Question: TCGA patient variable data dictionary
gravatar for Björn
12 months ago by
Björn40 wrote:

Hi, I downloaded miRNA seq and patient data from TCGA-PRAD. Is there a way to find out the explanation /dictionary on patient/clinical variable


 [1] "bcr_patient_barcode"                              "additional_studies"                              
 [3] "tumor_tissue_site"                                "other_dx"                                        
 [5] "gender"                                           "vital_status"                                    
 [7] "days_to_birth"                                    "days_to_death"                                   
 [9] "days_to_last_followup"                            "race_list"                                       
[11] "tissue_source_site"                               "patient_id"                                      
[13] "bcr_patient_uuid"                                 "history_of_neoadjuvant_treatment"                
[15] "informed_consent_verified"                        "icd_o_3_site"                                    
[17] "icd_o_3_histology"                                "icd_10"                                          
[19] "tissue_prospective_collection_indicator"          "tissue_retrospective_collection_indicator"       
[21] "days_to_initial_pathologic_diagnosis"             "age_at_initial_pathologic_diagnosis"             
[23] "year_of_initial_pathologic_diagnosis"             "person_neoplasm_cancer_status"                   
[25] "ethnicity"                                        "day_of_form_completion"                          
[27] "month_of_form_completion"                         "year_of_form_completion"                         
[29] "histological_type"                                "histological_type_other"                         
[31] "zone_of_origin"                                   "laterality"                                      
[33] "tumor_levels"                                     "initial_pathologic_diagnosis_method"             
[35] "days_to_bone_scan_performed"                      "bone_scan_results"                               
[37] "diagnostic_ct_abd_pelvis_performed"               "days_to_diagnostic_computed_tomography_performed"
[39] "diagnostic_ct_abd_pelvis_results"                 "diagnostic_mri_performed"                        
[41] "days_to_diagnostic_mri_performed"                 "diagnostic_mri_results"                          
[43] "lymphnodes_examined"                              "number_of_lymphnodes_examined"                   
[45] "number_of_lymphnodes_positive_by_he"              "residual_tumor"                                  
[47] "patient_death_reason"                             "source_of_patient_death_reason"                  
[49] "postoperative_rx_tx"                              "radiation_therapy"                               
[51] "primary_therapy_outcome_success"                  "biochemical_recurrence"                          
[53] "days_to_first_biochemical_recurrence"             "has_new_tumor_events_information"                
[55] "has_drugs_information"                            "has_radiations_information"                      
[57] "has_follow_ups_information"                       "stage_event_system_version"                      
[59] "stage_event_clinical_stage"                       "stage_event_pathologic_stage"                    
[61] "stage_event_tnm_categories"                       "stage_event_psa"                                 
[63] "stage_event_gleason_grading"                      "stage_event_ann_arbor"                           
[65] "stage_event_serum_markers"                        "stage_event_igcccg_stage"                        
[67] "stage_event_masaoka_stage"
mirna tcga • 847 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe49k • written 12 months ago by Björn40

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

ADD REPLYlink written 12 months ago by RamRS24k
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe49k
Kevin Blighe49k wrote:

There are different ways to do this.

first way

First, see my previous answers, here:

In a nutshell, if you want more comprehensive information on these terms, you should go by the Common Data Elements (CDE) ID of each. You should have the CDE ID, which likely appears in the third row of the data that you downloaded.

With the CDE ID, do the following:

  1. Go to CDE Browser
  2. Go to Public ID Search tab
  3. Put the numerical CDE ID into the Public ID search box
  4. Click on Search

second way

Just go to the GDC Data Dictionary (in particular, the Viewer), and you can find descriptions there, too).


ADD COMMENTlink written 12 months ago by Kevin Blighe49k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 776 users visited in the last hour