Results 1 to 10 of about 7,252,476 (351)

Deep Survey of GABAergic Interneurons: Emerging Insights From Gene-Isoform Transcriptomics. [PDF]

Front Mol Neurosci, 2019
GABAergic interneuron diversity is a key feature in the brain that helps to create different brain activity patterns and behavioral states. Cell type classification schemes—based on anatomical, physiological and molecular features—have provided us with a
Que L, Winterer J, Földy C.
europepmc   +2 more sources

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. [PDF]

Bioinformatics, 2018
Motivation Alternative splicing events (ASE) cause expression of a variable repertoire of potential protein products that are critical to carcinogenesis. Current methods to detect ASEs in tumor samples compare mean expression of gene isoforms relative to
Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ.   +15 more
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Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. [PDF]

Science
Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain.
Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, PsychENCODE Consortium†, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ, PsychENCODE Consortium.   +38 more
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IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing. [PDF]

Nucleic Acids Res, 2017
Allele-specific expression (ASE) is a fundamental problem in studying gene regulation and diploid transcriptome profiles, with two key challenges: (i) haplotyping and (ii) estimation of ASE at the gene isoform level.
Deonovic B, Wang Y, Weirather J, Wang XJ, Au KF.   +4 more
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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
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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
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A ratiometric catalog of protein isoform shifts in the cardiac fetal gene program [PDF]

JCI Insight
Pathological cardiac remodeling is associated with the reactivation of fetal genes, yet the extent of the heart’s fetal gene program and its impact on proteome compositions remain incompletely understood.
Yu Han, Shaonil Binti, Sara A. Wennersten, Boomathi Pandi, Dominic C.M. Ng, Edward Lau, Maggie P.Y. Lam   +6 more
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Transcription of a 5’ extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter [PDF]

eLife, 2017
Cell differentiation programs require dynamic regulation of gene expression. During meiotic prophase in Saccharomyces cerevisiae, expression of the kinetochore complex subunit Ndc80 is downregulated by a 5’ extended long undecoded NDC80 transcript ...
Minghao Chia, Amy Tresenrider, Jingxun Chen, Gianpiero Spedale, Victoria Jorgensen, Elçin Ünal, Folkert Jacobus van Werven   +6 more
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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
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Improving gene isoform quantification with miniQuant. [PDF]

Nat Biotechnol
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
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