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Table of Contents
Intro; Preface; Contents; Contributors; Chapter 1: Non-coding RNA Resources; 1.1 Introduction; 1.2 ncRNA Annotation Resources; 1.2.1 miRBase; 1.2.2 NONCODE; 1.2.3 LNCipedia; 1.2.4 LNCat; 1.3 ncRNA-Associated Disease Resources; 1.3.1 HMDD; 1.3.2 miR2Disease; 1.3.3 LncRNADisease; 1.3.4 Lnc2Cancer; 1.4 ncRNA-Related Variants Resources; 1.4.1 dPORE-miRNA; 1.4.2 miRdSNP; 1.4.3 miRNASNP; 1.4.4 MirSNP; 1.4.5 PolymiRTS; 1.4.6 MicroSNiPer; 1.4.7 lncRNASNP; 1.4.8 LincSNP; 1.5 Other ncRNA Resources; 1.5.1 DIANA-LncBase; 1.5.2 ChIPBase; 1.5.3 LncRNA2Target; 1.6 Perspectives and Conclusion; References
Chapter 2: Systematic Identification of Non-coding RNAs2.1 Introduction; 2.2 Methods; 2.2.1 Identification of miRNAs; 2.2.2 Identification of lncRNAs; 2.3 Results; 2.3.1 miRNA Transcriptome Detected by Small RNA-seq Annotation; 2.3.2 Re-annotation of Microarray for Revealing lncRNAs; 2.3.3 Summaries of lncRNA Annotation Resources; 2.3.4 Construction of miRNA and lncRNA Expression Profiles in Heart Failure (Based on miRNA-seq and RNA-seq); 2.4 Concluding Remarks; References; Chapter 3: Functional Characterization of Non-coding RNAs Through Genomic Data Fusion; 3.1 Introduction; 3.2 Methods
3.2.1 MiRNA Expression Data Sets3.2.2 Identification of Orthologous miRNAs; 3.2.3 Construction of a Conserved miRNA Co-expression Network; 3.2.4 MiRNA Genomic Location, Cluster, Family, TF, Targets and Disease Information; 3.2.5 Gene Expression Data from miRNA Knockout/Transfection Experiments; 3.2.6 Functional Enrichment Analysis; 3.3 Results; 3.3.1 Construction of a Conserved miRNA Co-expression Network; 3.3.2 Functional Relationships Between Conserved Co-expressed miRNA Pairs; 3.3.3 Dysfunction of miRNA Cooperation in Disease; 3.4 Concluding Remarks; References
Chapter 4: Genomic-Scale Prioritization of Disease-Related Non-coding RNAs4.1 Introduction; 4.2 Expression-Based Technologies; 4.3 Biological Network-Based Technologies; 4.4 Known Disease-ncRNA Association-Based Technologies; 4.5 Integrated Strategy Based Technologies; 4.6 Conclusions; References; Chapter 5: Genome-Wide Mapping of SNPs in Non-coding RNAs; 5.1 Introduction; 5.2 Mapping SNPs in Human miRNA Targets; 5.3 Mapping Disease-Associated SNPs in lncRNAs; 5.4 Identification of SNPs ́Effects on lncRNA Structure; 5.5 Mapping Disease-Associated SNPs in lncRNA TFBSs
5.6 Perspectives and ConclusionReferences; 6: Profiling DNA Methylation Patterns of Non-coding RNAs (ncRNAs) in Human Disease; 6.1 Introduction; 6.2 Re-annotation of Data from the Infinium 450 k Array to Construct lncRNA Methylation Profiles; 6.2.1 Probe Mapping; 6.2.2 DNA Methylation Level Evaluating; 6.2.3 LncRNAs Methylation Profiles Constructing and Methylation Pattern Detecting; 6.3 Classifying lncRNA Methylation Patterns in Cancers; 6.3.1 A Strategy for Methylation Pattern Classifying; 6.3.2 Analysis of Repetitive Elements at lncRNA Promoters
Chapter 2: Systematic Identification of Non-coding RNAs2.1 Introduction; 2.2 Methods; 2.2.1 Identification of miRNAs; 2.2.2 Identification of lncRNAs; 2.3 Results; 2.3.1 miRNA Transcriptome Detected by Small RNA-seq Annotation; 2.3.2 Re-annotation of Microarray for Revealing lncRNAs; 2.3.3 Summaries of lncRNA Annotation Resources; 2.3.4 Construction of miRNA and lncRNA Expression Profiles in Heart Failure (Based on miRNA-seq and RNA-seq); 2.4 Concluding Remarks; References; Chapter 3: Functional Characterization of Non-coding RNAs Through Genomic Data Fusion; 3.1 Introduction; 3.2 Methods
3.2.1 MiRNA Expression Data Sets3.2.2 Identification of Orthologous miRNAs; 3.2.3 Construction of a Conserved miRNA Co-expression Network; 3.2.4 MiRNA Genomic Location, Cluster, Family, TF, Targets and Disease Information; 3.2.5 Gene Expression Data from miRNA Knockout/Transfection Experiments; 3.2.6 Functional Enrichment Analysis; 3.3 Results; 3.3.1 Construction of a Conserved miRNA Co-expression Network; 3.3.2 Functional Relationships Between Conserved Co-expressed miRNA Pairs; 3.3.3 Dysfunction of miRNA Cooperation in Disease; 3.4 Concluding Remarks; References
Chapter 4: Genomic-Scale Prioritization of Disease-Related Non-coding RNAs4.1 Introduction; 4.2 Expression-Based Technologies; 4.3 Biological Network-Based Technologies; 4.4 Known Disease-ncRNA Association-Based Technologies; 4.5 Integrated Strategy Based Technologies; 4.6 Conclusions; References; Chapter 5: Genome-Wide Mapping of SNPs in Non-coding RNAs; 5.1 Introduction; 5.2 Mapping SNPs in Human miRNA Targets; 5.3 Mapping Disease-Associated SNPs in lncRNAs; 5.4 Identification of SNPs ́Effects on lncRNA Structure; 5.5 Mapping Disease-Associated SNPs in lncRNA TFBSs
5.6 Perspectives and ConclusionReferences; 6: Profiling DNA Methylation Patterns of Non-coding RNAs (ncRNAs) in Human Disease; 6.1 Introduction; 6.2 Re-annotation of Data from the Infinium 450 k Array to Construct lncRNA Methylation Profiles; 6.2.1 Probe Mapping; 6.2.2 DNA Methylation Level Evaluating; 6.2.3 LncRNAs Methylation Profiles Constructing and Methylation Pattern Detecting; 6.3 Classifying lncRNA Methylation Patterns in Cancers; 6.3.1 A Strategy for Methylation Pattern Classifying; 6.3.2 Analysis of Repetitive Elements at lncRNA Promoters