You are here

Home

Gene Ontology

Gene ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) Maintain and develop its controlled vocabulary of gene and gene product attributes; 2) Annotate genes and gene products, and assimilate and disseminate annotation data; and 3) Provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. [Source: Wikipedia]

NONCODE

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

NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of ncRNAs, except transfer RNAs and ribosomal RNAs. (ii) All ncRNA sequences and their related information (e.g.

Rating: 
5
Average: 5 (2 votes)

DIANA-miRPath

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

DIANA-mirPath is a web-based computational tool developed to identify molecular pathways potentially altered by the expression of single or multiple microRNAs. The software performs an enrichment analysis of multiple microRNA target genes comparing each set of microRNA targets to all known KEGG pathways. The combinatorial effect of co-expressed microRNAs in the modulation of a given pathway is taken into account by the simultaneous analysis of multiple microRNAs.

Rating: 
4
Average: 4 (1 vote)

g:Profiler

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

g:Profiler (http://biit.cs.ut.ee/gprofiler/) is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology (GO), pathway, or transcription factor binding site enrichments down to individual gene levels.

Rating: 
5
Average: 5 (2 votes)

SigTerms

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

MicroRNAs are short (approximately 22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches.

Rating: 
Average: 5 (1 vote)

miRo

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

miRò is a web-based knowledge base that provides users with miRNA-phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities. The main goal of miRò is the establishment of a knowledge base which allows non-trivial analysis through sophisticated mining techniques and the introduction of a new layer of associations between genes and phenotypes inferred based on miRNAs annotations.

Rating: 
Average: 5 (1 vote)

Empirical GO

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

Many studies have investigated the differential expression of microRNAs (miRNAs) in disease states and between different treatments, tissues and developmental stages. Given a list of perturbed miRNAs, it is common to predict the shared pathways on which they act. The standard test for functional enrichment typically yields dozens of significantly enriched functional categories, many of which appear frequently in the analysis of apparently unrelated diseases and conditions.

Rating: 
Average: 5 (1 vote)

Linc2GO

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

Large numbers of long intergenic non-coding RNA (lincRNA) have been detected through high-throughput sequencing technology. However, currently we still know very little about their functions. Therefore, a lincRNA function annotation database is needed to facilitate the study in this field. In this article, we present Linc2GO, a web resource that aims to provide comprehensive functional annotations for human lincRNA.

Rating: 
3
Average: 3 (2 votes)

miR2GO

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

miR2GO is a web-based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO and miRpair2GO. miRmut2GO implements a knowledge-based method to assess the functional effects of genetic and somatic mutations in microRNA seed regions. The functional effects of a mutation are analysed by semantic comparison of enriched gene ontology (GO) annotations of the target gene sets for the wild-type and mutated alleles.

Rating: 
Average: 5 (1 vote)

mdgsa

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

Functional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis Nevertheless, major limitations of this approach have already been described at the gene level, while some newer arise in the miRNA scenario.Here, we propose an enhanced methodology that builds on the well-established gene set analysis paradigm.

Rating: 
5
Average: 5 (2 votes)

CHNmiRD

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

MicroRNAs (miRNAs) play an important role in the development and progression of human diseases. The identification of disease-associated miRNAs will be helpful for understanding the molecular mechanisms of diseases at the post-transcriptional level. Based on different types of genomic data sources, computational methods for miRNA-disease association prediction have been proposed.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to Gene Ontology