Cleaned clinical, survival, and virome abundance data for patients with colon and rectal adenocarcinoma (TCGA PanCancer Atlas).
Format
A data frame with patient data in rows and variables in columns:
- sample_id
Unique TCGA patient identifier (character).
- time_months
Overall survival time (months), censored at 60 mos. (numeric).
- status
Overall survival status: 1 = deceased, 0 = alive (integer).
- age
Age at diagnosis (numeric).
- sex
Sex of the patient (character).
- race
Race of the patient (character).
- ethnicity
Ethnicity of the patient (character).
- stage
AJCC pathologic tumour stage (character).
- Alfamovirus
Normalised abundance (numeric).
- Allexivirus
Normalised abundance (numeric).
- Alphacoronavirus
Normalised abundance (numeric).
- Alphaentomopoxvirus
Normalised abundance (numeric).
- Alphafusellovirus
Normalised abundance (numeric).
- Alphapapillomavirus
Normalised abundance (numeric).
- Alphapartitivirus
Normalised abundance (numeric).
- Alpharetrovirus
Normalised abundance (numeric).
- Alphatorquevirus
Normalised abundance (numeric).
- Alphavirus
Normalised abundance (numeric).
- Ambidensovirus
Normalised abundance (numeric).
- Ampelovirus
Normalised abundance (numeric).
- Andromedalikevirus
Normalised abundance (numeric).
- Aparavirus
Normalised abundance (numeric).
- Aquamavirus
Normalised abundance (numeric).
- Arenavirus
Normalised abundance (numeric).
- Avastrovirus
Normalised abundance (numeric).
- Bacilladnavirus
Normalised abundance (numeric).
- Bafinivirus
Normalised abundance (numeric).
- Barnyardlikevirus
Normalised abundance (numeric).
- Batrachovirus
Normalised abundance (numeric).
- Bcep22likevirus
Normalised abundance (numeric).
- Betacoronavirus
Normalised abundance (numeric).
- Betaentomopoxvirus
Normalised abundance (numeric).
- Betapapillomavirus
Normalised abundance (numeric).
- Betapartitivirus
Normalised abundance (numeric).
- Betaretrovirus
Normalised abundance (numeric).
- Betatorquevirus
Normalised abundance (numeric).
- Bicaudavirus
Normalised abundance (numeric).
- Bracovirus
Normalised abundance (numeric).
- Bromovirus
Normalised abundance (numeric).
- Cafeteriavirus
Normalised abundance (numeric).
- Capripoxvirus
Normalised abundance (numeric).
- Carlavirus
Normalised abundance (numeric).
- Caulimovirus
Normalised abundance (numeric).
- Cavemovirus
Normalised abundance (numeric).
- Cervidpoxvirus
Normalised abundance (numeric).
- Chlorovirus
Normalised abundance (numeric).
- Closterovirus
Normalised abundance (numeric).
- Comovirus
Normalised abundance (numeric).
- Cp220likevirus
Normalised abundance (numeric).
- Crinivirus
Normalised abundance (numeric).
- Cripavirus
Normalised abundance (numeric).
- Cucumovirus
Normalised abundance (numeric).
- Cytomegalovirus
Normalised abundance (numeric).
- Deltabaculovirus
Normalised abundance (numeric).
- Dicipivirus
Normalised abundance (numeric).
- Dyopipapillomavirus
Normalised abundance (numeric).
- Emaravirus
Normalised abundance (numeric).
- Endornavirus
Normalised abundance (numeric).
- Enterovirus
Normalised abundance (numeric).
- Fabavirus
Normalised abundance (numeric).
- Flavivirus
Normalised abundance (numeric).
- Furovirus
Normalised abundance (numeric).
- Gammacoronavirus
Normalised abundance (numeric).
- Gammapapillomavirus
Normalised abundance (numeric).
- Gammaretrovirus
Normalised abundance (numeric).
- Gammatorquevirus
Normalised abundance (numeric).
- Hepacivirus
Normalised abundance (numeric).
- Hepatovirus
Normalised abundance (numeric).
- Higrevirus
Normalised abundance (numeric).
- Hordeivirus
Normalised abundance (numeric).
- Hypovirus
Normalised abundance (numeric).
- I3likevirus
Normalised abundance (numeric).
- Ichnovirus
Normalised abundance (numeric).
- Iflavirus
Normalised abundance (numeric).
- Ilarvirus
Normalised abundance (numeric).
- Influenzavirus_C
Normalised abundance (numeric).
- Isavirus
Normalised abundance (numeric).
- Kobuvirus
Normalised abundance (numeric).
- L5likevirus
Normalised abundance (numeric).
- Lambdalikevirus
Normalised abundance (numeric).
- Lambdapapillomavirus
Normalised abundance (numeric).
- Lentivirus
Normalised abundance (numeric).
- Leporipoxvirus
Normalised abundance (numeric).
- Lymphocryptovirus
Normalised abundance (numeric).
- Mamastrovirus
Normalised abundance (numeric).
- Mardivirus
Normalised abundance (numeric).
- Mastadenovirus
Normalised abundance (numeric).
- Microvirus
Normalised abundance (numeric).
- Mimivirus
Normalised abundance (numeric).
- Molluscipoxvirus
Normalised abundance (numeric).
- Muromegalovirus
Normalised abundance (numeric).
- Muscavirus
Normalised abundance (numeric).
- N4likevirus
Normalised abundance (numeric).
- Narnavirus
Normalised abundance (numeric).
- Nepovirus
Normalised abundance (numeric).
- Nyavirus
Normalised abundance (numeric).
- Omegapapillomavirus
Normalised abundance (numeric).
- Orthobunyavirus
Normalised abundance (numeric).
- Orthohepadnavirus
Normalised abundance (numeric).
- Orthopoxvirus
Normalised abundance (numeric).
- Ostreavirus
Normalised abundance (numeric).
- Parapoxvirus
Normalised abundance (numeric).
- Pecluvirus
Normalised abundance (numeric).
- Pestivirus
Normalised abundance (numeric).
- Phi29likevirus
Normalised abundance (numeric).
- Phikmvlikevirus
Normalised abundance (numeric).
- Phikzlikevirus
Normalised abundance (numeric).
- Piscihepevirus
Normalised abundance (numeric).
- Pithovirus
Normalised abundance (numeric).
- Polyomavirus
Normalised abundance (numeric).
- Pomovirus
Normalised abundance (numeric).
- Potexvirus
Normalised abundance (numeric).
- Potyvirus
Normalised abundance (numeric).
- Prasinovirus
Normalised abundance (numeric).
- Proboscivirus
Normalised abundance (numeric).
- Protoparvovirus
Normalised abundance (numeric).
- Prymnesiovirus
Normalised abundance (numeric).
- Ranavirus
Normalised abundance (numeric).
- Rhadinovirus
Normalised abundance (numeric).
- