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A Molecular Taxonomy of Urothelial Carcinoma
- Authors
- Sjödahl, GottfridLauss, MartinLindgren, DavidHöglund, Mattias
- Description
Gene expression profiles from 308 UC used to define seven molecular subtypes using step-by-step partitions and a bootstrap approach. Total RNA from fresh-frozen resection samples of 308 urothelial carcinomas was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip arrays (Illumina Inc) at the SCIBLU Genomics Centre at Lund University Sweden.
- Subject
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Gene Expression ProfilingUrinary Bladder Neoplasms
- Access Rights
- Free to All
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Acral Melanoma (TGEN, Genome Res 2017): Whole exome sequencing and transcriptome analysis of 34 Acral Melanoma patients (33 with matched normals)
- Authors
- Liang, Winnie S.Hendricks, WilliamKiefer, JeffreySchmidt, Jessica22 more author(s)...
- Description
This dataset contains summary data visualizations and clinical data from a comprehensive genomic and transcriptomic analysis of 34 acral lentiginous melanomas (ALM). The study was conducted to analyze ALM, a rare sun-shielded melanoma subtype of cutaneous melanoma (CM) which is associated with worse survival than other CM in an effort to delineate non-UV oncogenic mechanisms. The clinical data includes mutation count, information about mutated genes, patient demographics, disease status, therapeutic details and copy number alterations among other relevant data points.
- Subject
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Chromosome AberrationsDNA Mutational AnalysisMelanoma/geneticsMelanoma/pathologyTranscriptome
- Access Rights
- Free to All
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Acute Myeloid Leukemia (TCGA, Firehose Legacy)
- Description
TCGA Acute Myeloid Leukemia. Source data from GDAC Firehose. Previously known as TCGA Provisional. This dataset contains summary data visualizations and clinical data from a broad sampling of 200 carcinomas from 200 patients. The data was gathered as part of the Broad Institute of MIT and Harvard Firehose initiative, a cancer analysis pipeline. The clinical data includes mutation count, information about mutated genes, patient demographics, sample type, disease code, Abnormal Lymphocyte Percent, Atra Exposure, Basophils Cell Count, Blast Count, Cytogenetic abnormality type, and FAB. The dataset includes Next-Generation Clustered Heat Maps (NG-CHM) viewable via an embedded NG-CHM Heat Map Viewer, provided my MD Anderson Cancer Center, which provides a graphical environment for exploration of clustered or non-clustered heat map data. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
- Subject
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DNA Mutational AnalysisLeukemia, Myeloid, Acute
- Access Rights
- Free to All
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Acute Myeloid Leukemia (TCGA, PanCancer Atlas) data
- Description
This dataset contains summary data visualizations and clinical data from a broad sampling of over 200 acute myeloid leukemias. The data was gathered as part of the PanCancer Atlas initiative, which aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset. The clinical data includes mutation count, information about mutated genes, patient demographics, disease status, tumor typing, and chromosomal gain or loss. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
- Subject
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DNA Mutational AnalysisLeukemia, Myeloid, Acute
- Access Rights
- Free to All
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Adenoid Cystic Carcinoma Project (J Clin Invest 2019)
- Description
Multi-Institute Cohort of 1045 Adenoid Cystic Carcinoma patients. This dataset contains summary data visualizations and clinical data from a broad sampling of 1045 adenoid cystic carcinomas. The data was gathered in support of an article in the Journal of Clinical Investigation. The clinical data includes mutation count, information about mutational analysis, patient demographics, survival status, and tumor type (based on the opensource OncoTree ontology developed at MSK). The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
- Subject
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Carcinoma, Adenoid Cystic
- Access Rights
- Free to All
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Adrenocortical Carcinoma (TCGA, Firehose Legacy)
- Description
