1. Guide to OncoLnc: A new TCGA data portal
By Jordan Anaya

2. Point your browser to

3. Homepage

4. Enter a search term Case does not matter
mRNAs: Use a modern HUGO gene symbol or Entrez ID
miRNAs: mature miRBase name or accession number
lncRNAs: MiTranscriptome Beta name or transcript ID

5. Potential for name conflicts
There are name conflicts between MiTranscriptome Beta and TCGA Tier 3 data
OncoLnc will notify you of the conflict

6. Example

7. Results page Cancer: The TCGA cancer study
Cox coefficient: The coefficient from the gene term in a multivariate model run for that cancer study
P-value: The p-value for the gene term in a multivariate model run for that cancer study
FDR corrected: The BH-adjusted p-value. For each cancer study the Cox model is run for every single gene that meets the expression cutoff. The FDR correction is performed with all the genes run in an individual cancer study. mRNA, miRNA, lncRNA Cox models are run separately from each other.

8. Results page cont.
Rank: Where the gene ranks by p-value compared to all other genes in that cancer study. mRNAs, miRNAs, lncRNAs are ranked separately.
Median expression: Median expression of the gene. If a patient had more than one expression file they were averaged.
Mean expression: Mean expression of the gene. If a patient had more than one expression file they were averaged.
Kaplan: Go to an interactive Kaplan-Meier plotter

9. Notes about expression
Depending on the gene it may not be safe to compare expression between cancers:
MiTranscriptome Beta:
Normalized expression was used and I believe they were normalized across cancers.
TCGA Tier 3 mRNAs:
Normalized expression was used. I do not know if it is safe to compare expression across cancers.
TCGA Tier 3 miRNAs:
Expression was not normalized across cancers, it is not recommended to compare across cancers.

10. Kaplan-Meier Plotting Page

11. Enter how to divide patients
Enter numbers between 0 and 100 that do not sum to over 100.
Patients are sorted by expression of the gene.
Lower percentile is the low slice of patients, for example bottom quartile.
Upper percentile is the upper slice of patients, for example upper quartile.
If you want all data for that gene and cancer, input 100 for lower and 0 for upper.

12. Kaplan-Meier Plot

13. Below the plot is the data used in the plot

14. Please send any questions to omnesresnetwork@gmail.com
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