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Showing posts with label Gene expression database. Show all posts

Partek Express: Gene expression analysis Software

Partek Express is a streamlined, easy to use software analysis tool designed for scientists who are new to gene expression analysis. Partek Express will guide you through easily setting-up robust and powerful statistics tests to identify genes whose expression is changed across different experimental variables or combination of variables.

The software supports complex experimental designs with multiple experimental variables including paired designs. Also, technical variables, such as batch effects or operator differences, are automatically controlled. All analysis methodologies are fully disclosed with references to streamline authoring of a methods section of a pending publication.

Benefits of Partek Express for Your Gene Expression Data:
Identify outliers samples for quality control
Use visualization to see how your samples group together and define how each phenotype contributes to the overall expression profile
Find and visualize the genes that change across specific experimental variables or a combination of variables
Determine the optimal degree of replication using power analysi.

Software Link: Partek Express: Gene expression analysis Software

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Designed for expression profiling applications

The Agilent MassHunter Profiling software is specifically designed for expression profiling applications such as biomarker discovery. MassHunter Profiling software uses a unique feature extraction and correlation algorithm, that does a better job of locating all the components in even very complex peptide mixtures.

Features:
Unique feature extraction and correlation algorithm locates molecular features, not just chromatographic peaks
Visualization tools allow the identification of statistically meaningful differences between sample groups (e g., healthy versus disease)
Calculates abundance ratios and clearly identifies differentially expressed features
Flexible feature selection allows user selection of comparison criteria
Exports profile data for statistical data analysis by Agilent's GeneSpring MS software, other database search programs, identification environments, or statistical analysis packages
Supports additional workflows including pharmaceutical impurity analysis, forensic analysis, environmental analysis, and pesticide analysis

Software Link : Agilent MassHunter Profiling software - Expression profiling Software

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The foundation of Gene Logic's ToxExpress® Program is our ToxExpress® System. Developed in collaboration with major pharmaceutical companies, the ToxExpress® System is the largest database of its kind, comprised of over 14,000 individual vehicle and normal control and drug-treated animal tissue samples. A consortium of our customers stringently evaluates compound selection, study protocols, and in-life data, resulting in a consistent, robust database that serves as a premier reference source for both gene expression and related in-life toxicology data.

The ToxExpress® System is designed to help extensively characterize compounds, to facilitate the drug development process and aid in decision-making. The ToxExpress® System supports end-user research efforts and extensive knowledge building in four major areas:

Investigative Toxicology
Predictive Toxicology
Mechanistic Toxicology
Safety Biomarker Discovery

Software Link: ToxExpress - Gene expression database

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The Biomax Oncology Base is the first comprehensive index of virtually all published cancer-related genes (over 6000) and their associations to diseases and drug compounds. It is constructed from a mixture of automatic text mining of MEDLINE abstracts (using the BioLT Literature Mining Tool), semi-automatic verification, and manual validation and scoring of results. For each manually validated cancer gene, annotators read all the cancer-term-associated and drug-term-associated statements and add structured, controlled vocabularies describing the gene's role in the cancer and the associated evidence.

Integrates project data with clinical data and experimental data using the BioXM Knowledge Management Environment

Searches for networks of relationships and candidate genes
Connects information related to clinical conditions to the field of molecular biology
Finds connections between cancer sub-types, genes and compounds

Software Link: Biomax Oncology Base - Cancer Gene Databas

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The PEDANT Genome Database is a comprehensive collection of completely annotated genomes which enables users to explore and compare organisms previously analyzed with the Pedant-Pro Sequence Analysis Suite.

Software Link: PEDANT Genome Database

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The BioExpress® System offers in a single platform, all of the phenotypic, clinical and experimental information which is coupled seamlessly with high-quality Affymetrix GeneChip® microarray data. Unique software analysis tools enable researchers to maximize the benefit of the BioExpress® System data to quickly reach powerful conclusions.

You can access the BioExpress® System through flexible subscription terms that take into account your specific needs. You can choose a full subscription to the entire BioExpress® System or select specific sample subsets relevant to your therapeutic area of research. In addition to accessing the human and animal tissues and cell line samples, subscriptions also include on-site training and use of the Genesis Enterprise System® Software for enterprise-wide, rigorous, open-ended data mining and analysis.

The BioExpress® System offers data sets in therapeutic areas that accelerate today's most compelling research needs:

Oncology Suite
The BioExpress® Oncology Suite contains gene expression data from primary, metastatic, and benign tumor samples, and normal samples, including matched adjacent controls. The suite includes valuable hematological malignancy samples for many well-known cancers.

Inflammation Suite
The BioExpress® Inflammation Suite contains gene expression profiles for both autoimmune and inflammatory diseases. Due to the complex nature of inflammatory processes, targeted diseases represented in the BioExpress® Inflammation Suite include a combination of human clinical samples, animal models of disease development, and cellular systems.

Cardiovascular Suite
The BioExpress® Cardiovascular Suite is a large-scale, comprehensive reference data set consisting of gene expression profiles, clinical annotations, and histopathology information derived from the analysis of our collection of human tissues and complementary animal models related to cardiac and vascular diseases.

Central Nervous System Suite
The BioExpress® Central Nervous System (CNS) Suite is a large scale, comprehensive reference data set consisting of gene expression profiles, clinical annotations, and pathological information data derived from our collection of high-quality, well-documented psychiatric and neurodegenerative diseased human brain tissues and complementary animal models.

Metabolic Suite
The BioExpress® Metabolic Disorders Suite contains gene expression profiles for Type 2 diabetes, obesity, and metabolic syndromes. The data set contains several well-defined case study experiments involving animal and cell models.

Human Atlas Suite
The BioExpress® Atlas Reference Data Suite is a genomic database containing gene expression information gathered from a broad range of exceptionally high-quality normal human, mouse, and rat tissues. The BioExpress® Atlas Reference Data Suite allows the rapid determination of tissue specificity and range of gene expression profiles for genes of interest across the most relevant normal human organs and tissues and control animal models.

Software Link: BioExpress - Gene expression database