TCGA Adrenocortical Carcinoma; raw data at the NCI; source mutation data from GDAC Firehose. This dataset contains summary data visualizations and clinical data from a broad sampling of 92 adrenocortical carcinomas. The data was gathered as part of the Broad Institute of MIT and Harvard Firehose initiative, a cancer analysis pipeline. The clinical data includes mutation count, information about mutated genes, patient demographics, Adjuvant Postoperative Pharmaceutical Therapy Administered Indicator, tumor typing, disease status, Atypical Mitotic Figures, Capsular Invasion, Ct scan preop results, Cytoplasm Presence Less Than Equal 25 Percent, and Days to Sample Collection. The dataset includes Next-Generation Clustered Heat Maps (NG-CHM) viewable via an embedded NG-CHM Heat Map Viewer, provided my MD Anderson Cancer Center, which provides a graphical environment for exploration of clustered or non-clustered heat map data. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
- Subject
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Adrenocortical CarcinomaDNA Mutational Analysis
- Access Rights
- Free to All
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Adrenocortical Carcinoma (TCGA, PanCancer Atlas) data
- Description
This dataset contains summary data visualizations and clinical data from a broad sampling of 91 adrenocortical carcinomas. The data was gathered as part of the PanCancer Atlas initiative, which aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset. The clinical data includes mutation count, information about mutated genes, patient demographics, disease status, tumor typing, and chromosomal gain or loss. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
- Subject
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Adrenocortical CarcinomaDNA Mutational Analysis
- Access Rights
- Free to All
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Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016).
- Description
Exome sequencing analysis of 160 cancers arising in the periampullary region, 62 of these clearly arising from either the bile duct (n = 44) or the duodenum (n = 18) and 98 for which the epithelium of origin could not be clearly defined morphologically (AMPCA). This dataset contains summary data visualizations and clinical data from a sampling of 160 samples of ampullary adenocarcinomas from Baylor College of Medicine Elkins Pancreatic Center, Australian Pancreatic Cancer Genome Initiative, MD Anderson Cancer Center, and the Technical University of Dresden. The clinical data includes Patient ID, Sample ID, Mutation Count, Percent Intestinal, Associated Adenoma, Cllularity based on allele frequency, Data Source, Days to Last Followup, Immunohistochemistry Subtype, Morphology Other Features, Morphology Subtype, Neoplasm Histologic, Grade Note, Overall Survival (Months), Overall Survival Status, Patient's Vital Status, PB Blast Percentage, and Primary Tumor Site.
- Subject
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Ampulla of VaterCarcinoma
- Access Rights
- Free to All
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An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression
- Authors
- Albanese, Steven KyleParton, Daniel LawrenceIsik, MehtapRodriguez-Laureano, Lucelenie7 more author(s)...
- Description
Source code, assay data, full expression results for all ABL1 constructs, wild-type kinases, and ABL1 and SRC mutants, plasmid libraries, and other supporting material for the generation of a library of human kinase domain constructs for automated bacterial expression. From the publication abstract, "Kinases play a critical role in cellular signaling and are dysregulated in a number of diseases, such as cancer, diabetes, and neurodegeneration. Therapeutics targeting kinases currently account for roughly 50% of cancer drug discovery efforts. The ability to explore human kinase biochemistry and biophysics in the laboratory is essential to designing selective inhibitors and studying drug resistance. Bacterial expression systems are superior to insect or mammalian cells in terms of simplicity and cost effectiveness but have historically struggled with human kinase expression. Following the discovery that phosphatase coexpression produced high yields of Src and Abl kinase domains in bacteria, we have generated a library of 52 His-tagged human kinase domain constructs that express above 2 μg/mL of culture in an automated bacterial expression system utilizing phosphatase coexpression (YopH for Tyr kinases and lambda for Ser/Thr kinases). Here, we report a structural bioinformatics approach to identifying kinase domain constructs previously expressed in bacteria and likely to express well in our protocol, experiments demonstrating our simple construct selection strategy selects constructs with good expression yields in a test of 84 potential kinase domain boundaries for Abl, and yields from a high-throughput expression screen of 96 human kinase constructs. Using a fluorescence-based thermostability assay and a fluorescent ATP-competitive inhibitor, we show that the highest-expressing kinases are folded and have well-formed ATP binding sites. We also demonstrate that these constructs can enable characterization of clinical mutations by expressing a panel of 48 Src and 46 Abl mutations."
