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
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.
In all seriousness,use CiteAb and Antibodypedia, look for KO/KD validated antibodies, best - recombinant, second best - monoclonal, and if possible do your own KO/KD controls, or induction by ligand/small molecule,if not - compare hyperexpressing with low expressing cells (from depmap/protein atlas)
December 26, 2024 at 6:31 AM
In all seriousness,use CiteAb and Antibodypedia, look for KO/KD validated antibodies, best - recombinant, second best - monoclonal, and if possible do your own KO/KD controls, or induction by ligand/small molecule,if not - compare hyperexpressing with low expressing cells (from depmap/protein atlas)
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/#/
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
If you work on cancer, DepMap is a great resource to mine depmap.org/portal/home/#/
September 23, 2025 at 1:45 PM
If you work on cancer, DepMap is a great resource to mine depmap.org/portal/home/#/
Proud to announce that the 2nd European Cancer DepMap Symposium has the patronage of AIRC: the Italian Association for Cancer Research. Honoured by their support as we bring together leading scientists on cancer-dependencies functional-genomics CRISPR
🔗 humantechnopole.it/en/trainings...
#EuroDepMap
🔗 humantechnopole.it/en/trainings...
#EuroDepMap
June 19, 2025 at 11:40 AM
Proud to announce that the 2nd European Cancer DepMap Symposium has the patronage of AIRC: the Italian Association for Cancer Research. Honoured by their support as we bring together leading scientists on cancer-dependencies functional-genomics CRISPR
🔗 humantechnopole.it/en/trainings...
#EuroDepMap
🔗 humantechnopole.it/en/trainings...
#EuroDepMap
🧬 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
Our January issue is LIVE! Perfect Xmas reading! 🎁🎅It features articles on:
- Epigenomic heterogeneity as a source of #tumour evolution
- CSCs and immune evasion
- Convergent inducers & effectors of T cell paralysis in the TME
- The #Cancer DepMap
go.nature.com/41P09Nk
- Epigenomic heterogeneity as a source of #tumour evolution
- CSCs and immune evasion
- Convergent inducers & effectors of T cell paralysis in the TME
- The #Cancer DepMap
go.nature.com/41P09Nk
December 23, 2024 at 11:54 AM
Our January issue is LIVE! Perfect Xmas reading! 🎁🎅It features articles on:
- Epigenomic heterogeneity as a source of #tumour evolution
- CSCs and immune evasion
- Convergent inducers & effectors of T cell paralysis in the TME
- The #Cancer DepMap
go.nature.com/41P09Nk
- Epigenomic heterogeneity as a source of #tumour evolution
- CSCs and immune evasion
- Convergent inducers & effectors of T cell paralysis in the TME
- The #Cancer DepMap
go.nature.com/41P09Nk
Thrilled to share our first dive into generative models, integrating 7 distinct omics to generate a complete Synthetic Cancer Dependency Map for +1,500 cancer cell lines! Excited for what’s ahead. rdcu.be/d1TgQ #GarnettLab #CMRI #ProCan #INESC-ID #IST @naturecomms.bsky.social
Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning
Nature Communications - Multi-omics integration is often limited by data sparsity and heterogeneity. Here, the authors develop MOSA, a method designed to augment DepMap cell line data to...
rdcu.be
November 29, 2024 at 2:53 PM
Thrilled to share our first dive into generative models, integrating 7 distinct omics to generate a complete Synthetic Cancer Dependency Map for +1,500 cancer cell lines! Excited for what’s ahead. rdcu.be/d1TgQ #GarnettLab #CMRI #ProCan #INESC-ID #IST @naturecomms.bsky.social
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-HBS1L
Congratulations to the DepMap team! @vazquezf.bsky.social
#depmap #cancertarget #syntheticlethal
Frequent passenger mutations in genes involved in mRNA quality control lead to a dependency on PELO-HBS1L
Congratulations to the DepMap team! @vazquezf.bsky.social
#depmap #cancertarget #syntheticlethal
SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO - Nature
Analysis of large-scale CRISPR screening data, combined with experiments in patient-derived tumour organoid models, identifies PELO as a potential therapeutic target in chromosomal 9p21.3-deleted canc...
www.nature.com
February 5, 2025 at 10:01 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-HBS1L
Congratulations to the DepMap team! @vazquezf.bsky.social
#depmap #cancertarget #syntheticlethal
Frequent passenger mutations in genes involved in mRNA quality control lead to a dependency on PELO-HBS1L
Congratulations to the DepMap team! @vazquezf.bsky.social
#depmap #cancertarget #syntheticlethal
#PERSPECTIVE 🚨
Hahn, Vazquez & colleagues outline the current limitations and future strategies for enhancing the Cancer Dependency Map project.
