| General/Administrative Questions |
 1. I am unable to log in to Oncomine. (I can't remember my password.)
Confirm you are logging in at the correct site. Academic users should log in at www.oncomine.org and commercial users at www.oncomine.com. If you have forgotten your password, you can click the "forgot pasword?" link on the login page; your password will then be sent to your e-mail address. Also, please note that the username and password fields are case-sensitive. If you are still experiencing problems, please contact customer support. |
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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. |
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3. I cannot view heat maps and box plots.
Confirm that Adobe SVG Viewer has been installed. You can download the viewer by going to "About SVG" under Support in the main toolbar. |
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4. What web browser do you recommend for Oncomine?
We support Microsoft Internet Explorer version 6 or higher. Please refer to the system requirements for more information. |
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5. 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: Rhodes D. R. et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 6, 1-6. (2004). For further information, refer to the terms described in the licensing agreement. |
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6. Is there help available for Oncomine?
Detailed help pages can be accessed from the yellow question mark icons throughout the application. There are also Flash demonstrations and Quick Start Guides available under Support in the main toolbar. |
| Content/Interface Questions |
7. 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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8. 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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9. Why is there an asterisk next to some genes in Oncomine?
An asterisk denotes a gene with ambiguous mapping (i.e., one or more reporters mapping to this gene also map to another gene). |
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10. How do I access COPA results in Oncomine?
You can access COPA results from the Outlier tab in either the gene or profile search modules. |
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11. Why do only some search results return heat map icons?
The heat map icons only exist if co-expression results are available for the gene in the dataset. Co-expression is only available for the top 50% of variable genes per dataset. |
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12. Why do I get different gene search results when I select "Term Matched" instead of "Official Symbol"?
When the "Term Matched" is a reporter ID (as opposed to a gene symbol), the search will be conducted on all genes associated with that reporter. In contrast, a search by "Official Symbol" will yield results for all reporters associated with that gene. |
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13. Can I download data from Oncomine?
Normalized data is available for download for individual genes with the Data Download link in bar graphs and heatmaps. When available, links to source data are provided from the Study Details popup, which is available by clicking on a study name. |
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14. Is it possible to upload datasets to Oncomine?
Users cannot directly upload datasets into Oncomine. Please contact support to recommend a published dataset for analysis. |
| Analysis Questions |
15. 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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16. 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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17. What is the difference between profiles with one class, two classes, or more than two classes?
Differential expression analysis requires that samples be grouped into logical classes and then compared using a statistical technique. When logical groupings result in one class, Class 0 is compared relative to zero using Student's t-test. When the groups result in two classes (e.g., cancer vs. normal), Class 2 is compared relative to Class 1 using Students t-test. When the groupings contain more than two classes (e.g., Grade 1, Grade 2, Grade 3) they are compared using the Pearson Correlation.
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18. How are gene lists ranked?
Gene lists are ranked by significance determined by differential expression, correlation, meta-analysis, or COPA score, depending on the analysis. |
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