{"id":"W3137058839","doi":"10.1016/j.oraloncology.2021.105260","title":"All HPV-negative head and neck cancers are not the same: Analysis of the TCGA dataset reveals that anatomical sites have distinct mutation, transcriptome, hypoxia, and tumor microenvironment profiles","year":2021,"lang":"en","type":"article","venue":"Oral Oncology","topic":"Head and Neck Cancer Studies","field":"Medicine","cited_by":27,"is_retracted":false,"has_abstract":false,"ca_institutions":"Western University","funders":"Canadian Institutes of Health Research; National Institutes of Health; National Cancer Institute; Foundation for the National Institutes of Health","keywords":"Head and neck squamous-cell carcinoma; Tumor microenvironment; Biology; Bioconductor; Cancer research; Transcriptome; DNA methylation; Cancer; Head and neck cancer; Gene; Genetics; Gene expression","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001998637,0.0001562594,0.0007180859,0.00005072971,0.0001285721,0.00001206338,0.00007437415,0.00005957451,0.0000887202],"category_scores_gemma":[0.0001689715,0.00008997508,0.00008837126,0.0002234385,0.0005937043,0.00006060378,0.00009243811,0.0001767687,8.292014e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002195612,"about_ca_system_score_gemma":0.0001275335,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000638044,"about_ca_topic_score_gemma":0.007113631,"domain_scores_codex":[0.9987837,0.0002337992,0.0002735991,0.0003011555,0.0001747318,0.0002329913],"domain_scores_gemma":[0.9991087,0.0003339627,0.0001730959,0.0002435087,0.00004598779,0.00009478162],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005244401,0.0002361257,0.9570419,0.0001375752,0.00188511,0.0001112056,0.004331738,0.00000952113,0.01431679,0.00004203017,0.01881498,0.002548597],"study_design_scores_gemma":[0.001230954,0.0002600714,0.9721653,0.00004721982,0.001702022,0.00004296145,0.003432057,0.0001038221,0.006121328,0.00002767171,0.01476983,0.00009676634],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9800765,0.00174561,0.000005016829,0.01513836,0.0000596611,0.0003339103,0.002549918,0.00000537575,0.00008565627],"genre_scores_gemma":[0.9934472,0.0005069875,0.0003664244,0.005051223,0.00003785914,0.00005385606,0.0003683621,0.000009797315,0.0001583193],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01512341,"threshold_uncertainty_score":0.3969573,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0448142059241138,"score_gpt":0.333430312170274,"score_spread":0.2886161062461602,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}