👇 📖
https://bit.ly/42rDh...
Hahn, Vazquez & colleagues outline the current limitations and future strategies for enhancing the Cancer Dependency Map project.
👇 📖
https://bit.ly/42rDh...
The present and future of the Cancer Dependency Map - Nature Reviews Cancer
The Cancer Dependency Map (DepMap) is a data repository and research platform that can be utilized to systematically identify cancer vulnerabilities. Here Arafeh, Shibue et al. outline the current limitations and future strategies to enhance the DepMap project.
bit.ly
January 30, 2025 at 3:02 PM
#PERSPECTIVE 🚨
Hahn, Vazquez & colleagues outline the current limitations and future strategies for enhancing the Cancer Dependency Map project.
👇 📖
https://bit.ly/42rDh...
Hahn, Vazquez & colleagues outline the current limitations and future strategies for enhancing the Cancer Dependency Map project.
👇 📖
https://bit.ly/42rDh...
Thanks to @researchireland.ie for funding, and to the DepMap teams @broadinstitute.org and @sangerinstitute.bsky.social for generating the data that our approach depends on 9/9
January 29, 2026 at 9:29 AM
Thanks to @researchireland.ie for funding, and to the DepMap teams @broadinstitute.org and @sangerinstitute.bsky.social for generating the data that our approach depends on 9/9
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!
KF: 41% of highest-ranking cancer dependencies are transcxription factors in DepMap data #AACRprecmed25
Analyses of Genes Critical to Tumor Survival Reveal Potential ‘Supertargets’: Focus on Transcription
The identification of mechanisms that underlie the biology of individual tumors is aimed at the development of personalized treatment strategies. Herein, we performed a comprehensive search of genes (termed Supertargets) vital for tumors of particular tissue origin. In so doing, we used the DepMap database portal that encompasses a broad panel of cell lines with individual genes knocked out by CRISPR/Cas9 technology. For each of the 27 tumor types, we revealed the top five genes whose deletion was lethal in the particular case, indicating both known and unknown Supertargets. Most importantly, the majority of Supertargets (41%) were represented by DNA-binding transcription factors. RNAseq data analysis demonstrated that a subset of Supertargets was deregulated in clinical tumor samples but not in the respective non-malignant tissues. These results point to transcriptional mechanisms as key regulators of cell survival in specific tumors. Targeted inactivation of these factors emerges as a straightforward approach to optimize therapeutic regimens.
www.mdpi.com
March 11, 2025 at 9:45 PM
KF: 41% of highest-ranking cancer dependencies are transcxription factors in DepMap data #AACRprecmed25
If you work on cancer, DepMap is a great resource to mine depmap.org/portal/home/#/
August 7, 2026 at 2:15 PM
If you work on cancer, DepMap is a great resource to mine depmap.org/portal/home/#/
For #genomics #datasets, I often use these 4 portals:
🧬TCGA - www.cancer.gov/ccg/research...
🧬DepMap - depmap.org/portal/
🧬1000 Genomes - www.internationalgenome.org
🧬recount3 - rna.recount.bio
Are there better resources you use for genomics datasets? What am I missing?
🧬TCGA - www.cancer.gov/ccg/research...
🧬DepMap - depmap.org/portal/
🧬1000 Genomes - www.internationalgenome.org
🧬recount3 - rna.recount.bio
Are there better resources you use for genomics datasets? What am I missing?
September 24, 2026 at 2:43 PM
For #genomics #datasets, I often use these 4 portals:
🧬TCGA - www.cancer.gov/ccg/research...
🧬DepMap - depmap.org/portal/
🧬1000 Genomes - www.internationalgenome.org
🧬recount3 - rna.recount.bio
Are there better resources you use for genomics datasets? What am I missing?
🧬TCGA - www.cancer.gov/ccg/research...
🧬DepMap - depmap.org/portal/
🧬1000 Genomes - www.internationalgenome.org
🧬recount3 - rna.recount.bio
Are there better resources you use for genomics datasets? What am I missing?
