Category Cross-Omics>Data/Text Mining Systems/Tools

Abstract GENECHASER is a gene-specific search tool that can be used to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.

It automatically reannotates and analyzes all Gene Expression Omnibus (GEO) data sets (GDS) (see G6G Abstract Number 20013), performs all group versus group comparisons, identifies all experimental conditions where the 'expression levels' of a gene or set of genes is significantly changed, and displays them graphically with statistical comparisons and sort/filter functions.

GENECHASER also provides access to the raw data in the original studies.

GENECHASER has the ability to analyze all GEO data sets in an automated way to quickly deliver 'gene expression profiles' under 12,658 experimental conditions across all species to the hands of biologists and clinicians without bioinformatics skills.

To create the database that GENECHASER accesses the manufacturer downloaded and parsed all SOFT files of GDS into a relational database using AILUN (see G6G Abstract Number 20400).

The manufacturer saved all performed comparisons via AILUN, in a table in MySQL database, which contains 12,658 comparisons.

All differentially expressed genes along with their q values, fold changes, and rank percentiles were saved in a table, which contains 28 million entries.

The whole process from data downloads, platform annotation, and gene identification, to database development was fully automated.

GENECHASER Single Gene Search -- In single gene search, the input is a gene identifier, such as a gene symbol.

For example, a search for "Nanog" returns a list of matching IDs from 'Entrez Gene' and Homologene.

Clicking an 'Entrez Gene ID' returns experimental conditions in a single species, while clicking a 'Homologene ID' returns experimental conditions in all species.

For example, Nanog was measured in 5,706 comparisons, and differentially expressed in 217 (q = 0.05, fold > 2).

Each row in the output table lists Nanog expression in an identified comparison, and includes the rank of comparison, species, study title, a color bar representing the significance of the comparison, comparison type, fold change, rank percentile among all changing genes with q- value = 0.2 in the comparison, and q-value.

The color represents the q-value, with redder colors indicating higher significance.

Bar length represents fold change with longer lengths for larger changes. Bar width represents rank percentile with greater widths for higher percentiles.

Clicking on the title opens the original study with the raw GEO data. Clicking on the colored bar opens the original expression values for the probe in GEO, including present/absent calls for Affymetrix arrays.

The two groups under comparison are listed under the color bar.

For example, the first row indicates that Nanog was 1000-fold up- regulated (q = 0.006, rank = 0.2%ile) in embryonic stem cell compared to hematopoietic stem cell in mice.

More detailed description is available by clicking 'Legends'.

Results can be threshold filtered by q-value, fold, rank percentile, and comparison types. Comparison types are defined by GEO.

The comparison type filter is convenient for quickly identifying conditions of interest.

For example, 'disease state' lists all diseases where Nanog was differentially expressed. 'Genotype/variation' and 'strain' return mutation and knockout studies.

'Agent' suggests drugs for regulating Nanog expression. Other frequently used comparison types include infection, protocol, tissue, cell type, cell line, development, and age.

The user can also use keywords to filter study titles. Results are initially sorted by q-values, but can be re-sorted by fold change, title, rank percentile, and species.

Changes to filter thresholds and sort selections are retained if a user selects 'Start Over' for a new search.

Results can be displayed graphically or as text in 'Display Results'.

Graphical results can be saved in a high quality Portable Network Graphics (PNG) file using 'Create Image'.

Textual results can be downloaded as a tabbed text file for detailed analysis.

A permanent link can be created by 'Link to this page'. which can be forwarded to collaborators.

Similar to 'single gene search', 'multiple gene search' takes a list of up- and down regulated genes as input and displays differentially expressed comparisons with average fold changes and q-values.

Clicking the average values opens individual values for each input gene.

System Requirements

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Manufacturer Web Site GENECHASER

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G6G Abstract Number 20399

G6G Manufacturer Number 102506