Results 71 to 80 of about 184,470 (334)

TCGADownloadHelper: simplifying TCGA data extraction and preprocessing [PDF]

Frontiers in Genetics
The Cancer Genome Atlas (TCGA) provides comprehensive genomic data across various cancer types. However, complex file naming conventions and the necessity of linking disparate data types to individual case IDs can be challenging for first-time users. While other tools have been introduced to facilitate TCGA data handling, they lack a straightforward ...
Alexandra Anke Baumann, Alexandra Anke Baumann, Olaf Wolkenhauer, Olaf Wolkenhauer, Olaf Wolkenhauer, Markus Wolfien, Markus Wolfien   +6 more
openaire   +3 more sources

Chemoresistome mapping in individual breast cancer patients unravels diversity in dynamic transcriptional adaptation

Molecular Oncology, EarlyView.
This study used longitudinal transcriptomics and gene‐pattern classification to uncover patient‐specific mechanisms of chemotherapy resistance in breast cancer. Findings reveal preexisting drug‐tolerant states in primary tumors and diverse gene rewiring patterns across patients, converging on a few dysregulated functional modules. Despite receiving the
Maya Dadiani, Gilgi Friedlander, Gili Perry, Nora Balint‐Lahat, Shlomit Gilad, Dana Morzaev‐Sulzbach, Anjana Shenoy, Noa Bossel Ben‐Moshe, Anya Pavlovsky, Rinat Bernstein‐Molho, Eytan Domany, Iris Barshack, Tamar Geiger, Bella Kaufman, Einav Nili Gal‐Yam   +14 more
wiley   +1 more source

M1 macrophage-related prognostic model by combining bulk and single-cell transcriptomic data in NSCLC [PDF]

Exploration of Medicine
Aim: Lung cancer is the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC) is the most common subtype. Despite recent advancements in diagnostics and therapies, only a small percentage of patients benefit from ...
Zhe Liu, Fang Liu, Olutomilayo Olayemi Petinrin, Muhammad Toseef, Nanjun Chen, Zhongxu Zhu, Ka-Chun Wong   +6 more
doaj   +1 more source

A Comprehensive Analysis of Prognostic Indicators in Serous Ovarian Cancer Based on Leukocyte Migration and Immune Microenvironment

Frontiers in Bioscience-Landmark, 2023
Background: High-grade serous ovarian cancer (HGSOC) treatment is facing clinical challenges. The tumor immune microenvironment (TME) has recently been shown to perform a critical function in the prediction of clinical outcomes as well as the ...
Junping Pan, Xiaochuan Chen, Lin Yang, Yanwen Song, Jing Liu, Li Li, Yibin Lin, Lina Tang, Sufang Qiu, Qin Xu   +9 more
doaj   +1 more source

Expression and DNA methylation of 20S proteasome subunits as prognostic and resistance markers in cancer

Molecular Oncology, EarlyView.
Comprehensive analysis of genomic mutations, gene expression, DNA methylation, and pathway analysis of TCGA data was carried out to define cancer types in which proteasome subunits expression is associated with worse survival. Albeit the effect of specific proteasome subunits on cellular function, the main role of the proteasome is better evaluated ...
Ruba Al‐Abdulla, Simone Venz, Ruslan Al‐Ali, Martin Wendlandt, Mandy Radefeldt, Elke Krüger   +5 more
wiley   +1 more source

GWAS Meets TCGA to Illuminate Mechanisms of Cancer Predisposition [PDF]

Cell, 2013
Genome-wide association studies (GWASs) have unraveled a large number of cancer risk alleles. Understanding how these allelic variants predispose to disease is a major bottleneck confronting translational application. In this issue, Li and colleagues combine GWASs with The Cancer Genome Atlas (TCGA) to disambiguate the contributions of germline and ...
Hyun Seok Kim, Michael A. White, John D. Minna   +2 more
openaire   +4 more sources

Detecting homologous recombination deficiency for breast cancer through integrative analysis of genomic data

Molecular Oncology, EarlyView.
This study develops a semi‐supervised classifier integrating multi‐genomic data (1404 training/5893 validation samples) to improve homologous recombination deficiency (HRD) detection in breast cancer. Our method demonstrates prognostic value and predicts chemotherapy/PARP inhibitor sensitivity in HRD+ tumours.
Rong Zhu, Katherine Eason, Suet‐Feung Chin, Paul A. W. Edwards, Raquel Manzano Garcia, Richard Moulange, Jia Wern Pan, Soo Hwang Teo, Sach Mukherjee, Maurizio Callari, Carlos Caldas, Stephen‐John Sammut, Oscar M. Rueda   +12 more
wiley   +1 more source

Data‐driven discovery of gene expression markers distinguishing pediatric acute lymphoblastic leukemia subtypes

Molecular Oncology, EarlyView.
This study investigates gene expression differences between two major pediatric acute lymphoblastic leukemia (ALL) subtypes, B‐cell precursor ALL, and T‐cell ALL, using a data‐driven approach consisting of biostatistics and machine learning methods. Following analysis of a discovery dataset, we find a set of 14 expression markers differentiating the ...
Mona Nourbakhsh, Nikola Tom, Anna Schrøder Lassen, Helene Brasch Lind Petersen, Ulrik Kristoffer Stoltze, Karin Wadt, Kjeld Schmiegelow, Matteo Tiberti, Elena Papaleo   +8 more
wiley   +1 more source

Pan-cancer adaptive immune resistance as defined by the Tumor Inflammation Signature (TIS): results from The Cancer Genome Atlas (TCGA)

Journal of Immunotherapy for Cancer, 2018
The Tumor Inflammation Signature (TIS) is an investigational use only (IUO) 18-gene signature that measures a pre-existing but suppressed adaptive immune response within tumors.
P. Danaher, S. Warren, Rongze Lu, J. Samayoa, A. Sullivan, I. Pekker, B. Wallden, F. Marincola, A. Cesano   +8 more
semanticscholar   +1 more source

Ten-year outcomes of uveal melanoma based on The Cancer Genome Atlas (TCGA) classification in 1001 cases

Indian Journal of Ophthalmology, 2021
Purpose: To understand the prognostic value of The Cancer Genome Atlas (TCGA) for uveal melanoma metastasis, using a simplified 4-category classification, based on tumor DNA.
C. Shields, Eileen L. Mayro, Z. Baş, P. Dockery, Antonio Yaghy, S. Lally, A. Ganguly, J. Shields   +7 more
semanticscholar   +1 more source