scholarly journals A bioinformatics framework for the identification of active regulatory elements through the integrative analysis of high-throughput genomic data

2012 ◽  
Vol 18 (A) ◽  
pp. 45
Author(s):  
G Malagoli Tagliazucchi ◽  
A Miccio ◽  
A Cavazza ◽  
V Poletti ◽  
C Peano ◽  
...  
Keyword(s):  
High Throughput ◽  
Genomic Data ◽  
Regulatory Elements ◽  
Integrative Analysis

Latent feature decompositions for integrative analysis of diverse high-throughput genomic data

2012 ◽  
Author(s):  
Karl B. Gregory ◽  
Kevin R. Coombes ◽  
Amin Momin ◽  
Luc Girard ◽  
Lauren A. Byers ◽  
...  
Keyword(s):  
High Throughput ◽  
Genomic Data ◽  
Integrative Analysis

scholarly journals Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

2012 ◽  
Vol 40 (19) ◽  
pp. 9379-9391 ◽  
Author(s):  
Shihua Zhang ◽  
Chun-Chi Liu ◽  
Wenyuan Li ◽  
Hui Shen ◽  
Peter W. Laird ◽  
...  
Keyword(s):  
Genomic Data ◽  
Integrative Analysis

scholarly journals HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

2014 ◽  
Vol 15 (1) ◽  
pp. 280 ◽  
Author(s):  
Huihuang Yan ◽  
Jared Evans ◽  
Mike Kalmbach ◽  
Raymond Moore ◽  
Sumit Middha ◽  
...  
Keyword(s):  
High Throughput ◽  
Integrative Analysis

scholarly journals SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool

2014 ◽  
Vol 2014 ◽  
pp. 1-4 ◽  
Author(s):  
Santosh Kumar Upadhyay ◽  
Shailesh Sharma
Keyword(s):  
Operating Systems ◽  
High Throughput ◽  
Genomic Data ◽  
Prediction Tool ◽  
High Demand ◽  
Specific Target ◽  
Target Sites ◽  
High Throughput Detection ◽  
User Friendly

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.

scholarly journals Functional characterization of splicing regulatory elements

2021 ◽  
Author(s):  
Scott I Adamson ◽  
Lijun Zhan ◽  
Brenton R Graveley
Keyword(s):  
High Throughput ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Small Subset ◽  
General Sequence ◽  
Splicing Regulators ◽  
Splicing Regulatory Elements

Background: RNA binding protein-RNA interactions mediate a variety of processes including pre-mRNA splicing, translation, decay, polyadenylation and many others. Previous high-throughput studies have characterized general sequence features associated with increased and decreased splicing of certain exons, but these studies are limited by not knowing the mechanisms, and in particular, the mediating RNA binding proteins, underlying these associations. Results: Here we utilize ENCODE data from diverse data modalities to identify functional splicing regulatory elements and their associated RNA binding proteins. We identify features which make splicing events more sensitive to depletion of RNA binding proteins, as well as which RNA binding proteins act as splicing regulators sensitive to depletion. To analyze the sequence determinants underlying RBP-RNA interactions impacting splicing, we assay tens of thousands of sequence variants in a high-throughput splicing reporter called Vex-seq and confirm a small subset in their endogenous loci using CRISPR base editors. Finally, we leverage other large transcriptomic datasets to confirm the importance of RNA binding proteins which we designed experiments around and identify additional RBPs which may act as additional splicing regulators of the exons studied. Conclusions: This study identifies sequence and other features underlying splicing regulation mediated specific RNA binding proteins, as well as validates and identifies other potentially important regulators of splicing in other large transcriptomic datasets.

scholarly journals High-throughput identification of long-range regulatory elements and their target promoters in the human genome

2013 ◽  
Vol 41 (9) ◽  
pp. 4835-4846 ◽  
Author(s):  
Yih-Chii Hwang ◽  
Qi Zheng ◽  
Brian D. Gregory ◽  
Li-San Wang
Keyword(s):  
Human Genome ◽  
Long Range ◽  
High Throughput ◽  
Regulatory Elements ◽  
Target Promoters

scholarly journals Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns

2018 ◽  
Vol 9 ◽  
Author(s):  
Jinyu Chen ◽  
Shihua Zhang
Keyword(s):  
Genomic Data ◽  
Integrative Analysis

scholarly journals Robust Selection of Cancer Survival Signatures from High-Throughput Genomic Data Using Two-Fold Subsampling

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e108818 ◽  
Author(s):  
Sangkyun Lee ◽  
Jörg Rahnenführer ◽  
Michel Lang ◽  
Katleen De Preter ◽  
Pieter Mestdagh ◽  
...  
Keyword(s):  
High Throughput ◽  
Cancer Survival ◽  
Genomic Data ◽  
Selection Of
Sign in / Sign up

Export Citation Format

Share Document