- Subject
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Bacteria/metabolismBinding sitesEscherichia coli/metabolismPhosphorylationProtein Structure, SecondaryProtein-Tyrosine KinasesProto-Oncogene Proteins c-ablsrc-Family Kinases
- Access Rights
- Free to AllFee Required
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Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytoma (MSKCC, Neuro Oncol 2017): Genomic characterization using next generation sequencing (NGS) in 22 Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas.
- Authors
- Thomas, Alissa A.Abrey, Lauren E.Terziev, RobertRaizer, Jeffrey J.24 more author(s)...
- Description
This dataset contains summary data visualizations and sequencing data of anaplastic oligodendroglioma (AO) and anaplastic oligoastrocytoma (AOA) tumors following a trial using induction temozolomide (TMZ) followed by myeloablative high-dose chemotherapy (HDC) with autologous stem-cell transplant (ASCT) as a potential strategy to defer radiotherapy. The clinical data includes mutation count, information about mutated genes, patient demographics, disease progression among other relevant data points. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
- Subject
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Brain NeoplasmsChemoradiotherapyDNA Mutational AnalysisOligodendrogliomaTemozolomide
- Access Rights
- Free to All
Filter by
Subject
- DNA Mutational Analysis 89
- Adenocarcinoma 13
- Urinary Bladder Neoplasms 11
- Breast Neoplasms 10
- Gene Expression Profiling 10
- Carcinoma, Renal Cell 9
- Cholangiocarcinoma 9
- Carcinoma, Squamous Cell 8
- Prostatic Neoplasms 8
- Brain Neoplasms 7
- Melanoma 7
- Transcriptome 7
- Uterine Neoplasms 7
- Carcinoma, Hepatocellular 6
- Gallbladder Neoplasms 6
- Immunotherapy 6
- Lung Neoplasms 6
- Sarcoma, Synovial 6
- Carcinoma, Non-Small-Cell Lung 5
- Colorectal Neoplasms 5
- Cystadenocarcinoma, Serous 5
- Ovarian Neoplasms 5
- Adenocarcinoma of Lung 4
- Endometrial Neoplasms 4
- Esophageal Neoplasms 4
- Genomics 4
- Kidney Neoplasms 4
- Killer Cells, Natural 4
- Mesothelioma 4
- Pancreatic Neoplasms 4
- Sarcoma 4
- Skin Neoplasms 4
- Stomach Neoplasms 4
- Transcription Factors 4
- Bile Duct Neoplasms 3
- Carcinoma, Ductal, Breast 3
- Carcinoma, Endometrioid 3
- Carcinoma, Lobular 3
- Carcinosarcoma 3
- Gene Expression 3
- Gene Expression Regulation, Neoplastic 3
- Glioblastoma 3
- Liposarcoma 3
- Liver Neoplasms 3
- Lymphocytes, Tumor-Infiltrating 3
- Mutation 3
- Neurofibroma 3
- Oligodendroglioma 3
- Pheochromocytoma 3
- Rectal Neoplasms 3
- Squamous Cell Carcinoma of Head and Neck 3
