The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data!
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
September 20, 2025 at 7:43 AM
The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data!
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.
Start mining data now: dataminer.depmap.sanger.ac.uk
Latest version of #depmap added to r2platform.com
R2: academic open online nocode data science platform for biomedical research
#DataScientist #biologist #clinician #genomics #Cancer
R2: academic open online nocode data science platform for biomedical research
#DataScientist #biologist #clinician #genomics #Cancer
October 18, 2025 at 7:14 PM
Latest version of #depmap added to r2platform.com
R2: academic open online nocode data science platform for biomedical research
#DataScientist #biologist #clinician #genomics #Cancer
R2: academic open online nocode data science platform for biomedical research
#DataScientist #biologist #clinician #genomics #Cancer
🧬Integration with DepMap highlighted the pivotal role of epigenetic regulation and splicing pathways in shaping cellular responses to pro-rejuvenating signals, and of mitochondrial translation and type I interferon in responses to pro-aging signals. #RegenerativeMedicine
June 5, 2025 at 10:03 AM
🧬Integration with DepMap highlighted the pivotal role of epigenetic regulation and splicing pathways in shaping cellular responses to pro-rejuvenating signals, and of mitochondrial translation and type I interferon in responses to pro-aging signals. #RegenerativeMedicine
2/5. We further found that housekeeping genes (involved in ribosomes, transport, and metabolism) show a common decrease in expression across both neurons and glia. Conversely, neuron-specific gene expression generally remains stable throughout life.
September 3, 2025 at 5:46 PM
2/5. We further found that housekeeping genes (involved in ribosomes, transport, and metabolism) show a common decrease in expression across both neurons and glia. Conversely, neuron-specific gene expression generally remains stable throughout life.
Multiple convergent lines of evidence led us to PHIP as a functional partner for PHF6:
1) Highest co-dependency score in DepMap.
2) Rare germline mutations in both produce overlapping neurodevelopmental disorders.
3) PHIP was recently reported to be mutated in AML (Stiff et al, Nat Gen 2024). (6/n)
1) Highest co-dependency score in DepMap.
2) Rare germline mutations in both produce overlapping neurodevelopmental disorders.
3) PHIP was recently reported to be mutated in AML (Stiff et al, Nat Gen 2024). (6/n)
December 4, 2024 at 5:55 PM
Multiple convergent lines of evidence led us to PHIP as a functional partner for PHF6:
1) Highest co-dependency score in DepMap.
2) Rare germline mutations in both produce overlapping neurodevelopmental disorders.
3) PHIP was recently reported to be mutated in AML (Stiff et al, Nat Gen 2024). (6/n)
1) Highest co-dependency score in DepMap.
2) Rare germline mutations in both produce overlapping neurodevelopmental disorders.
3) PHIP was recently reported to be mutated in AML (Stiff et al, Nat Gen 2024). (6/n)
Exciting new synthetic lethal target emerging from #depmap data 🧪🧬
Frequent passenger mutations in genes involved in mRNA quality control lead to a dependency on PELO
#depmap #cancertarget #syntheticlethal
Frequent passenger mutations in genes involved in mRNA quality control lead to a dependency on PELO
#depmap #cancertarget #syntheticlethal
Scientists have discovered a genetic vulnerability — found in 5 percent of adult cancers — that could be a promising drug target.
@nature.com #Science #Cancer @vazquezf.bsky.social
@nature.com #Science #Cancer @vazquezf.bsky.social
Mutations in two gene pairs point to a promising drug target in 5 percent of adult cancers
Targeting the PELO gene could be a way to kill tumor cells in cancers with one of two common genetic mutations.
www.broadinstitute.org
February 5, 2025 at 9:56 PM
Exciting new synthetic lethal target emerging from #depmap data 🧪🧬
Frequent passenger mutations in genes involved in mRNA quality control lead to a dependency on PELO
#depmap #cancertarget #syntheticlethal
Frequent passenger mutations in genes involved in mRNA quality control lead to a dependency on PELO
#depmap #cancertarget #syntheticlethal
We’re kicking off the first DepMap post with a bang!
