ArticleNucleic acids research2014
SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Exploration of prognosis and immunometabolism landscapes in ER+ breast cancer based on a novel lipid metabolism-related signature.Frontiers in immunology · 2023Article
- ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events.Genomics, proteomics & bioinformatics · 2022Article
- A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data.Methods (San Diego, Calif.) · 2021Article
- A general index for linear and nonlinear correlations for high dimensional genomic data.BMC genomics · 2020Article
- Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis.BMC genomics · 2019Article
- Gene co-expression analysis for functional classification and gene-disease predictions.Briefings in bioinformatics · 2018Article
- Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples.PloS one · 2018Article
- Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing.Current protocols in bioinformatics · 2017Article
- Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models.Human molecular genetics · 2016Article
- A Network of Splice Isoforms for the Mouse.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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Abstract
Conventionally, overall gene expressions from microarrays are used to infer gene networks, but it is challenging to account splicing isoforms. High-throughput RNA Sequencing has made splice variant profiling practical. However, its true merit in quantifying splicing isoforms and isoform-specific exon expressions is not well explored in inferring gene networks. This study demonstrates SpliceNet, a method to infer isoform-specific co-expression networks from exon-level RNA-Seq data, using large dimensional trace. It goes beyond differentially expressed genes and infers splicing isoform network changes between normal and diseased samples. It eases the sample size bottleneck; evaluations on simulated data and lung cancer-specific ERBB2 and MAPK signaling pathways, with varying number of samples, evince the merit in handling high exon to sample size ratio datasets. Inferred network rewiring of well established Bcl-x and EGFR centered networks from lung adenocarcinoma expression data is in good agreement with literature. Gene level evaluations demonstrate a substantial performance of SpliceNet over canonical correlation analysis, a method that is currently applied to exon level RNA-Seq data. SpliceNet can also be applied to exon array data. SpliceNet is distributed as an R package available at http://www.jjwanglab.org/SpliceNet.
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