Results 131 to 140 of about 591,228 (346)

Models for transcript quantification from RNA-Seq [PDF]

, 2011
RNA-Seq is rapidly becoming the standard technology for transcriptome analysis. Fundamental to many of the applications of RNA-Seq is the quantification problem, which is the accurate measurement of relative transcript abundances from the sequenced reads.
Pachter, Lior
core  

Redox regulation meets metabolism: targeting PRDX2 to prevent hepatocellular carcinoma

Molecular Oncology, EarlyView.
PRDX2 acts as a central redox hub linking metabolic dysfunction‐associated steatohepatitis (MASH) to hepatocellular carcinoma (HCC). In normal hepatocytes, PRDX2 maintains redox balance and metabolic homeostasis under oxidative stress. In contrast, during malignant transformation, PRDX2 promotes oncogenic signaling, stemness, and tumor initiation ...
Naroa Goikoetxea‐Usandizaga, María Luz Martinez‐Chantar, Carolina Conter   +2 more
wiley   +1 more source

Single-cell total-RNA profiling unveils regulatory hubs of transcription factors

Nature Communications
Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from unspliced RNA to spliced RNA (i.e., mature RNA) to degradation. To feed this kinetic analysis, simultaneous measurement of unspliced RNA and
Yichi Niu, Jiayi Luo, Chenghang Zong
doaj   +1 more source

Simulating multiple faceted variability in single cell RNA sequencing. [PDF]

, 2019
The abundance of new computational methods for processing and interpreting transcriptomes at a single cell level raises the need for in silico platforms for evaluation and validation.
Xu, Chenling, Yosef, Nir, Zhang, Xiuwei
core  

Correlation of the differential expression of PIK3R1 and its spliced variant, p55α, in pan‐cancer

Molecular Oncology, EarlyView.
PIK3R1 undergoes alternative splicing to generate the isoforms, p85α and p55α. By combining large patient datasets with laboratory experiments, we show that PIK3R1 spliced variants shape cancer behavior. While tumors lose the protective p85α isoform, p55α is overexpressed, changes linked to poorer survival and more pronounced in African American ...
Ishita Gupta, Yang Song, Madeleine Ndahayo, Anirudh Saxena, Theresa Guo, Dylan Z. Kelley, Jessica Gore, Andrew Hennigan, Alexa Anderson, John C. Papadimitriou, Daria A. Gaykalova   +10 more
wiley   +1 more source

RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation

Scientific Reports
This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC ...
Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U. Shanthappa, Anna Butusova, Sofia Menshikova, Anna Belozerova, Anastasia Shvyrkova, Arina Tkachuk, Olga Khatenkova, Linda Balabanian, Ekaterina Postovalova, Jochen K. Lennerz, Funda Meric-Bernstam, Alexander Bagaev   +15 more
doaj   +1 more source

Statistical calibration of qRT-PCR, microarray and RNA-Seq gene expression data with measurement error models

, 2014
The accurate quantification of gene expression levels is crucial for transcriptome study. Microarray platforms are commonly used for simultaneously interrogating thousands of genes in the past decade, and recently RNA-Seq has emerged as a promising ...
Kuczek, Thomas, Sun, Zhaonan, Zhu, Yu
core   +1 more source

Basroparib inhibits YAP‐driven cancers by stabilizing angiomotin

Molecular Oncology, EarlyView.
Basroparib, a selective tankyrase inhibitor, suppresses Wnt signaling and attenuates YAP‐driven oncogenic programs by stabilizing angiomotin. It promotes AMOT–YAP complex formation, enforces cytoplasmic YAP sequestration, inhibits YAP/TEAD transcription, and sensitizes YAP‐active cancers, including KRAS‐mutant colorectal cancer, to MEK inhibition.
Young‐Ju Kwon, Dong Young Kim, Yuna Kim, Uk‐Il Kim, Jae‐Sung Kim   +4 more
wiley   +1 more source

Integrated Analysis of Single-Cell RNA-seq and Bulk RNA-seq in the Identification of a Novel ceRNA Network and Key Biomarkers in Diabetic Kidney Disease

International Journal of General Medicine, 2022
Yuejun Wang,1 Mingming Zhao,2 Yu Zhang2 1Department of Nephrology, Zhejiang Aged Care Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, People’s Republic of China; 2Department of Nephrology, Xiyuan Hospital, China Academy of Chinese Medical ...
Wang Y, Zhao M, Zhang Y
doaj  

RaMBat: Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects

Molecular Oncology, EarlyView.
To integrate multiple transcriptomics data with severe batch effects for identifying MB subtypes, we developed a novel and accurate computational method named RaMBat, which leveraged subtype‐specific gene expression ranking information instead of absolute gene expression levels to address batch effects of diverse data sources.
Mengtao Sun, Jieqiong Wang, Shibiao Wan
wiley   +1 more source