Hi,
I am absolutely new to gene expression using microarray analysis. I have been handed a task to look for a certain gene and its related interactions during certain conditions, using microarray data.
I have all XLS files and no CLE files, or anything similar. Could someone tell me if there are free programs available that will take the XLS data and give me some clues of up- or down-regulated genes? How can I further relate this information to a pathway?
It should at least be able to give me a clue of up- and down-regulation of gene sets.
You should give more information. What are the columns in your xls files?
Many softwares allow reading different file types including xls.
Is your data is pre-processed by any body? Is it normalized?
What is your control?
Do you know the format of the microarrays? That's going to drive what you use to do the analysis.
R can read in Excel files and do analysis. I frequently use the Bioconductor package marray for 2-color spotted arrays. There's also affy for Affymetrix arrays. This is a great basic overview of what is available: http://www.bioconductor.org/help/workflows/arrays/
@omer Faruk : Its just the raw data. the columns are probe ID, Signal & Detection & P values, Gene ID, Ensmble etc.,
@Thomas Mohr: I understand it can be done in that manner.... a person with no programming expereince, It is a daunting task.
Hi Sri,
Try InSilico DB, a tool built for biomedical scientists who have the expertise to interpret biological data but not necessarily have programming or IT skills (https://insilicodb.com). You can upload your excel file and generate heatmaps in a couple of minutes to visualize differential gene expression in your data, clusters, fold changes, venn diagrams, etc.
Here is a blog and video tutorial to get you started:
https://insilicodb.com/analyze-my-excel-data-and-compute-a-differential-gene-expression-analysis/
https://insilicodb.com/webinar-august-20th-2014/
Best,
Alain
If you are not familiar with R, don't try to use it by yourself. Plus, it is too much data. I strongly advise you to ask for help from someone used to do such analyses. Otherwise you may take a long time to understand how to treat and interpret results.
Anyway, there is also BRB Tools, which I think is paid but user-friendly, then MeV software (free).
Try Ingenuıty pathway analyses and Genego software. They can be helpful to you. They are pretty easy and you would not need any to do coding.
http://www.ingenuity.com/products/ipa
https://portal.genego.com/
http://thomsonreuters.com/metacore/?subsector=systems-biology
They have trials for few weeks but you will need only few hours after you understand how to use them. Let me know if you need any help in using these tools.
The quickest way might be using SAM (significance analysis of microarrays). It directly takes XLS files. For pathway analysis, you can plug in the genes you identify as differentially expressed to DAVID to see what pathways are significantly enriched in these genes. Both tools are easy to learn. You should be able to get them running for you quickly.
http://statweb.stanford.edu/~tibs/SAM/
http://david.abcc.ncifcrf.gov/tools.jsp
Hi Sri,
Could you show us an entry from your xls files. And explain what exactly you're trying to do, as well as what the experimental design is.
Good luck,
Aliaksei.
Cytoscape and DAVID could help you to analyse your data and determine the possible pathways that could be of interest for your disease model
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