⭐ 35 CRISPR screens
⭐ NEW data from our Pediatric Dependencies Accelerator Program (learn more at PedDep.org)
⭐ First 281 WES -> WGS
⭐ New Resources page
📣 DepMap is now on dbGaP (phs003444.v1.p1)
Read our release notes for more info!
⭐ 35 CRISPR screens
⭐ NEW data from our Pediatric Dependencies Accelerator Program (learn more at PedDep.org)
⭐ First 281 WES -> WGS
⭐ New Resources page
📣 DepMap is now on dbGaP (phs003444.v1.p1)
Read our release notes for more info!
December 18, 2024 at 7:07 PM
We’re kicking off the first DepMap post with a bang!
⭐ 35 CRISPR screens
⭐ NEW data from our Pediatric Dependencies Accelerator Program (learn more at PedDep.org)
⭐ First 281 WES -> WGS
⭐ New Resources page
📣 DepMap is now on dbGaP (phs003444.v1.p1)
Read our release notes for more info!
⭐ 35 CRISPR screens
⭐ NEW data from our Pediatric Dependencies Accelerator Program (learn more at PedDep.org)
⭐ First 281 WES -> WGS
⭐ New Resources page
📣 DepMap is now on dbGaP (phs003444.v1.p1)
Read our release notes for more info!
If you work on cancer, DepMap is a great resource to mine depmap.org/portal/home/#/
May 26, 2025 at 1:45 PM
If you work on cancer, DepMap is a great resource to mine depmap.org/portal/home/#/
🧬 Excited to announce the 2nd Euro Cancer DepMap Symposium bringing together leading minds in functional genomics, cancer vulnerabilities, AI, CRISPR and anti-cancer target discovery.📍Join us in Milan for cutting-edge science, open discussion & collaboration. #EuroDepMap #CancerResearch #CRISPR
June 11, 2025 at 3:00 PM
🧬 Excited to announce the 2nd Euro Cancer DepMap Symposium bringing together leading minds in functional genomics, cancer vulnerabilities, AI, CRISPR and anti-cancer target discovery.📍Join us in Milan for cutting-edge science, open discussion & collaboration. #EuroDepMap #CancerResearch #CRISPR
Explore the latest #DepMap resource in a data-driven UMAP embedding in the R2 open online #genomics #data #science platform ( r2.amc.nl )
The R2 'sample maps' section contains embeddings for hundreds of different public resources, like #UMAP, t-SNE, and manuscript figure data, ready for exploration
The R2 'sample maps' section contains embeddings for hundreds of different public resources, like #UMAP, t-SNE, and manuscript figure data, ready for exploration
May 2, 2025 at 1:37 PM
Our top hits were GGNBP2, CNOT10 and CNOT11. The three proteins interact and are top co-dependencies in Depmap suggesting a functional link across cell types.
Incredibly, KO of GGNBP2 rescues editing-deficient cells even better than KO of MDA5, and completely blocked induction of ISGs by qPCR! 6/X
Incredibly, KO of GGNBP2 rescues editing-deficient cells even better than KO of MDA5, and completely blocked induction of ISGs by qPCR! 6/X
December 6, 2024 at 1:31 AM
Our top hits were GGNBP2, CNOT10 and CNOT11. The three proteins interact and are top co-dependencies in Depmap suggesting a functional link across cell types.
Incredibly, KO of GGNBP2 rescues editing-deficient cells even better than KO of MDA5, and completely blocked induction of ISGs by qPCR! 6/X
Incredibly, KO of GGNBP2 rescues editing-deficient cells even better than KO of MDA5, and completely blocked induction of ISGs by qPCR! 6/X
🧬 Excited to announce the 2nd Euro Cancer DepMap Symposium bringing together leading minds in functional genomics, cancer vulnerabilities, AI, CRISPR and anti-cancer target discovery.📍Join us in Milan for cutting-edge science, open discussion & collaboration. #EuroDepMap #CancerResearch #CRISPR
🔬 Join us in Milan for the 2nd European Cancer Dependency Map Symposium #ECDM25! A key event for scientists in functional genomics & target discovery. Talks, panels, AI & poster sessions await.
Register now 👉 humantechnopole.it/en/trainings...
Register now 👉 humantechnopole.it/en/trainings...
