| General/Administrative Questions |
 1. I am unable to log in to Oncomine.
- If you have forgotten your password for Oncomine 4, then enter your username in the text box provided in the login box and click the "forgot password" link. Our system will generate a new password and send it to your e-mail account.
- If you wish to customize your password, then use the change password functionality in the tools menu within the application.
- If you need to register for Oncomine, please click on the "Not a user? Register now!" link at the bottom of the login box.
- If you are a trial user of Oncomine Research Premium Edition, then you must go to www.oncomine.com to log in.
- If you try to log in unsuccessfully eight times, then your account will be locked out. You will need to contact support to unlock your account.
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2. How can I gain access to Oncomine?
Commercial organizations should contact sales. Academic / non-profit users can register for access at www.oncomine.org. If academic users are interested in a subscription version of Oncomine, please click here for more information. |
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3. What web browser do you recommend for Oncomine?
Please review the system requirements. |
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4. Can I cite Oncomine or use images from Oncomine in my own publication?
Images from Oncomine may be used in publications with proper citation. The citation for Oncomine is as follows: Oncomine™ (Compendia Bioscience, Ann Arbor, MI) was used for analysis and visualization. |
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5. Is there help available for Oncomine?
In the upper right corner of Oncomine 4, click the Help button and choose Oncomine Help or Support Documents and FAQ. These open new windows, which contains an Online Help Guide and other resources (Quick Start Guides, FAQs, System Requirements, Flash demos), respectively. |
| Content/Interface Questions |
1. What is the source of the datasets in Oncomine?
The datasets have been retrieved from public repositories including GEO, SMD, and ArrayExpress, as well as through direct correspondence with the publication authors. |
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2. How do you map reporter IDs to gene symbols?
We map reporter IDs to gene symbols by first retrieving the corresponding GenBank accession number and then using Entrez-supplied data to map from GenBank accession number to Entrez Gene ID. If the GenBank accession number has not been mapped by Entrez, but has been clustered by UniGene, we apply the UniGene-supplied mapping to Entrez Gene ID. |
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3. Can I download data from Oncomine?
Normalized data is available for download for a subset of genes with the Export link on the right of the Visualize pane. This is exclusively available through the subscription editions of Oncomine. |
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4. Is it possible to upload datasets to Oncomine?
Users cannot directly upload datasets into Oncomine. This is exclusively available through the subscription editions of Oncomine.
Please contact support to recommend a published dataset for analysis.
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| Analysis Questions |
1. What do the numbers in "t-test" and "p-Value" represent?
The t-test value is the t-test statistic derived from the Student's t-test. The larger the absolute value of the t-test statistic, the greater the effect size between the two classes. The p-Value reflects the significance of the differential expression observed. The lower the p-Value, the greater the significance. P-Values are often used to reject null hypotheses (no difference between the classes) at a particular confidence interval. |
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2. How are datasets normalized in Oncomine?
All mRNA datasets have been log-2 transformed, with the median set to zero (0) and standard deviation set to one (1). For DNA copy number datasets, no standard deviation is applied. For additional details, click here. |
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