should exercise caution when interpreting results outside the experimental context.
Recommendations
Users should consult the references provided to better understand the experimental design and limitations. The dataset is best suited for research applications in cancer genomics, genetic interactions, and therapeutic target discovery.
Citation
BibTeX:
@article{
doi:10.1126/sciadv.abm6638,
author = {Xu Feng and Mengfan Tang and Merve Dede and Dan Su and Guangsheng Pei and Dadi Jiang and Chao Wang and Zhen Chen and Mi Li and Litong Nie and Yun Xiong and Siting Li and Jeong-Min Park and Huimin Zhang and Min Huang and Klaudia Szymonowicz and Zhongming Zhao and Traver Hart and Junjie Chen },
title = {Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors},
journal = {Science Advances},
volume = {8},
number = {19},
pages = {eabm6638},
year = {2022},
doi = {10.1126/sciadv.abm6638},
URL = {https://www.science.org/doi/abs/10.1126/sciadv.abm6638},
eprint = {https://www.science.org/doi/pdf/10.1126/sciadv.abm6638},
abstract = {Exploiting cancer vulnerabilities is critical for the discovery of anticancer drugs. However, tumor suppressors cannot be directly targeted because of their loss of function. To uncover specific vulnerabilities for cells with deficiency in any given tumor suppressor(s), we performed genome-scale CRISPR loss-of-function screens using a panel of isogenic knockout cells we generated for 12 common tumor suppressors. Here, we provide a comprehensive and comparative dataset for genetic interactions between the whole-genome protein-coding genes and a panel of tumor suppressor genes, which allows us to uncover known and new high-confidence synthetic lethal interactions. Mining this dataset, we uncover essential paralog gene pairs, which could be a common mechanism for interpreting synthetic lethality. Moreover, we propose that some tumor suppressors could be targeted to suppress proliferation of cells with deficiency in other tumor suppressors. This dataset provides valuable information that can be further exploited for targeted cancer therapy. Whole-genome CRISPR screens uncover synthetic lethal interactions for tumor suppressors.}
}
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