The Cancer Dependency Map advances cancer therapy by identifying vulnerabilities across diverse cancer models, despite its current limitations.
by Arafeh R, Shibue T (...) Vazquez F et 2 al. in Nat Rev Cancer #MedSky
📖 read the article:
by Arafeh R, Shibue T (...) Vazquez F et 2 al. in Nat Rev Cancer #MedSky
📖 read the article:
The present and future of the Cancer Dependency Map - Nature Reviews Cancer
The Cancer Dependency Map (DepMap) is a data repository and research platform that can be utilized to systematically identify cancer vulnerabilities. Here Arafeh, Shibue et al. outline the current limitations and future strategies to enhance the DepMap project.
www.nature.com
January 10, 2025 at 2:31 PM
The Cancer Dependency Map advances cancer therapy by identifying vulnerabilities across diverse cancer models, despite its current limitations.
by Arafeh R, Shibue T (...) Vazquez F et 2 al. in Nat Rev Cancer #MedSky
📖 read the article:
by Arafeh R, Shibue T (...) Vazquez F et 2 al. in Nat Rev Cancer #MedSky
📖 read the article:
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
(1/3) Excited to share our latest work using
@depmap.org to uncover a new synthetic lethality in two distinct patient populations!
We found that SKI complex inactivation through two independent genomic alterations creates a dependency on PELO
#CancerResearch #SyntheticLethality #Genomics #DepMap
@depmap.org to uncover a new synthetic lethality in two distinct patient populations!
We found that SKI complex inactivation through two independent genomic alterations creates a dependency on PELO
#CancerResearch #SyntheticLethality #Genomics #DepMap
SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO - Nature
Analysis of large-scale CRISPR screening data, combined with experiments in patient-derived tumour organoid models, identifies PELO as a potential therapeutic target in chromosomal 9p21.3-deleted canc...
nature.com
February 6, 2025 at 1:07 PM
(1/3) Excited to share our latest work using
@depmap.org to uncover a new synthetic lethality in two distinct patient populations!
We found that SKI complex inactivation through two independent genomic alterations creates a dependency on PELO
#CancerResearch #SyntheticLethality #Genomics #DepMap
@depmap.org to uncover a new synthetic lethality in two distinct patient populations!
We found that SKI complex inactivation through two independent genomic alterations creates a dependency on PELO
#CancerResearch #SyntheticLethality #Genomics #DepMap
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
Test the genes as a result of your Claude prompt in >550,000 bulk samples with ease in R2: the open online data science platform for biomedical research r2platform.com
R2 provides instant access to nearly 3,000 public resources including #TCGA, #GTeX, #DepMap, #TARGET, RNA atlas, etc.
R2 provides instant access to nearly 3,000 public resources including #TCGA, #GTeX, #DepMap, #TARGET, RNA atlas, etc.
April 3, 2026 at 6:13 AM
Test the genes as a result of your Claude prompt in >550,000 bulk samples with ease in R2: the open online data science platform for biomedical research r2platform.com
R2 provides instant access to nearly 3,000 public resources including #TCGA, #GTeX, #DepMap, #TARGET, RNA atlas, etc.
R2 provides instant access to nearly 3,000 public resources including #TCGA, #GTeX, #DepMap, #TARGET, RNA atlas, etc.
Tell your stories in data.
R2: The open online data science platform for biomedical researchers. No coding skills required
Secure your FREE account Today at r2platform.com
2,750 open access resources (e.g. TCGA,DepMap,GTeX,etc)
2,975 pubmed citations
#genomics #datascience #nocode #storytelling
R2: The open online data science platform for biomedical researchers. No coding skills required
Secure your FREE account Today at r2platform.com
2,750 open access resources (e.g. TCGA,DepMap,GTeX,etc)
2,975 pubmed citations
#genomics #datascience #nocode #storytelling
July 19, 2025 at 12:28 PM
Tell your stories in data.
