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Functional prioritization
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Unraveling functional noncoding variants associated with complex diseases is still a great challenge. We present a novel algorithm, Prioritization And Functional Assessment (PAFA), that prioritizes and assesses the functionality of genetic variants by introducing population differentiation measures and recalibrating training variants.
18p
vibransone
28-03-2024
1
1
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The extent to which changes in gene expression can influence cardiovascular disease risk across different tissue types has not yet been systematically explored. We have developed an analysis pipeline that integrates tissue-specific gene expression, Mendelian randomization and multiple-trait colocalization to develop functional mechanistic insight into the causal pathway from a genetic variant to a complex trait.
15p
vibransone
28-03-2024
4
2
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The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying “personal” gene regulatory network.
13p
vioraclene
31-03-2024
4
2
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Patients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes. We introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization information to improve the power to detect de novo mutations influencing disease risk.
11p
vioraclene
31-03-2024
1
1
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5’ untranslated regions (5’UTRs) are essential modulators of protein translation. Predicting the impact of 5’UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5’UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs).
21p
vicwell
29-02-2024
3
1
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Continued part 1, part 2 of ebook "Axiomatic design in large systems: Complex products, buildings and manufacturing systems" presents the following content: application of axiomatic design to the design of the built environment - a literature review; applying axiomatic design to prefabricated building design in the housing industry - a case study analysis; an application of quality function deployment and axiomatic design to the conceptual design of temporary housing; manufacturing systems; design and implementation approach for distributed manufacturing networks using axiomatic design;...
170p
dieptieuung
14-07-2023
4
3
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Apoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, proteincoding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis.
40p
lyhuyenthu
31-01-2023
9
2
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We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated “gold standard” positively selected variants and simulations.
18p
vialfrednobel
29-01-2022
11
0
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Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson’s disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants.
26p
vialfrednobel
29-01-2022
15
0
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A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method for prioritizing cancer genes accounting not only for mutations in individual genes but also in their neighbors in functional networks, MUFFINN (MUtations For Functional Impact on Network Neighbors).
16p
viaristotle
29-01-2022
8
0
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A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction.
19p
viaristotle
29-01-2022
11
0
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Constructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module identification, gene function prediction, and disease-gene prioritization.
26p
viarchimedes
26-01-2022
8
0
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RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation and disease. Their binding sites cover more of the genome than coding exons; nevertheless, most noncoding variant prioritization methods only focus on transcriptional regulation. Here, we integrate the portfolio of ENCODE-RBP experiments to develop RADAR, a variant-scoring framework.
13p
viarchimedes
26-01-2022
13
0
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Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected from 19 normal tissues across six vertebrate species.
14p
viarchimedes
26-01-2022
10
0
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Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary.
15p
vibeauty
23-10-2021
8
1
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Enhancers are distal cis-regulatory elements that control gene expression. Despite an increasing appreciation of the importance of enhancers in cellular function and disease, our knowledge of enhancer-regulated transcription is very limited.
18p
vitzuyu2711
29-09-2021
11
1
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An unfavorable genetic correlation between milk production and fertility makes simultaneous improvement of milk production and fertility difficult in cattle breeding. Rapid genetic improvement in milk production traits in dairy cattle has been accompanied by decline in cow fertility.
9p
visilicon2711
20-08-2021
6
1
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Aim of the present study was first to identify genetic variants associated with egg number (EN) in female broilers, second to describe the mode of their gene action (additive and/or dominant) and third to provide a list with implicated candidate genes for the trait.
12p
vijeeni2711
24-07-2021
11
0
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Prioritizing genetic variants is a challenge because disease susceptibility loci are often located in genes of unknown function or the relationship with the corresponding phenotype is unclear. A global data-mining exercise on the biomedical literature can establish the phenotypic profile of genes with respect to their connection to disease phenotypes.
13p
vikentucky2711
26-11-2020
10
1
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Biological data has grown explosively with the advance of nextgeneration sequencing. However, annotating protein function with wet lab experiments is time-consuming. Fortunately, computational function prediction can help wet labs formulate biological hypotheses and prioritize experiments.
16p
vikentucky2711
24-11-2020
12
2
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