Data Analysis Solutions

Facility Prepared Analysis.

Our facility is able to provide you with a custom analysis of your gene expression experiments. We can provide reports of fold changes for treatment groups as well as collated changes amongst individual samples. Through R, we can also give you custom report summaries and figures including boxplots, volcano plots, and heatmaps of expression changes. With Fluidigm RealTime PCR experiments, we can prepare custom report summaries with pivot tables, delta CT changes, Endogenous control analysis with correlations and plots.

 

Expression Console. 

This software is available free of charge online from Affymetrix.com. We use it to convert scanned microarray fluorescent images into spreadsheets of usable numerical data. This offers the most basic analysis and provides a table of raw signals for the user.

 

TAC (Transcriptome Analysis Software).

This software is available free of charge online from Affymetrix.com. It has the same features as “Expression Console”, but also provides a more in depth analysis through fold changes, volcano plots, and some limited pathway analysis (through Wikipathways).

 

SAM (Significance Analysis of Microarray Data). 

This software is available to all academics, free of charge, as an Excel addin, from Robert Tibshirani website, UC Stanford, CA. SAM analysis was the original tool of choice when trying to confer significance upon observed differences in gene expression levels in the very complex arena of microarray.

 

QCmiRNA ver2. 

Analysis and QC of miRNA microarrays. On Facility-User computer. Available free of charge to users from Affymetrix.com.

 

Integrative Genome Viewer (IGV).

This software is freely available from the Broad Institute. This is a tool for high-performance visualization for interactive exploration of large, integrated datasets.

DAVID Functional Annotation Tool.

We use the web-accessible NCBI package called “DAVID” to mine pattern in microarray based projects.

 

Ingenuity Pathway Analysis (IPA).

This is a popular, commercially available software with many bioinformatics features. We use it to gain insight from high dimension microarray and RNAseq results.

 

Sequence Detection System (SDS) version 2.3. 

Analysis software for real time PCR studies from Life technologies (formerly ABI). On the Facility-User computer.

 

Fluidigm Real-Time PCR Analysis (ver. 4.3.1).

This is Fluidigm’s proprietary software for use with the medium-throughput nano-fluidic Biomark system. It is available as a free download from the Fluidigm Website.

 

GEO (Gene Expression Omnibus). 

Online general microarray database resource. Accessible free of charge at NCBI website.

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