- Thyroid Cancer, Papillary 3
- Tumor Microenvironment/immunology 3
- Uveal Neoplasms 3
- Adenocarcinoma, Mucinous 2
- Adrenocortical Carcinoma 2
- Carcinoma, Embryonal 2
- Carcinoma, Papillary 2
- Carcinoma, Papillary, Follicular 2
- Chromosome Aberrations 2
- Colonic Neoplasms 2
- Cystadenocarcinoma, Papillary 2
- DNA Methylation 2
- Fibromatosis, Aggressive 2
- Fibrosarcoma 2
- Histiocytoma, Malignant Fibrous 2
- Interferon Regulatory Factors 2
- Leiomyosarcoma 2
- Leukemia, Myeloid, Acute 2
- Lymphoma, Large B-Cell, Diffuse 2
- Melanoma/genetics 2
- Melanoma/pathology 2
- Mouse Cytomegalovirus 2
- Neoplasms, Squamous Cell 2
- Nerve Sheath Neoplasms 2
- Paraganglioma 2
- Plasmacytoma/genetics 2
- Receptors, Antigen, T-Cell 2
- Seminoma 2
- T-Lymphocytes, Cytotoxic 2
- Testicular Neoplasms 2
- Thymoma 2
- Thyroid Neoplasms 2
- Ureteral Neoplasms 2
- Uterine Cervical Neoplasms 2
- Viral Infections 2
- Adenocarcinoma, Papillary 1
- Adenoma, Liver Cell 1
- Adenosine 1
- Ampulla of Vater 1
- Anticodon/chemistry 1
- Anticodon/metabolism 1
- Astrocytoma 1
- Bacteria/genetics 1
- Bacteria/metabolism 1
- Bacterial Proteins 1
- Bacterial Toxins 1
- Bayes Theorem 1
- Binding sites 1
- Carcinoma 1
OncoTree Cancer Tag
- CHOL 9
- BLCA 8
- LUAD 8
- BRCA 7
- BREAST 7
- GBM 7
- IHCH 7
- CCRCC 6
- COAD 6
- IDC 6
- ILC 6
- SKCM 6
- SYNS 6
- ACRM 5
- COADREAD 5
- EGC 5
- ESCA 5
- GBC 5
- HCC 5
- LUSC 5
- NSCLC 5
- ODG 5
- PAAD 5
- PRAD 5
- SSRCC 5
- STAD 5
- UEC 5
- USC 5
- AASTR 4
- AODG 4
- ASTR 4
- BRCNOS 4
- CESC 4
- CHRCC 4
- ECAD 4
- EHCH 4
- ESCC 4
- HNSC 4
- LUNE 4
- MDLC 4
- MEL 4
- OAST 4
- PHC 4
- PLEMESO 4
- PRCC 4
- READ 4
- SRCBC 4
- UCS 4
- UM 4
- UTUC 4
- ACC 3
- ADNOS 3
- AMPCA 3
- AOAST 3
- ARMM 3
- BLADDER 3
- BRAIN 3
- BRCANOS 3
- CUP 3
- DDLS 3
- DIFG 3
- EMBCA 3
- FLC 3
- GEJ 3
- GSARC 3
- HGGNOS 3
- LGGNOS 3
- LMS 3
- MACR 3
- MBC 3
- MFH 3
- MFS 3
- MNET 3
- MPNST 3
- MSTAD 3
- MUP 3
- NSCLCPD 3
- NSGCT 3
- OVARY 3
- PDC 3
- PGNG 3
- PLBMESO 3
- PLLS 3
- PLMESO 3
- PROSTATE 3
- RCC 3
- SARCL 3
- SDCA 3
- SEM 3
- SOC 3
- THPA 3
- THPD 3
- THYM 3
- TSTAD 3
- UAD 3
- UCCC 3
- UCEC 3
- UMEC 3
- ACBC 2
Repository
- cBioPortal 89
- GEO 17
- GitHub 3
- ENA 2
- dbGaP 2
- Addgene 1
- BioProject 1
- CPTAC 1
- Figshare 1
- FlowRepository 1
- GtRNAdb 1
- MicrobesOnline 1
- PATRIC 1
- PanCanAtlas 1
Data Tools
- MSK-IMPACT 17
Analytical/Collection Software
Author
- Carr, Ambrose James 4
- Lau, Colleen M. 4
- Lowe, Scott W. 4
- Massagué, Joan 4
- Pe'er, Dana 4
- Sun, Joseph C. 4
- Azizi, Elham 3
- Banito, Ana Cristina Tome Moita 3
- Choi, Kristy 3
- Cornish, Andrew Erickson 3
