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GO-Elite

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. The results can be visualized on WikiPathways or as networks.

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START

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The serial analysis of chromatin occupancy technique (SACO) promises to become a widely used method for the unbiased genome-wide experimental identification of loci bound by a transcription factor of interest. We describe the first web-based automatic tool, termed sequence tag analysis and reporting tool (START), for processing SACO data generated by experiments performed for the yeast, fruit fly, mouse, rat or human genomes.

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At_miRNA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs are small, endogenous RNAs found in many different species and are known to have an influence on diverse biological phenomena. They also play crucial roles in plant biological processes, such as metabolism, leaf sidedness and flower development. However, the functional roles of most microRNAs are still unknown. The identification of closely related microRNAs and target genes can be an essential first step towards the discovery of their combinatorial effects on different cellular states.

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HCCNet

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Abstract is not available.[1]

 

 

 

 

 

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Tools4miRs

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods.

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ncRNAppi

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Currently, there are a number of databases which store microRNA (miRNA) information, and tools available which provide miRNA target prediction. In this article, we describe a novel web-based tool that integrate the miRNA-targeted mRNA data, protein-protein interactions (PPI) records, tissues, biochemical pathways, human disease and gene function information to establish a disease-related miRNA target pathway database. This database is unique in the sense that it links miRNA target genes with their PPI partners according to being tissue- and diseases-specific or both.

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mirnanalyze

Submitted by ChenLiang on Thu, 04/06/2017 - 19:32

The current state-of-the-art in cancer diagnosis and treatment is not ideal; diagnostic tests are accurate but invasive, and treatments are "one-size fits-all" instead of being personalized. Recently, miRNA's have garnered significant attention as cancer biomarkers, owing to their ease of access (circulating miRNA in the blood) and stability. There have been many studies showing the effectiveness of miRNA data in diagnosing specific cancer types, but few studies explore the role of miRNA in predicting treatment outcome.

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DynaMod

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

A comprehensive analysis of enriched functional categories in differentially expressed genes is important to extract the underlying biological processes of genome-wide expression profiles. Moreover, identification of the network of significant functional modules in these dynamic processes is an interesting challenge. This study introduces DynaMod, a web-based application that identifies significant functional modules reflecting the change of modularity and differential expressions that are correlated with gene expression profiles under different conditions.

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SlideBase

Submitted by ChenLiang on Mon, 01/09/2017 - 11:33

Genomics consortia have produced large datasets profiling the expression of genes, micro-RNAs, enhancers and more across human tissues or cells. There is a need for intuitive tools to select subsets of such data that is the most relevant for specific studies. To this end, we present SlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders.

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The Porcine Translational Research Database

Submitted by ChenLiang on Sun, 09/10/2017 - 20:18

The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation.

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