GeneSifter™ Analysis Edition

Category Genomics>Gene Expression Analysis/Profiling/Tools and Cross-Omics>Next Generation Sequence Analysis/Tools

Abstract GeneSifter™ Analysis Edition is an advanced data analysis product. With it, Geospiza delivers complete end-to-end systems for data-intensive genetic analysis applications like microarrays and Next Gen sequencing-based transcription.

GeneSifter Analysis Edition helps biologists readily incorporate sophisticated data management and computational analysis into their research efforts. The results include improved quality and productivity in the experimental and decision-making processes.

Identifying Biological Significance --

To understand the biology underlying complex 'expression patterns' in microarray data, you must determine both the statistical and biological significance. GeneSifter’s unique ease-of-use enables you, the scientist, to explore the statistically significant interplay of your data with factors of biological relevance.

Note: GeneSifter's sophisticated statistical tools now support Next Gen data. The upcoming spring release will offer additional support for Next Gen - contact the manufacturer for more information.

Ease-of-Use -- GeneSifter offers award winning ease-of-use, enabling you to understand the biological significance of your data and draw meaningful conclusions quickly.

Within this easy-to-use analysis platform, you can produce comprehensive reports for over 30 types of validated data analysis techniques. Or, for fast results, you can use the manufacturer's One- Click Gene Summary™ merging the latest annotation from 11 independent sources.

Sophisticated Statistical Analysis -- Combined with its unique ease-of- use, GeneSifter offers a robust statistical framework with 15 advanced options, including 2-way ANOVA, PCA, PAM, hierarchical clustering, CLARA, false discovery rate (FDR), family wise error rate (FWER), RMA, Max T and more.

Through a web-based interface, GeneSifter provides “R” platform biostatistics and Integrated Gene Ontology (GO) and pathways analysis. For validation, MIAME-compliant protocols are also available.

Anytime, Anywhere Access -- GeneSifter provides its product through a secure web-based interface, offering convenience and performance. Keep your data secure with password protected access to your individual account or opt to share your findings worldwide through web- based collaboration - the choice is yours.

GeneSifter takes care of your data security and management with its state-of-the-art hosting facility and daily back-ups of your critical data.

Focus on the science, Not the software with the tools you need to understand the data:

1) Pairwise Analysis - Define two groups then apply normalization, statistical analysis and quality metrics to create lists of differentially expressed genes.

2) Filtering - Apply fold change cutoffs, statistical analysis and quality metrics to create lists of differentially expressed genes.

3) Interactive Scatter Plot - Provides visualization of the entire array data set and identification of individual genes.

4) Cluster Samples - Use hierarchical clustering to determine the relationship of samples based on a gene list.

5) Project Analysis - Define and analyze groups across multiple conditions.

6) Function Navigation - Rapidly identify and group genes based on function using Gene Ontology terms.

7) Ontology Report - Summarize the ontology terms for a gene list or use Z-Scores to assess biological significance.

8) Pattern Navigation - Define and identify patterns of gene expression with supervised clustering.

Biological analysis features include:

1) One-Click Gene Summary™ with information from, and links to, external databases such as Gene Ontology™, GenBank, UniGene, NetAffx™, Homologene, OMIM, Entrez Gene; 2) Pathway Report;

3) Z-score Report - automatically shows the most significant ontologies for your experiment;

4) Gene Ontology tree structures and individual designations extracted for visualization in One-Click Gene Summary™;

5) One-Click Gene Summary access to PubGene™ (see G6G Abstract Number 20251) for identification of putative relationships between genes based on scientific literature;

6) GeneCards™ (see G6G Abstract Number 20170) , PubGene™ and KEGG metabolic pathway diagrams for each gene on an array;

7) Automatic import of data from NCBI's Gene Expression Omnibus (GEO) (see G6G Abstract Number 20013) data repository;

8) Retrieve sequences and store as part of annotation for genes on array;

9) Enhanced metabolic pathways information and diagram links included in One-Click Gene Summaries;

10) UniGene and Entrez Gene organism-specific information automatically parsed and presented in One-Click Gene Summaries™;

11) Search, filter and group genes by chromosome, KEGG metabolic pathway, probe set ID, Gene Ontology (GO) biological process, molecular function or cellular component.

Supported Platforms --

1) Applied Biosystems - Capillary Electrophoresis and SOLiD Sequencers

2) Illumina - Genome Analyzer and iScan System for BeadArrays

3) Roche - Genome Sequencer FLX™ System and NimbleGen Array System

4) Affymetrix - GeneChip Microarray System

5) Helicos - Single Molecule Sequencer

File formats accepted -- GeneSifter accepts Affymetrix CHP files (native or text), CEL files, or tab-delimited text files, including the standard output from Illumina BeadStudio and Codelink Expression Analysis software.

Customers with data in Gene List formats that they have obtained from a GeneSifter enabled core lab can also analyze those results using GeneSifter Analysis Edition. Several of the upload tools also accept ZIP archives of the above file types.

System Requirements

GeneSifter will run on anything with a browser and connection to the Internet.


Manufacturer Web Site Geospiza, Inc.

Price Contact manufacturer.

G6G Abstract Number 20005A

G6G Manufacturer Number 101124