Curator Dashboard

PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologs (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene. We brought this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indexes (NCBI Gene), and by the use of associated orthology relationships (HomoloGene). PhenomicDB is thought as a first step towards comparative phenomics and will improve the understanding of the gene functions by combining the knowledge about phenotypes from several organisms. It is not intended to compete with the much more dedicated primary source databases but tries to compensate its partial loss of depth by linking back to the primary sources. The basic functional concept of PhenomicDB is an integrated meta-search-engine for phenotypes. Users should be aware that comparison of genotypes or even phenotypes between organisms as different as yeast and man can have serious scientific hurdles. Nevertheless finding that the phenotype of a given mouse gene is described as ��similar to psoriasis�� and at the same time that the human ortholog has been described as a gene causing skin defects can lead to novelty and interesting hypotheses. Similarly, a gene involved in cancer in mammalian organisms could show a proliferation phenotype in a lower organism such as yeast and thus, give further insights to a researcher.

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• SciCrunch
• 17 years ago - by Anonymous

Software designed to detect single nucleotide variants from next generation sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

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• SciCrunch
• 13 years ago - by Anonymous

Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

It consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites. The literature based information in RegTransBase is a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains various types of experimental data, in particular: * the activation or repression of transcription by an identified direct regulator * determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA * mapping or prediction of binding sites for a regulatory protein * characterization of regulatory mutations The analysis section of RegtransBase is based on a set of manually curated alignments of transcription factor binding sites and allows you to search for new binding sites and verify conservation of bindings sites across multiple species through the use of web based analysis tools.

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• SciCrunch
• 17 years ago - by Anonymous

Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).

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• SciCrunch
• 13 years ago - by Anonymous

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.

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• SciCrunch
• 13 years ago - by Anonymous

A C++ software program for multipoint IBD estimation based on high density SNP genotype data.

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• SciCrunch
• 13 years ago - by Anonymous

Project to study human gene expression and regulation in multiple tissues, providing valuable insights into mechanisms of gene regulation and its disease related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. Includes initiatives: Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis ,Laboratory, Data Analysis, and Coordinating Center (LDACC), caHUB Acquisition of Normal Tissues in Support of GTEx Project.

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• SciCrunch
• 13 years ago - by Anonymous

Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.

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• 13 years ago - by Anonymous

A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.

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• SciCrunch
• 13 years ago - by Anonymous

An Algorithm based on a BivAriate CUmulative Statistic to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.

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• 13 years ago - by Anonymous

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

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• SciCrunch
• 13 years ago - by Anonymous

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

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• SciCrunch
• 13 years ago - by Anonymous

A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.

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• SciCrunch
• 13 years ago - by Anonymous

AUTOmated server for predicting functional consequences of amino acid MUTations in protEins.

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• SciCrunch
• 13 years ago - by Anonymous

Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

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• SciCrunch
• 17 years ago - by Anonymous