UPEFinder: A Bioinformatic Tool for the Study of Uncharacterized Proteins Based on Gene Expression Correlation and the PageRank Algorithm

Analyzing biological data using pathways helps identify trends in data tied to the function of a network. A large number of pathway-based analysis tools have been developed toward this goal. These pathways are often manually curated and thus associations are subject to the biases of the curator. A potentially attractive alternative is to define pathways based on the inherent functionality and connectivity of the network itself. Within metabolism, functionality is defined by the production and consumption of metabolites, and connectivity by metabolites participating in reactions through common enzymes. In this work, we present an algorithm, termed MetPath, that calculates pathways for production and consumption of metabolites. We show how these pathways have attractive properties, such as the ability to integrate multiple data types and weight contribution of genes within the pathway by their functional contribution to metabolite production/consumption. Pathways calculated in this manner are condition-specific and thus are custom tailored to the system of interest, in contrast to curated pathways. We find that these pathways predict gene expression correlation better compared to manually-curated pathways. Additionally, we find that these pathways can be used to understand gene expression changes between growth conditions and between cell types. This work serves to better understand the functional pathway structure underlying cell metabolism and helps to enable systems analyses of high-throughput data.

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Comprehensive Identification and Alternative Splicing of Microexons in Drosophila

Frontiers in Genetics ◽

10.3389/fgene.2021.642602 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ting-Lin Pang ◽

Zhan Ding ◽

Shao-Bo Liang ◽

Liang Li ◽

Bei Zhang ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Sex Determination ◽

Rna Splicing ◽

Critical Role ◽

Regulation Of Gene Expression ◽

Pathway Gene ◽

Mrna Transcripts ◽

Bioinformatic Tool ◽

Alternatively Spliced

Interrupted exons in the pre-mRNA transcripts are ligated together through RNA splicing, which plays a critical role in the regulation of gene expression. Exons with a length ≤ 30 nt are defined as microexons that are unique in identification. However, microexons, especially those shorter than 8 nt, have not been well studied in many organisms due to difficulties in mapping short segments from sequencing reads. Here, we analyzed mRNA-seq data from a variety of Drosophila samples with a newly developed bioinformatic tool, ce-TopHat. In addition to the Flybase annotated, 465 new microexons were identified. Differentially alternatively spliced (AS) microexons were investigated between the Drosophila tissues (head, body, and gonad) and genders. Most of the AS microexons were found in the head and two AS microexons were identified in the sex-determination pathway gene fruitless.

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