As an example, let's consider transcriptomics or gene expression. One goal of such experiments is to compare the relative gene expression between cells to see how different genes are up or down regulated as the cells change over time or respond to some sort of treatment.
The general process, whether it involves microarrays or Next Gen sequencing, is to measure the number of RNA molecules for a given gene, either over a period of time or after different treatments. Laboratory processes create the molecules to assay, the molecules are measured, data are collected, and we process the data to produce tables of information. These tables are then compared with one another to identify genes that are differentially expressed. With the gene expression results in hand, one can delve deeper by utilizing other databases like Entrez Gene or pathway sites to learn about gene function and gain insights.From a systems perspective, you need a LIMS to define sample information and keep track of workflow steps and the data generated at the bench. You will also need to track which samples are on a slide, or lane, or well when the data are collected. You will need to store and organize the data by sample. Then, you will need to analyze the data through multiple programs in a pipelined process (filter, align ...) to produce information, like gene lists, that can be compared for each sample. You may want to review this information to see that your experiments are on track and then, if they are, you will want to compare the gene lists from different experiments to tell a story.
FinchLab, combined with Geospiza’s hosted Software as a Service (SaaS) delivery, solves challenges related to IT, LIMS, and the core data analysis. GeneSifter completes the process by delivering a software solution that lets you compare your gene lists. GeneSifter provides information about the relative gene expression between samples and links gene information to key public resources to uncover additional details.It's an exciting time for those in the genetic analysis and genomics fields. New high throughput data collection technologies are giving scientists the ability to interrogate systems and understand biology in a whole new way. As we come to the end of 2008 and think about 2009, Geospiza is excited to think about how we will integrate and extend our products to further develop end to end systems for a wide variety of genomics applications that target basic and clinical research to help us improve human health and well being.
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