June 11, 2025 at 3:02 PM
🧬 Excited to announce the 2nd Euro Cancer DepMap Symposium bringing together leading minds in functional genomics, cancer vulnerabilities, AI, CRISPR and anti-cancer target discovery.📍Join us in Milan for cutting-edge science, open discussion & collaboration. #EuroDepMap #CancerResearch #CRISPR
DepMap Miner features:
· Tailor model data selections
· Explore relationships between 'omics' data
· customisable plots
· Visualise gene dependencies across 900+ cell lines
· Export data easily to continue exploring
Discover more: dataminer.depmap.sanger.ac.uk
· Tailor model data selections
· Explore relationships between 'omics' data
· customisable plots
· Visualise gene dependencies across 900+ cell lines
· Export data easily to continue exploring
Discover more: dataminer.depmap.sanger.ac.uk
September 20, 2025 at 7:43 AM
DepMap Miner features:
· Tailor model data selections
· Explore relationships between 'omics' data
· customisable plots
· Visualise gene dependencies across 900+ cell lines
· Export data easily to continue exploring
Discover more: dataminer.depmap.sanger.ac.uk
· Tailor model data selections
· Explore relationships between 'omics' data
· customisable plots
· Visualise gene dependencies across 900+ cell lines
· Export data easily to continue exploring
Discover more: dataminer.depmap.sanger.ac.uk
Prior CRISPR screens have focused on EITHER regulatory elements OR protein-coding genes.
And these have been wonderfully successful: e.g. Cancer DepMap in 1,000+ human cell lines for protein-coding genes, or the sickle-cell cure CASGEVY discovered in a noncoding CRISPR screen.
And these have been wonderfully successful: e.g. Cancer DepMap in 1,000+ human cell lines for protein-coding genes, or the sickle-cell cure CASGEVY discovered in a noncoding CRISPR screen.
December 26, 2024 at 3:01 AM
Prior CRISPR screens have focused on EITHER regulatory elements OR protein-coding genes.
And these have been wonderfully successful: e.g. Cancer DepMap in 1,000+ human cell lines for protein-coding genes, or the sickle-cell cure CASGEVY discovered in a noncoding CRISPR screen.
And these have been wonderfully successful: e.g. Cancer DepMap in 1,000+ human cell lines for protein-coding genes, or the sickle-cell cure CASGEVY discovered in a noncoding CRISPR screen.
2️⃣ We analyzed DepMap pooled genome-wide CRISPRCas9 screens and identified complex genetic interactions specific to chr4p deletion in basal breast cancer cell models.
October 17, 2025 at 5:57 PM
2️⃣ We analyzed DepMap pooled genome-wide CRISPRCas9 screens and identified complex genetic interactions specific to chr4p deletion in basal breast cancer cell models.
The R2 platform : Democratizing bioinformatics through an easily accessible public online software platform for non-experts in the field of Genomics
r2.amc.nl
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
r2.amc.nl
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
November 1, 2025 at 10:42 PM
The R2 platform : Democratizing bioinformatics through an easily accessible public online software platform for non-experts in the field of Genomics
r2.amc.nl
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
r2.amc.nl
#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap
Our goal here was to begin to establish something like the Cancer DepMap — which looks at how loss of protein-coding genes impacts growth in >1,000 cell lines — but for noncoding regions. 📕📗📘📙
depmap.org/portal/
depmap.org/portal/
DepMap: The Cancer Dependency Map Project at Broad Institute
depmap.org
March 3, 2025 at 2:40 AM
Our goal here was to begin to establish something like the Cancer DepMap — which looks at how loss of protein-coding genes impacts growth in >1,000 cell lines — but for noncoding regions. 📕📗📘📙
depmap.org/portal/
depmap.org/portal/
BAF chromatin remodeler subunit BRG1 (SMARCA4) is another AMKL-specific DepMap vulnerability--Remarkably, BRG1 sits right at the CBF promoter, is enriched in MEPs, and a BRG/BRM inhibitor kills AMKL cell lines and increases survival in mice w/AMKL xenografts. 5/6
September 6, 2023 at 6:13 PM
BAF chromatin remodeler subunit BRG1 (SMARCA4) is another AMKL-specific DepMap vulnerability--Remarkably, BRG1 sits right at the CBF promoter, is enriched in MEPs, and a BRG/BRM inhibitor kills AMKL cell lines and increases survival in mice w/AMKL xenografts. 5/6
To prioritize targets, we cross-evaluated our siRNA screening results with the CRISPR loss-of-function screen dataset from the Cancer Dependency Map Project (@Depmap ou @BroadInstitute) and confirmed 9 targetable core vulnerabilities.