- Prabhakaran, Sandhya 3
- Socci, Nicholas D. 3
- Al-Ahmadie, Hikmat 2
- Ariyan, Charlotte Eielson 2
- Basnet, Harihar 2
- Berger, Michael Forman 2
- Chan-On, Waraporn 2
- Dao, The Phuong 2
- Fromme, Rachel M. 2
- Kadaveru, Krishna 2
- Kiseliovas, Vaidotas 2
- Konopacki, Catherine Ann 2
- Liang, Winnie S. 2
- Mazutis, Linas 2
- McConkey, David J. 2
- McKenney, Peter Timothy 2
- Nainys, Juozas 2
- Plitas, George 2
- Reuter, Victor 2
- Rudensky, Alexander Y. 2
- Sanchez-Vega, Francisco 2
- Schultz, Nikolaus D. 2
- Setty, Manu 2
- Solit, David 2
- Sosman, Jeffrey 2
- Su, Xiaoping 2
- Teh, Bin Tean 2
- Trent, Jeffrey 2
- Wasti, Ruby C. 2
- Wu, Kenmin 2
- Abrey, Lauren E. 1
- Adileh, Mohammad 1
- Adkins, Jonathan 1
- Aguilar, Julio Garcia 1
- Akbani, Rehan 1
- Albanese, Steven Kyle 1
- Amin, Sadaf 1
- Arcila, Maria Eugenia 1
- Bacusmo, Jo Marie 1
- Bagrodia, Aditya 1
- Bai, Jianbo 1
- Bajorin, Dean 1
- Barlas, Afsar 1
- Behr, Julie Marie 1
- Bellmunt, Joaquim 1
- Bochner, Bernard 1
- Brennan, Cameron 1
- Briggs, Samuel Royden 1
- Bullman, Susan 1
- Busam, Klaus J. 1
- Cairncross, J. Gregory 1
- Carpten, John 1
- Carvalho, Benilton 1
- Castro, Mauro A. A. 1
- Cercek Hanjis, Andrea 1
- Cha, Eugene K. 1
- Chagas, Vinicius S. 1
- Chakravarty, Debyani 1
- Chen, Chin-Tung 1
- Chen, Shuibing 1
- Chen, Xi 1
- Chen, Ye-Guang 1
- Chen, Yingbei 1
- Cherniack, Andrew D. 1
- Chodera, John Damon 1
- Choi, Seo-Hyun 1
- Choi, Woonyoung 1
- Choo, Caleb 1
- Clevers, Hans 1
- Cook, Brandoch 1
- Craig, David W. 1
- Crandall, Holly 1
- Crespo, Miguel 1
- Cutcutache, Ioana 1
- Cuyugan, Lori 1
- Czerniak, Bogdan A. 1
- Dalbagni, Guido 1
- De Angelis, Lisa 1
- DeMatteo, Ronald P. 1
- DeMott, Michael 1
- Dedon, Peter C. 1
- Deluca, Valerie 1
- Deng, Haiteng 1
- Desai, Neil B. 1
- Deutsch, Chris 1
- Dow, Lukas 1
- Elfarash, Ameer 1
- Elghouayel, Arthur 1
- Evans, Todd 1
Publisher
- The Cancer Genome Atlas (TCGA) 33
- Broad Institute 32
- Memorial Sloan Kettering Cancer Center 19
- Duke-NUS Graduate Medical School 2
- Australian Pancreatic Cancer Genome Initiative 1
- Baylor College of Medicine Elkins Pancreatic Center 1
- Charles Rudin Lab 1
- Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar Technische Universität München 1
- MD Anderson Cancer Center 1
- National Cancer Centre Singapore 1
- National Cancer Institute (U.S.) 1
- National Cancer Institute - Office of Cancer Clinical Proteomics Research 1
- Technische Universität Dresden 1
- The Lowe Lab 1
- United States - National Institutes of Health (NIH) - National Cancer Institute (NCI) 1
- Virtual Institute for Microbial Stress and Survival 1