NDLI: Systematic reconstruction of splicing regulatory modules by integrating many RNA-seq datasets

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2011 IEEE International Conference on Systems Biology (ISB)

Contents

Robustness of CDK2 in triggering cellular senescence based on probability of DNA-damaged cells passing G1/S checkpoint

The role of GSH depletion in Resveratrol induced HeLa cell apoptosis

Inferring gene regulatory networks from multiple time course gene expression datasets

Predicting functional impact of single amino acid polymorphisms by integrating sequence and structural features

Kinetics of muller's ratchet from adaptive landscape viewpoint

NRProF: Neural response based protein function prediction algorithm

Pathogenesis of axial spondyloarthropathy in a network perspective

Copy number detection using self-weighted least square regression

Detecting protein complexes in PPI networks: The roles of interactions

Characterizing criticality of proteins by system dynamics

Extrinsic vs. intrinsic noises in phage lambda genetic switch

An edge based core-attachment method to detect protein complexes in PPI networks

Evaluating the denoising techniques in protein-protein interaction prediction

RNADAP—RNA-Seq data annotation pipeline

Application of an improved K-means algorithm in gene expression data analysis

Detecting B-cell lymphomas dysregulation modules based on molecular interaction network

The calibration method research for biology image

Time delay-accelerated transition of gene switch and -enhanced stochastic resonance in a bistable gene regulatory model

Phenotype-difference oriented identification of molecular functions for diabetes progression in Goto-Kakizaki rat

Identifying positional homologs as bidirectional best hits of sequence and gene context similarity

Comparative genomics revealed a novel DNA-binding regulatory protein involved in homologous recombination in bacteria

Protein interaction prediction for mouse pdz domains using dipeptide composition features

Antiallodynic effects of microglial interleukin-1β inhibition in the spinal cord

Analysis of gene expression profile triggered by signal peptide of eosinophil cationic protein

A general shape equation for local regular structure of biomolecular chains

Genomic signatures for metagenomic data analysis: Exploiting the reverse complementarity of tetranucleotides

Bifurcation of an epidemic model with sub-optimal immunity and saturated recovery rate

WinBEST-KIT for analyzing multilayer and multicellular systems

A modified newton's method for inverse problem of Probabilistic Boolean Networks with gene perturbations

Parallel-META: A high-performance computational pipeline for metagenomic data analysis

Floral structure and pollination in relation to fruit set in cynanchum otophyllum schneid

Synchronization feature of coupled cell-cycle oscillators

Identification of master regulator candidates for diabetes progression in Goto-Kakizaki Rat by a computational procedure

MicroRNA expression analysis reveals significant biological pathways in human prostate cancer

The preservation of bidirectional promoter architecture in Eukaryotes - Functional or co-regulation constraint?

Predicting MicroRNA targets by integrating sequence and expression data in cancer

Context-specific miRNA regulation network predicts cancer prognosis

Dynamics of HBV model with intermittent antiviral therapy

A linear programming model for identifying non-redundant biomarkers based on gene expression profiles

A quantitative framework of transcriptional dynamics by integrating multiple sources of knowledge

Stability analysis and simulation of an anti-HBV therapy mathematical model with time-delay immune response

Systematic reconstruction of splicing regulatory modules by integrating many RNA-seq datasets

Finding optimal control policy by using dynamic programming in conjunction with state reduction

Gradient-based high precision alignment of cryo-electron subtomograms

Discriminative random field approach to prediction of protein residue contacts

Dynamic remodeling of context-specific miRNAs regulation networks facilitate in silico cancer drug screening

Heavy metal tolerance of an antarctic bacterial Strain O5 and its antioxidant enzyme activity changes induced by $Cu^{2+}$

Evolutionary sequence divergence predicts protein sub-cellular localization signals

Global analysis of a general HBV infection model

Identifying biomarkers for acupuncture treatment via an optimization model

Parallel metabolomics of urine and serum revealed systematic alteration associated with renal disease

Neural fate decisions mediated by notch-delta signaling

A dynamical method to extract communities induced by low or middle-degree nodes

Cross-species identification of hydroxylation sites for ARD and FIH interaction

Analyzing time-course gene expression data using profile-state hidden Markov model

Intrinsic noise induced state transition in coupled positive and negative feedback genetic circuit

The early warning signal of complex diseases based on the network transition entropy

Identifying temporal trace of biological process during phase transition

Inferring domain-domain interactions using an extended parsimony model

An identification of secondary structure conserved elements in mammalian syntenic regions

Exploring drug combinations in a drug-cocktail network

Detecting coherent local patterns from time series gene expression data by a temporal biclustering method

Author index

Systematic reconstruction of splicing regulatory modules by integrating many RNA-seq datasets

Content Provider	IEEE Xplore Digital Library
Author	Chao Dai Wenyuan Li Liu, J. Zhou, X.J.
Copyright Year	2011
Description	Author affiliation: Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, 90089, USA (Wenyuan Li; Zhou, X.J.) \|\| School of Computer, Wuhan University, 430072, China (Chao Dai; Liu, J.)
Abstract	Alternative splicing is a ubiquitous gene regulatory mechanism that dramatically increases the complexity of the proteome. In this paper we study splicing module, which we define as a set of cassette exons co-regulated by the same splicing factors. We have designed a tensor-based approach to identify co-splicing clusters that appear frequently across multiple conditions, thus very likely to represent splicing modules - a unit in the splicing regulatory network. In particular, we model each RNA-seq dataset as a co-splicing network, where the nodes represent exons and the edges are weighted by the correlations between exon inclusion rate profiles. We apply our tensor-based method to the 19 co-splicing networks derived from RNA-seq datasets and identify an atlas of frequent co-splicing clusters. We demonstrate that these identified clusters represent splicing modules by validating against four biological knowledge databases. The likelihood that a frequent co-splicing cluster is biologically meaningful increases with its recurrence across multiple datasets, highlighting the importance of the integrative approach. We also demonstrate that the co-splicing clusters reveal novel functional groups which cannot be identified by co-expression clusters, and that the same exons can dynamically participate in different pathways depending on different conditions and different other exons that are co-spliced.
Starting Page	267
Ending Page	273
File Size	970820
Page Count	7
File Format	PDF
ISBN	9781457716614
e-ISBN	9781457716669
e-ISBN	9781457716652
DOI	10.1109/ISB.2011.6033164
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-09-02
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Tensile stress Correlation Databases Splicing Power capacitors Optimization
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Discovery of Protein–lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets

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