• ToppGene Suite

  • Referenced in 5 articles [sw30169]
  • Suite for gene list enrichment analysis and candidate gene prioritization. ToppGene Suite (http://toppgene.cchmc.org; this ... enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification ... interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure ... PPIN)-based disease candidate gene prioritization uses social and Web networks analysis algorithms (extended versions...
  • SNPs3D

  • Referenced in 5 articles [sw30035]
  • about the relationships between sets of candidate genes. The third module analyzes the likely impact ... SNPs on protein function. Disease/candidate gene relationships and gene-gene relationships are derived from ... context, mouse knockout information and papers. Gene-gene interactions are presented in an interactive graphical ... impact analysis, a knowledge based network of gene relationships and candidate genes, and access...
  • FREGAT

  • Referenced in 0 articles [sw18946]
  • Several approaches to the region-based association analysis of quantitative traits have recently been developed ... association studies of quantitative traits and candidate gene analysis. FREGAT offers many useful options...
  • SoDA2

  • Referenced in 3 articles [sw23149]
  • candidates for a given Ig gene, but have different consequences in an analysis ... used to compute the posterior probabilities of candidate rearrangements and to find those with...
  • MLPAstats

  • Referenced in 1 article [sw18851]
  • package for the integrated analysis of copy number alterations using MLPA data. Background: Multiplex-Dependent ... candidate gene studies, aimed at the identification of copy number alterations. The analysis of such ... integrate the methods for exploring different analysis scenarios in a reliable ... analysis tool that promotes the use of cost-effective MLPA suitable for candidate gene studies...
  • dmGWAS

  • Referenced in 2 articles [sw29291]
  • candidate genes, including some well-studied genes not detected in the single-marker analysis...
  • ProDiGe

  • Referenced in 2 articles [sw12407]
  • genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide ... tens or hundreds of disease gene candidates, the identification of disease genes among the candidates...
  • Signal-3L

  • Referenced in 16 articles [sw26857]
  • finding new drugs or reprogramming cells for gene therapy. To effectively and timely use such ... composition spaces; (2) selecting a set of candidates for the possible signal peptide cleavage sites ... alignment outcome for each of the aforementioned candidates through a voting system. Signal ... hence is particularly useful for the analysis of large-scale datasets. Signal-3L is freely...
  • ProMiR II

  • Referenced in 3 articles [sw29582]
  • ratio, conservation score and entropy of candidate sequences, for more controllable prediction of miRNAs ... services, e.g. the prediction of miRNA genes in long nonrelated sequences such as viral genomes ... structured in the MySQL database for efficient analysis. The ProMiR II web server is available...
  • antiSMASH

  • Referenced in 1 article [sw17019]
  • rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal ... cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes ... rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens ... Here, we present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable...
  • MetaOmics

  • Referenced in 1 article [sw16608]
  • differentially expressed gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides ... criteria for meta-analysis. MetaDE and MetaPath were developed for candidate marker and pathway detection...
  • MOPAC

  • Referenced in 2 articles [sw02841]
  • experiments comes from DNA Microarray analysis of the bacterium E. coli in response to recovery ... upregulated genes and will not be present in the upstream regions of genes that showed ... genes and not present in the control set, which is the set of genes whose ... regulated genes under different control mechanisms among the co-expressed genes, we do not want...
  • GSPPCA

  • Referenced in 4 articles [sw25977]
  • probabilistic PCA. Sparse versions of principal component analysis (PCA) have imposed themselves as simple ... allows to find a path of candidate models using a variational expectation-maximization algorithm ... shown to infer biologically relevant subsets of genes. According to a metric based on pathway...
  • FUNC

  • Referenced in 2 articles [sw16930]
  • gene candidates, which must then be further analysed and interpreted. Information about these genes ... ontologies, such as the Gene Ontology. Relationships between the gene sets identified by experimental methods ... available methods to identify significant associations between gene sets and ontological annotations. Implemented are several ... versatile and useful tool for the analysis of genome-wide data. It is freely available...
  • MiRFinder

  • Referenced in 3 articles [sw29577]
  • important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important ... hairpin candidates and 2) exclusion of the non-robust structures based on analysis...
  • CGMIM

  • Referenced in 2 articles [sw30050]
  • identify genetically-associated cancers and candidate genes. Background: Online Mendelian Inheritance in Man (OMIM ... computerized database of information about genes and heritable traits in human populations, based on information ... There were 45 genes related to cancer of the esophagus, 121 genes related to cancer ... stomach, and 21 genes related to both. Analysis of CGMIM results indicate that fewer than...
  • GeneLibrarian

  • Referenced in 1 article [sw30046]
  • GeneLibrarian generates a summarized viewgraph of candidate genes for a user based on his/her preference ... algorithm and Gene Ontology-based clustering method to enable the discovery of gene relations. Conclusion ... expanding the number of potential genes for further analysis. This study concentrates on providing well...
  • REGANOR

  • Referenced in 1 article [sw23031]
  • allow for a meaningful comparative analysis, gene prediction of the various genomes should ... state of genome annotation requires automated gene identification methods to cope with the influence ... high-quality gene predictions. The web server is a resource for gene identification in prokaryote ... previously described, accurate gene finding method REGANOR. We also provide novel gene predictions...
  • R

  • Referenced in 7624 articles [sw00771]
  • R is a language and environment for statistical...
  • TSPLIB

  • Referenced in 653 articles [sw00983]
  • TSPLIB is a library of sample instances for...