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Gene Search


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Gene Search

  1. 1. TUTORIAL - GENE SEARCH Search for a gene of interest and have a overview of the implication of this gene in cancer
  2. 2. STEP 1Go Click Browser
  3. 3. STEP 2 Type the name of the gene of interest and click search STEP 3Click the EnsemblID of the gene ofinterest
  4. 4. STEP 4 Click on the tab Tumor type to go to the tumor types table for the gene.These values are based on This box indicates that This box shows somepredictions by CGPrio this gene is in the Cancer gene details and linkmethod. Genes with higher Gene Census, and it give to ensemblprobability rank are more details about the type oflikely to be involved in mutations identified.cancer.see Furney et al., NAR2008
  5. 5. We are in the page for MYC for all experiments and all tumor types. This table gives information of known cancer alterations found in MYC geneThese columns indicatethe number of sampleswith mutations and thenumber of samplesanalyzed for this genein each tumor type.This data is fromCOSMIC.
  6. 6. These colors indicateColor scale of corrected p- significance. Colorvalues: toward red meansGray = no significantly altered that this gene isRed/Yellow = significantly significantly altered inaltered this tumor type. Gray means that this White means that gene is not there is no data for significantly altered in this gene in this this tumor type. tumor type.
  7. 7. You can sort the table by clicking to the title of any column.Note that you canretrieve the data intable format byclicking on ‘CSV file’under ‘Export”. With this links you can go to the next page to see the rest of the tumor types
  8. 8. STEP 5 Sort the table by clicking to the Gain title, to have the tumor types in which this gene has the most significant copy number gain on top. STEP 6Click on “breast” tosee details of MYCalterations in breastcancer
  9. 9. STEP 7 Click on Tumor types Note that now we are Tab in the page of MYC for breast cancer This box shows the p-value for copy number alterations of MYC in breast cancer.This box shows details of This box shows somemutations of MYC in gene details and linkbreast cancer from the to ensemblCancer Gene Census
  10. 10. STEP 8 Now click on Experiments TabThis table gives informationon the alterations found inMYC in differentmorphologies of breastcancer.
  11. 11. This is the list of experimentsthat have analyzed MYC inbreast cancer. N = number of samples analyzed White cells means no data. In this case it means that this experiment has not analyzed transcriptomic alterations. The color shows that there is copy number gain for this gene in a significant number of samples of the 76 samples that were analyzed.
  12. 12. STEP 9 Click on the Gain column to sort by significance of copy number gain. STEP 9Click on Chin SF et alto see the details ofthis experiment.
  13. 13. Note that now we are in the page of MYC for a STEP 10 particular experiment of breast cancer.This box give details This box gives details ofof the experiment, copy number gain of MYCincluding authors, in this experiment. 76title and link to the samples have beenpublication and analyzed, of which 36original source of have a gain in this gene. This table givedata. The expected number of information of the tumor samples with alteration type and morphology by chance is about 5.2. type analyzed by this This is highly significant experiment copy number alteration.
  14. 14. STEP 10To explore other genesinvolved in breast cancerclick all in Experimentsand all in Genes/Modules
  15. 15. Note that now we are in a page for all experiments for this tumor type, and all genes and modules. STEP 11Change tothe Genestab in thebrowser. This Table gives the list of experiments analyzed for this tumor topography and morphology.
  16. 16. Note that now we are in a page for all experiments of Breast Cancer/Infiltrating duct carcinoma, and all genes.Note that you canretrieve the data intable format byclicking on ‘CSV file’under ‘Export”. This table summarizes the evidence for alterations of each gene involved in this tumor type.
  17. 17. THANKS FOR USING INTOGEN You will find more tutorials and documentation in