Search Results for "gene regulatory networks"
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Showing 57 open source projects for "gene regulatory networks"
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC... -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
The Boolean implication networks outperformed Bayesian networks, Pearson’s correlation networks, and other Boolean networks in constructing genome-scale co-expression networks evaluated with comprehensive biological pathways and Gene Ontology in MSigDB. References: Guo NL, Wan YW. Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artificial Intelligence in Medicine 2012 Jun;55(2):97-105. Ye Q, Singh S, Qian PR, Guo NL... -
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TSMiner is a software program for reconstructing time-specific regulatory networks for time-series expression data. TSMiner has three key modules: first, predicting the time-specific activated/repressed transcription factors (TFs); second, predicting the biological pathways associated with the predicted TFs; third, merging the TFs and pathways into time-specific regulatory networks. TSMiner provides extensive interactive operations to help users explore the results of each module. For example...
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data... -
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PPIXpress
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal... -
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RWRMTN
Predicting disease-associated miRNAs on a miRNA-target gene network
The misregulations of microRNA have been shown the contribution to diseases. Recently, we have proposed a computational method based on a random walk framework on a microRNA-target gene network to predict disease-associated microRNAs. This was shown superior when compared to existing state-of-the-art network- and machine learning-based methods since it well exploits mutual regulation between miRNAs and their target genes in microRNA-target gene networks. To facilitate the use of this method... -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein... -
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MPICorMat
Parallel tool to construct correlation similarity matrices
MPICorMat is a parallel tool to construct correlation similarity matrices as part of the procedure to generate gene co-expression networks. This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of the first module of the RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). RMTGeneNet users can exchange this CCM module by MPICorMat, benefit from its fast computation to generate the similarity... -
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OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.
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Grinn
graph database and R package for omic data integration
http://kwanjeeraw.github.io/grinn/ -
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We introduce a nonparametric Bayesian clustering method for inhomogeneous Poisson processes to detect heterogeneous binding patterns of multiple proteins including transcription factors. The estimated protein clusters form regulatory modules in different chromatin states, which help explain how proteins work together in regulating gene expression. We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins...
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PD_BiochemicalSystemsTheory
A model of Parkinson’s disease using biochemical systems theory
Major pathways involving in Parkinson's disease (PD) such as alphasynuclein aggregation, dopamine synthesis, lewy body formation, tau phosphorylation, parkin, and apoptosis were modeled using stochastic differential equations. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. The model allows a qualitative analysis of PD... -
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EDCC-CNG
Exploration and categorization of CREs and CRMs
Cis-regulatory elements (CREs) and cis-regulatory modules (CRMs) play an important role in temporal and spatial regulation of gene expression, which is a common process in eukaryotic organisms. We developed two programs that serve as exploratory tools in the analysis of CRM-mediated control of gene expression: “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG). EDCC correlates the presence and positions of CREs/CRMs with gene expression data and identifies... -
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MPIGeneNet
Parallel tool to construct gene co-expression networks
MPIGeneNet is a parallel tool to construct gene co-expression networks using Pearson’s correlation and Random Matrix Theory (RMT). This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). MPIGeneNet integrates the whole procedure of creating the in one program, which makes the tool easier to work with (the users only have to launch... -
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AccNET
AccNET: Accessory Genome Constellation Network.
AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical... -
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... modularity and robustness is conserved in a large set of randomly structured networks. The app provides various visualization modes to better elucidate topological relations between modules, and tabular results of centrality and gene ontology enrichment analyses of modules.
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STON
Translator of SBGN PD and AF maps into Neo4j graph database.
STON, Sbgn TO Neo4j, is a Java-based framework that imports and translates metabolic, signalling and gene regulatory pathways presented in SBGN (Systems Biology Graphical Notation, http://www.sbgn.org) Process Description (PD) and Activity Flow (AF) languages to a graph-oriented format compatible with Neo4j (http://neo4j.com/). STON1.2 allows also to link common processes between two different PD maps. This framework uses two sets of libraries: LibSBGN and Neo4j libraries... -
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BaseNet
Bacterial sRNA analysis tool
Perform gene expression profiling and predict novel sRNAs and automatically correlate co-differentially expressed sRNA-mRNA pairs to enhance target prediction and construct sRNA-mediated regulatory network. -
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came
Identification of chromatin accessibility from NOMe-seq
Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. However... -
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GenNet
A Tool for Qualitative and Quantitative Modeling of Gene Regulatory Ne
A Tool for Qualitative and Quantitative Modeling of Gene Regulatory Networks. GenNet is a Java based tool called that facilitate the model checking user by providing a unique GUI layout for both qualitative and quantitative modeling of GRNs. GenNet also assists the modeling users by providing some extra features i.e. CTL editor, parameters filtering and input/output files management. Download pre-installed GenNet Virtual Box Image here https://www.dropbox.com/s/9ryvs1f22zc181y/GenNet-1.3.28... -
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CoGA
R package for differential co-expression analysis
CoGA (Co-expression Graph Analyzer) is an R package to identify differentially co-expressed gene sets between two phenotypes. The software infers gene regulatory networks from gene expression data, and compares structural properties of the inferred networks based on their spectrum distributions. It also compares the networks in terms of their gene centralities, clustering coefficients and shortest path lengths. In addition to the differential co-expression analyses, the tool provides graphical... -
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nagnag
Identifyng and Quantifying NAGNAG Alternative Splicing
The NAGNAG alternative splicing is a regulatory process that controls the mRNA splicing from one gene. NAGNAG alternative splicing has attracted intensive attentions for last decades because of its unique property: inclusion or exclusion of three nucleotides results in difference of one or two amino acids in the final proteins. -
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DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
Living cells are complex, dynamic, self-regulatory, interactive systems, showing differential states across time and space. Complexity of cellular systems is highlighted with the multi-layered regulatory mechanisms involving the interactions between bio-molecules (such as DNA, RNA, mi-RNA and proteins). These interactions are analyzed in the form of static networks. Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid... -
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Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.