Gene function similarity
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The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful.
20p viellison 28-03-2024 1 1 Download
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Hox transcription factors specify segmental diversity along the anterior-posterior body axis in metazoans. While the different Hox family members show clear functional specificity in vivo, they all show similar binding specificity in vitro and a satisfactory understanding of in vivo Hox target selectivity is still lacking.
19p vigalileogalilei 27-02-2022 13 1 Download
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In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partitioning of duplicated genes among different tissues. Many studies of the tissue-specific homeolog expression partitioning have focused on allopolyploids that have very different parental genomes, while few studies have focused on autopolyploids or allopolyploids that have similar parental genomes.
10p vitzuyu2711 29-09-2021 5 1 Download
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Inference of protein’s membership in metabolic pathways has become an important task in functional annotation of protein. The membership information can provide valuable context to the basic functional annotation and also aid reconstruction of incomplete pathways. Previous works have shown success of inference by using various similarity measures of gene ontology.
10p vitzuyu2711 29-09-2021 19 1 Download
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Zebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types such as the oocyte.
15p vijeeni2711 24-07-2021 10 0 Download
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Recent advances in single-cell RNA sequencing have allowed researchers to explore transcriptional function at a cellular level. In particular, single-cell RNA sequencing reveals that there exist clusters of cells with similar gene expression profiles, representing different transcriptional states.
10p vijeeni2711 30-06-2021 10 1 Download
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The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic genome, suggesting the role of chromatin-level gene regulation in shaping the physical distribution of coordinated genes.
8p viwyoming2711 16-12-2020 15 0 Download
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The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses.
13p viwyoming2711 16-12-2020 10 1 Download
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Protein function prediction is to assign biological or biochemical functions to proteins, and it is a challenging computational problem characterized by several factors: (1) the number of function labels (annotations) is large; (2) a protein may be associated with multiple labels; (3) the function labels are structured in a hierarchy; and (4) the labels are incomplete.
12p vikentucky2711 26-11-2020 13 1 Download
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Measuring semantic similarities by combining gene ontology annotations and gene co-function networks
Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the limited proportion of genes that are annotated to GO in most organisms.
14p vikentucky2711 26-11-2020 13 1 Download
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The Gene Ontology (GO) is a dynamic, controlled vocabulary that describes the cellular function of genes and proteins according to tree major categories: Biological process, molecular function and cellular component.
14p vioklahoma2711 19-11-2020 13 2 Download
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Identifying relatedness among diseases could help deepen understanding for the underlying pathogenic mechanisms of diseases, and facilitate drug repositioning projects. A number of methods for computing disease similarity had been developed; however, none of them were designed to utilize information of the entire protein interaction network, using instead only those interactions involving disease causing genes.
13p vioklahoma2711 19-11-2020 15 2 Download
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In recent years, many measures of gene functional similarity have been proposed and widely used in all kinds of essential research. These methods are mainly divided into two categories: pairwise approaches and group-wise approaches.
14p vioklahoma2711 19-11-2020 8 1 Download
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RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies.
8p vioklahoma2711 19-11-2020 6 0 Download
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Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regulating miRNAs is limited.
12p vioklahoma2711 19-11-2020 6 1 Download
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MiRNAs play a critical role in the response of plants to abiotic and biotic stress. However, the functions of most plant miRNAs remain unknown. Inferring these functions from miRNA functional similarity would thus be useful. This study proposes a new method, called PPImiRFS, for inferring miRNA functional similarity.
11p vioklahoma2711 19-11-2020 6 1 Download
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Loss-of-function phenotypes are widely used to infer gene function using the principle that similar phenotypes are indicative of similar functions. However, converting phenotypic to functional annotations requires careful interpretation of phenotypic descriptions and assessment of phenotypic similarity.
12p vioklahoma2711 19-11-2020 10 1 Download
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The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation.
13p vioklahoma2711 19-11-2020 13 0 Download
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Functional annotation of bacterial genomes is an obligatory and crucially important step of information processing from the genome sequences into cellular mechanisms. However, there is a lack of computational methods to evaluate the quality of functional assignments.
11p viflorida2711 30-10-2020 6 1 Download
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Long non-coding RNA (lncRNA) plays important roles in many biological and pathological processes, including transcriptional regulation and gene regulation. As lncRNA interacts with multiple proteins, predicting lncRNA-protein interactions (lncRPIs) is an important way to study the functions of lncRNA.
8p viflorida2711 30-10-2020 14 2 Download