R2: The open online data science platform for biomedical researchers. No coding skills required
Secure your FREE account Today at r2platform.com
2,750 open access resources (e.g. TCGA,DepMap,GTeX,etc)
2,975 pubmed citations
#genomics #datascience #nocode #storytelling
R2: The open online data science platform for biomedical researchers. No coding skills required
Secure your FREE account Today at r2platform.com
2,750 open access resources (e.g. TCGA,DepMap,GTeX,etc)
2,975 pubmed citations
#genomics #datascience #nocode #storytelling
𝗧𝘄𝗼 𝗶𝗻𝗱𝗲𝗽𝗲𝗻𝗱𝗲𝗻𝘁 analyses, 𝗼𝗻𝗲 𝗰𝗼𝗻𝘃𝗲𝗿𝗴𝗶𝗻𝗴 𝘀𝘁𝗼𝗿𝘆: here is 𝗈𝗎𝗋 𝗇𝖾𝗐 𝗌𝗍𝗎𝖽𝗒, 𝗋𝖾𝗅𝖾𝖺𝗌𝖾𝖽 𝖺𝗅𝗈𝗇𝗀𝗌𝗂𝖽𝖾 𝖺𝗇 𝗂𝗇𝖽𝖾𝗉𝖾𝗇𝖽𝖾𝗇𝗍 𝗐𝗈𝗋𝗄 𝖿𝗋𝗈𝗆 𝗍𝗁𝖾 𝗖𝗶𝗿𝗶𝗲𝗹𝗹𝗼 𝗴𝗿𝗼𝘂𝗽 (𝗦𝗲𝘀𝗶𝗮 𝗲𝘁 𝗮𝗹.), 𝗐𝗁𝖾𝗋𝖾 𝖢𝖱𝖨𝖲𝖯𝖱 𝖽𝖾𝗉𝖾𝗇𝖽𝖾𝗇𝖼𝗒 𝗆𝖺𝗉𝗌 𝖺𝗋𝖾 𝗎𝗌𝖾𝖽 𝗍𝗈 𝗍𝖺𝖼𝗄𝗅𝖾 𝗍𝗁𝖾 𝗌𝖺𝗆𝖾 𝖼𝗁𝖺𝗅𝗅𝖾𝗇𝗀𝖾: 𝗆𝖺𝗄𝗂𝗇𝗀 𝗌𝖾𝗇𝗌𝖾 𝗈𝖿 𝖼𝖺𝗇𝖼𝖾𝗋 𝘷𝘢𝘳𝘪𝘢𝘯𝘵𝘴 𝘰𝘧 𝘶𝘯𝘬𝘯𝘰𝘸𝘯 𝘴𝘪𝘨𝘯𝘪𝘧𝘪𝘤𝘢𝘯𝘤𝘦 using DepMap data. Links 👇
January 26, 2026 at 5:22 PM
𝗧𝘄𝗼 𝗶𝗻𝗱𝗲𝗽𝗲𝗻𝗱𝗲𝗻𝘁 analyses, 𝗼𝗻𝗲 𝗰𝗼𝗻𝘃𝗲𝗿𝗴𝗶𝗻𝗴 𝘀𝘁𝗼𝗿𝘆: here is 𝗈𝗎𝗋 𝗇𝖾𝗐 𝗌𝗍𝗎𝖽𝗒, 𝗋𝖾𝗅𝖾𝖺𝗌𝖾𝖽 𝖺𝗅𝗈𝗇𝗀𝗌𝗂𝖽𝖾 𝖺𝗇 𝗂𝗇𝖽𝖾𝗉𝖾𝗇𝖽𝖾𝗇𝗍 𝗐𝗈𝗋𝗄 𝖿𝗋𝗈𝗆 𝗍𝗁𝖾 𝗖𝗶𝗿𝗶𝗲𝗹𝗹𝗼 𝗴𝗿𝗼𝘂𝗽 (𝗦𝗲𝘀𝗶𝗮 𝗲𝘁 𝗮𝗹.), 𝗐𝗁𝖾𝗋𝖾 𝖢𝖱𝖨𝖲𝖯𝖱 𝖽𝖾𝗉𝖾𝗇𝖽𝖾𝗇𝖼𝗒 𝗆𝖺𝗉𝗌 𝖺𝗋𝖾 𝗎𝗌𝖾𝖽 𝗍𝗈 𝗍𝖺𝖼𝗄𝗅𝖾 𝗍𝗁𝖾 𝗌𝖺𝗆𝖾 𝖼𝗁𝖺𝗅𝗅𝖾𝗇𝗀𝖾: 𝗆𝖺𝗄𝗂𝗇𝗀 𝗌𝖾𝗇𝗌𝖾 𝗈𝖿 𝖼𝖺𝗇𝖼𝖾𝗋 𝘷𝘢𝘳𝘪𝘢𝘯𝘵𝘴 𝘰𝘧 𝘶𝘯𝘬𝘯𝘰𝘸𝘯 𝘴𝘪𝘨𝘯𝘪𝘧𝘪𝘤𝘢𝘯𝘤𝘦 using DepMap data. Links 👇
DepMap keeps growing—and so does the portal!
To help navigate the portal, new in 24Q4 we’ve launched a new resource page 🚀! Check it out and share your feedback.
To help navigate the portal, new in 24Q4 we’ve launched a new resource page 🚀! Check it out and share your feedback.
Depmap Resources | Depmap Portal
depmap.org
December 20, 2024 at 8:03 AM
DepMap keeps growing—and so does the portal!
To help navigate the portal, new in 24Q4 we’ve launched a new resource page 🚀! Check it out and share your feedback.
To help navigate the portal, new in 24Q4 we’ve launched a new resource page 🚀! Check it out and share your feedback.