scholarly journals Functional annotation of HOT regions in the human genome: implications for human disease and cancer

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Hao Li ◽  
Hebing Chen ◽  
Feng Liu ◽  
Chao Ren ◽  
Shengqi Wang ◽  
...  
Keyword(s):  
Human Genome ◽  
Human Disease ◽  
Functional Annotation

scholarly journals dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiaoming Liu ◽  
Chang Li ◽  
Chengcheng Mou ◽  
Yibo Dong ◽  
Yicheng Tu
Keyword(s):  
Web Service ◽  
Human Genome ◽  
Exome Sequencing ◽  
Splice Site ◽  
Human Disease ◽  
Functional Annotation ◽  
Current Version ◽  
Functional Annotations ◽  
Whole Exome ◽  
Gene Level

AbstractWhole exome sequencing has been increasingly used in human disease studies. Prioritization based on appropriate functional annotations has been used as an indispensable step to select candidate variants. Here we present the latest updates to dbNSFP (version 4.1), a database designed to facilitate this step by providing deleteriousness prediction and functional annotation for all potential nonsynonymous and splice-site SNVs (a total of 84,013,093) in the human genome. The current version compiled 36 deleteriousness prediction scores, including 12 transcript-specific scores, and other variant and gene-level functional annotations. The database is available at http://database.liulab.science/dbNSFP with a downloadable version and a web-service.

scholarly journals Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Chao Ren ◽  
Feng Liu ◽  
Zhangyi Ouyang ◽  
Gaole An ◽  
Chenghui Zhao ◽  
...  
Keyword(s):  
Human Genome ◽  
Human Disease ◽  
Functional Annotation

scholarly journals Intron and Its Splicing Mechanism and Their Connection with Human Disease

2016 ◽  
Vol 15 (3) ◽  
pp. 307-312
Author(s):  
Mine Dosay-Akbulut
Keyword(s):  
Human Genome ◽  
Human Disease ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Developmental Disorders ◽  
Regulation Of Gene Expression ◽  
Medical Science ◽  
Intronless Genes ◽  
Different Types ◽  
Extra Difficulty

In the maturation mechanism of a messenger RNA, splicing play an important role with removing the noncoding introns and ligating the coding exons. Alternative splicing (AS) gives an extra difficulty to this mechanism and to the regulation of gene expression. The possible disturbing in the alternative RNA splicing mechanism can be a reason to several diseases like cancers and neurodegenerative disorders. Intronless genes (IGs) are seen in almost 3% of the human genome. Functionality of IGs has an important role in signal transduction genes and related regulatory proteins. This diversity can be reason to IG-associated diseases, especially neuropathies, developmental disorders, and cancer. The retroelements can be seen in almost half of the human genome. The known informations indicate that insertion of retroelement into exons and introns of genes promote different types of genetic disease, including cancer. The retroelement connected mutagenesis cause to fifty different types of human disease. The molecular informations and bioinformatic analyses can be used to explain the connection with splicing mutations and genetic mechanisms of several different human disease and understanding of this mechanism play an important role in the formation of treatment programme against to these diseases.Bangladesh Journal of Medical Science Vol.15(3) 2016 p.307-312

scholarly journals MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

2017 ◽  
Vol 100 (6) ◽  
pp. 843-853 ◽  
Author(s):  
Julia Wang ◽  
Rami Al-Ouran ◽  
Yanhui Hu ◽  
Seon-Young Kim ◽  
Ying-Wooi Wan ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Human Genome ◽  
Functional Annotation ◽  
Model Organism

Therapeutic Antisense Oligonucleotides Are Coming of Age

2019 ◽  
Vol 70 (1) ◽  
pp. 307-321 ◽  
Author(s):  
C. Frank Bennett
Keyword(s):  
Human Genome ◽  
Genome Sequence ◽  
Human Disease ◽  
Antisense Oligonucleotide ◽  
Antisense Oligonucleotides ◽  
Genetic Basis ◽  
Coming Of Age ◽  
Technology Platform ◽  
Therapeutic Applications ◽  
Monogenic Diseases

The first published description of therapeutic applications of antisense oligonucleotide (ASO) technology occurred in the late 1970s and was followed by the founding of commercial companies focused on developing antisense therapeutics in the late 1980s. Since the late 1980s, there has been steady progress in improving the technology platform, taking advantage of advances in oligonucleotide chemistry and formulations as well as increased understanding of the distribution and safety of ASOs. There are several approved ASO drugs and a broad pipeline in development. In addition, advances in understanding human disease, including the genetic basis for most monogenic diseases and the availability of the full human genome sequence, have created numerous therapeutic applications for the technology. I summarize the state of the technology and highlight how advances in the technology position ASOs to be an important contributor to future medicines.

scholarly journals Major functional bias for mitochondrial complexes in genome-wide CRISPR screens

2020 ◽  
Author(s):  
Mahfuzur Rahman ◽  
Maximilian Billmann ◽  
Michael Costanzo ◽  
Michael Aregger ◽  
Amy H. Y. Tong ◽  
...  
Keyword(s):  
Protein Stability ◽  
Human Genome ◽  
Cell Line ◽  
Functional Annotation ◽  
Reference Standards ◽  
Time Resolved ◽  
Genome Wide ◽  
Crispr Screen ◽  
Mitochondrial Complexes ◽  
Analyze Data

We present FLEX (Functionalevaluation of experimental perturbations), a pipeline that leverages several functional annotation resources to establish reference standards for benchmarking human genome-wide CRISPR screen data and methods for analyzing them. We apply FLEX to analyze data from the diverse cell line screens generated by the DepMap project. We identify a dominant mitochondria-associated signal, which our time-resolved CRISPR screens and analysis suggests may reflect screen dynamics and protein stability effects rather than genetic dependencies.

scholarly journals Mouse phenogenomics, toolbox for functional annotation of human genome

BMB Reports ◽  
2010 ◽  
Vol 43 (2) ◽  
pp. 79-90 ◽  
Author(s):  
Il-Yong Kim ◽  
Jae-Hoon Shin ◽  
Je-Kyung Seong
Keyword(s):  
Human Genome ◽  
Functional Annotation

Multi-omics annotation of human long non-coding RNAs

2020 ◽  
Vol 48 (4) ◽  
pp. 1545-1556 ◽  
Author(s):  
Qianpeng Li ◽  
Zhao Li ◽  
Changrui Feng ◽  
Shuai Jiang ◽  
Zhang Zhang ◽  
...  
Keyword(s):  
Human Genome ◽  
Functional Annotation ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Rna World ◽  
Omics Data ◽  
Biological Processes ◽  
Sequencing Technologies ◽  
Non Coding Rnas ◽  
Powerful Strategy

LncRNAs (long non-coding RNAs) are pervasively transcribed in the human genome and also extensively involved in a variety of essential biological processes and human diseases. The comprehensive annotation of human lncRNAs is of great significance in navigating the functional landscape of the human genome and deepening the understanding of the multi-featured RNA world. However, the unique characteristics of lncRNAs as well as their enormous quantity have complicated and challenged the annotation of lncRNAs. Advances in high-throughput sequencing technologies give rise to a large volume of omics data that are generated at an unprecedented rate and scale, providing possibilities in the identification, characterization and functional annotation of lncRNAs. Here, we review the recent important discoveries of human lncRNAs through analysis of various omics data and summarize specialized lncRNA database resources. Moreover, we highlight the multi-omics integrative analysis as a powerful strategy to efficiently discover and characterize the functional lncRNAs and elucidate their potential molecular mechanisms.

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