Results 1 to 10 of about 470,447 (304)

Improving gene isoform quantification with miniQuant. [PDF]

Nat Biotechnol
Abstract RNA sequencing has been widely applied for gene isoform quantification, but limitations exist in quantifying isoforms of complex genes accurately, especially for short reads. Here we identify genes that are difficult to quantify accurately with short reads and illustrate the information benefit of using long reads to quantify these ...
Li H, Wang D, Gao Q, Tan P, Wang Y, Cai X, Li A, Zhao Y, Thurman AL, Malekpour SA, Zhang Y, Sala R, Cipriano A, Wei CL, Sebastiano V, Song C, Zhang NR, Au KF.   +17 more
europepmc   +3 more sources

A bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data [PDF]

BMC Genomics
Background Even though alternative RNA splicing was discovered nearly 50 years ago (1977), we still understand very little about most isoforms arising from a single gene, including in which tissues they are expressed and if their functions differ.
Madeline L. Page, Bernardo Aguzzoli Heberle, J. Anthony Brandon, Mark E. Wadsworth, Lacey A. Gordon, Kayla A. Nations, David W. Fardo, Mark T. W. Ebbert   +7 more
doaj   +2 more sources

Dissecting the Biological Functions of Various Isoforms of Ferredoxin Reductase for Cell Survival and DNA Damage Response [PDF]

Cells
The ferredoxin reductase (FDXR) gene is expressed as seven isoforms: 1–6 by alternative splicing and 7 by an alternative promoter according to the Entrez Gene Database.
Ken-ichi Nakajima, Shakur Mohibi, Kyle Hong, Xinbin Chen, Jin Zhang   +4 more
doaj   +2 more sources

Gene isoform specificity through enhancer-associated antisense transcription. [PDF]

PLoS ONE, 2012
Enhancers and antisense RNAs play key roles in transcriptional regulation through differing mechanisms. Recent studies have demonstrated that enhancers are often associated with non-coding RNAs (ncRNAs), yet the functional role of these enhancer:ncRNA ...
Courtney S Onodera, Jason G Underwood, Sol Katzman, Frank Jacobs, David Greenberg, Sofie R Salama, David Haussler   +6 more
doaj   +4 more sources

Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation [PDF]

Nature Communications
We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele ...
Chunyu Liu, Roby Joehanes, Jiantao Ma, Jiuyong Xie, Jian Yang, Mengyao Wang, Tianxiao Huan, Shih-Jen Hwang, Jia Wen, Quan Sun, Cumhur Y. Demirkale, Nancy L. Heard-Costa, Peter Orchard, April P. Carson, Jeffrey W. Haessler, Laura M. Raffield, Alex P. Reiner, Nora Franceschini, Paul L. Auer, Charles Kooperberg, Yun Li, George O’Connor, Joanne M. Murabito, Peter Munson, Daniel Levy   +24 more
doaj   +2 more sources

Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers

Computational and Structural Biotechnology Journal, 2021
Transcript isoforms regulated by alternative splicing can substantially impact carcinogenesis, leading to a need to obtain clues for both gene differential expression and malfunctions of isoform distributions in cancer studies.
Tzu-Hsien Yang, Yu-Hsuan Chiang, Sheng-Cian Shiue, Po-Heng Lin, Ya-Chiao Yang, Kai-Chi Tu, Yan-Yuan Tseng, Joseph T. Tseng, Wei-Sheng Wu   +8 more
doaj   +1 more source

Isoform function prediction by Gene Ontology embedding

Bioinformatics, 2022
AbstractMotivationHigh-resolution annotation of gene functions is a central task in functional genomics. Multiple proteoforms translated from alternatively spliced isoforms from a single gene are actual function performers and greatly increase the functional diversity.
Sichao Qiu, Guoxian Yu, Xudong Lu, Carlotta Domeniconi, Maozu Guo   +4 more
openaire   +2 more sources

Characterization of Rubisco Activase Genes in Maize: An α-Isoform Gene Functions alongside a β-Isoform Gene [PDF]

Plant Physiology, 2014
Rubisco activase (RCA) catalyzes the activation of Rubisco in vivo and plays a crucial role in regulating plant growth. In maize (Zea mays), only β-form RCA genes have been cloned and characterized. In this study, a genome-wide survey revealed the presence of an α-form RCA gene and a β-form RCA gene in the maize genome, herein referred to as ZmRCAα and
Zhitong Yin, Zhenliang Zhang, Dexiang Deng, Maoni Chao, Qingsong Gao, Yijun Wang, Zefeng Yang, Yunlong Bian, Derong Hao, Chenwu Xu   +9 more
openaire   +2 more sources

The actin gene family: Function follows isoform [PDF]

Cytoskeleton, 2010
AbstractAlthough actin is often thought of as a single protein, in mammals it actually consists of six different isoforms encoded by separate genes. Each isoform is remarkably similar to every other isoform, with only slight variations in amino acid sequence.
Perrin, Benjamin J, Ervasti, James M
openaire   +2 more sources

TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing

Nature Communications, 2023
Single-molecule Real-time Isoform Sequencing (Iso-seq) of transcriptomes by PacBio can generate very long and accurate reads, thus providing an ideal platform for full-length transcriptome analysis.
Yuchao Xia, Zijie Jin, Chengsheng Zhang, Linkun Ouyang, Yuhao Dong, Juan Li, Lvze Guo, Biyang Jing, Yang Shi, Susheng Miao, Ruibin Xi   +10 more
doaj   +1 more source