5/n
5/n
August 31, 2023 at 6:53 PM
To prioritize targets, we cross-evaluated our siRNA screening results with the CRISPR loss-of-function screen dataset from the Cancer Dependency Map Project (@Depmap ou @BroadInstitute) and confirmed 9 targetable core vulnerabilities.
5/n
5/n
Seamlessly explore >2600 public data resources (incl. TCGA, DepMap, GTEx)
Delve deeper into your #research questions with a few clicks that enable inter-connected follow-up analyses & visualizations. No bioinformatics/programming skills required ( #nocode)
Secure your free account Today r2.amc.nl
Delve deeper into your #research questions with a few clicks that enable inter-connected follow-up analyses & visualizations. No bioinformatics/programming skills required ( #nocode)
Secure your free account Today r2.amc.nl
March 8, 2025 at 6:59 PM
I'm considering writing a machine learning book that covers conventional models like PCA, clustering, linear regression, random forests, XGBoost, and SVM. The book will use real-world biological data from sources such as TCGA and DepMap.
May 18, 2025 at 2:53 PM
I'm considering writing a machine learning book that covers conventional models like PCA, clustering, linear regression, random forests, XGBoost, and SVM. The book will use real-world biological data from sources such as TCGA and DepMap.
Here's the library comparison figure. A very efficient way to screen the genome and not miss important paralogs – for example, if one looks at DepMap would not learn that MAPK signaling is important in cancer, due to paralog buffering of ERK1 with ERK2 and MEK1 with MEK2.
September 6, 2023 at 10:42 AM
Here's the library comparison figure. A very efficient way to screen the genome and not miss important paralogs – for example, if one looks at DepMap would not learn that MAPK signaling is important in cancer, due to paralog buffering of ERK1 with ERK2 and MEK1 with MEK2.
3. depmap portal depmap.org/portal/inte... Cancer Cell Line Encyclopedia
May 29, 2025 at 1:45 PM
3. depmap portal depmap.org/portal/inte... Cancer Cell Line Encyclopedia
Another example: Werner helicase (WRN) for MSI colorectal cancer.
One (of several) papers that used DepMap info to find the synthetic lethal context: www.nature.com/articles/s41...
Novartis drug trial currently enrolling to test a WRNi: clinicaltrials.gov/study/NCT058...
One (of several) papers that used DepMap info to find the synthetic lethal context: www.nature.com/articles/s41...
Novartis drug trial currently enrolling to test a WRNi: clinicaltrials.gov/study/NCT058...
WRN helicase is a synthetic lethal target in microsatellite unstable cancers - Nature
Depletion of the DNA helicase WRN induced double-stranded DNA breaks, and promoted apoptosis and cell cycle arrest selectively in cancers with microsatellite instability, indicating that WRN is a prom...
www.nature.com
February 15, 2025 at 4:09 PM
Another example: Werner helicase (WRN) for MSI colorectal cancer.
One (of several) papers that used DepMap info to find the synthetic lethal context: www.nature.com/articles/s41...
Novartis drug trial currently enrolling to test a WRNi: clinicaltrials.gov/study/NCT058...
One (of several) papers that used DepMap info to find the synthetic lethal context: www.nature.com/articles/s41...
Novartis drug trial currently enrolling to test a WRNi: clinicaltrials.gov/study/NCT058...
I respectfully disagree. An open database is an open database. It's an invaluable tool for anyone in the community regardless of the fact if they can pay 600 or not. It can be integrated with existing databases, like depmap does for cancer cells.
November 21, 2024 at 6:13 AM
I respectfully disagree. An open database is an open database. It's an invaluable tool for anyone in the community regardless of the fact if they can pay 600 or not. It can be integrated with existing databases, like depmap does for cancer cells.