You are here

Home

Dead

siRNAs with high specificity to the target

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

'Off-target' silencing effect hinders the development of siRNA-based therapeutic and research applications. Common solution to this problem is an employment of the BLAST that may miss significant alignments or an exhaustive Smith-Waterman algorithm that is very time-consuming. We have developed a Comprehensive Redundancy Minimizer (CRM) approach for mapping all unique sequences ("targets") 9-to-15 nt in size within large sets of sequences (e.g. transcriptomes). CRM outputs a list of potential siRNA candidates for every transcript of the particular species.

Rating: 
Average: 5 (1 vote)

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.

Rating: 
Average: 5 (1 vote)

AraPath

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

Studying plants using high-throughput genomics technologies is becoming routine, but interpretation of genome-wide expression data in terms of biological pathways remains a challenge, partly due to the lack of pathway databases. To create a knowledgebase for plant pathway analysis, we collected 1683 lists of differentially expressed genes from 397 gene-expression studies, which constitute a molecular signature database of various genetic and environmental perturbations of Arabidopsis.

Rating: 
Average: 5 (1 vote)

application in consensus ranking of microRNA targets

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

MicroRNAs are very recently discovered small noncoding RNAs, responsible for negative regulation of gene expression. Members of this endogenous family of small RNA molecules have been found implicated in many genetic disorders. Each microRNA targets tens to hundreds of genes. Experimental validation of target genes is a time- and cost-intensive procedure. Therefore, prediction of microRNA targets is a very important problem in computational biology.

Rating: 
Average: 5 (1 vote)

ed_scan

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

Growing evidence demonstrates that local well-ordered structures are closely correlated with cis-acting elements in the post-transcriptional regulation of gene expression. The prediction of a well-ordered folding sequence (WFS) in genomic sequences is very helpful in the determination of local RNA elements with structure-dependent functions in mRNAs.

Rating: 
Average: 5 (1 vote)

DSTHO

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

Existing treatments of human cancer, which is characterized by abnormal proliferation of cells often lead to fatal outcomes. Sequence selective silencing of oncogene expression using siRNA technology is emerging as a potential solution for cancer treatment. The exclusive selectivity and easy application to virtually any therapeutic target including intracellular factors and transcription factors renders siRNA oligonucleotide applications very promising. However, synthesis of siRNA having sufficient knockdown efficiency is laborious and cost intensive.

Rating: 
Average: 5 (1 vote)

EGs

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

A set of genes and their gene expression levels are used to classify disease and normal tissues. Due to the massive number of genes in microarray, there are a large number of edges to divide different classes of genes in microarray space. The edging genes (EGs) can be co-regulated genes, they can also be on the same pathway or deregulated by the same non-coding genes, such as siRNA or miRNA. Every gene in EGs is vital for identifying a tissue's class. The changing in one EG's gene expression may cause a tissue alteration from normal to disease and vice versa.

Rating: 
Average: 5 (1 vote)

BiCliques Merging

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

MicroRNAs (miRNAs) are post-transcriptional regulators that repress the expression of their targets. They are known to work cooperatively with genes and play important roles in numerous cellular processes. Identification of miRNA regulatory modules (MRMs) would aid deciphering the combinatorial effects derived from the many-to-many regulatory relationships in complex cellular systems. Here, we develop an effective method called BiCliques Merging (BCM) to predict MRMs based on bicliques merging.

Rating: 
4
Average: 4 (2 votes)

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.

Rating: 
Average: 5 (1 vote)

OligoMatcher

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

OligoMatcher is a web-based tool for analysis and selection of unique oligonucleotide sequences for gene silencing by antisense oligonucleotides (ASOs) or small interfering RNA (siRNA). A specific BLAST server was built for analysing sequences of ASOs that target pre-mRNA in the cell nucleus. Tissue- and cell-specific expression data of potential cross-reactive genes are integrated in the OligoMatcher program, which allows biologists to select unique oligonucleotide sequences for their target genes in specific experimental systems.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to Dead