UBC

ubiquitin C

Dependent Cell Lines

CRISPR: 750/769 COMMON ESSENTIAL

RNAi: 368/711 STRONGLY SELECTIVE

Gene Effect


Dependent Cell Line: A cell line is considered dependent if it has a probability of dependency greater than 0.5.
Probability of Dependency: Probabilities of dependency are calculated for each gene score in a cell line as the probability that score arises from the distribution of essential gene scores rather than nonessential gene scores. See here for details.
Gene Effect: Outcome from DEMETER2 or CERES. A lower score means that a gene is more likely to be dependent in a given cell line. A score of 0 is equivalent to a gene that is not essential whereas a score of -1 corresponds to the median of all common essential genes.
Strongly Selective: A gene whose dependency is at least 100 times more likely to have been sampled from a skewed distribution than a normal distribution (i.e. skewed-LRT value > 100).
Common Essential: A gene which, in a large, pan-cancer screen, ranks in the top X most depleting genes in at least 90% of cell lines. X is chosen empirically using the minimum of the distribution of gene ranks in their 90th percentile least depleting lines.


Enriched Lineages

CRISPR

Gene Effect (CERES)

1. Melanoma (3.1e-07) n=47
2. Skin (6.9e-07) n=54

RNAi

Gene Effect (DEMETER2)

1. MSI (2.7e-06) n=16
2. High Grade Serous (1.2e-05) n=15
3. Colorectal Adenocarcinoma (7.5e-05) n=44
4. B-cell (7.9e-05) n=8
5. Colorectal (9.4e-05) n=46
6. Astrocytoma (1.1e-04) n=11


Enriched lineages have p-values < 0.0005 (shown in parentheses). n= indicates the number of cell lines plotted in that lineage.


Expression & CN

Expression


Copy Number log2(relative to ploidy + 1)


Expression: RNASeq files are aligned with STAR and quantified with RSEM, then TPM-normalized. Reported values are log2(TPM+1).

Copy number: The relative copy number pipeline used varies by cell line. For around 1000 lines, Sanger WES data was used, while for around 700 lines, Broad WES data was used. The remaining lines use SNP array data as explained in 10.1038/s41586-019-1186-3. See 10.1101/720243 for details on how CN source is chosen per line. Lines with WES data were processed through GATK using PONs from TCGA without matched normals and transformed by log2(x+1).



Top Co-dependencies

CRISPR (Avana) Public 20Q2

GenePearson correlation
PlotHNRNPK0.31
PlotSF10.27
PlotSNRPG0.27
PlotUSP140.27
PlotHCFC1R10.26

Combined RNAi (Broad, Novartis, Marcotte)

GenePearson correlation
PlotPOLR2A0.38
PlotARMH40.32
PlotARMH40.32
PlotSH3D190.28
PlotSH3D190.28

Target Tractability



Mutations

# of cell lines



Description

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Mutation Public 20Q2

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Fusion 20Q2

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Methylation (1kb upstream TSS) (12 125399587-125400587)

CpG Methylation

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  • Official symbol: UBC
  • Full name: ubiquitin C
  • Location:
  • Also known as:
  • Entrez ID: 7316
  • Ensembl ID: ENSG00000150991

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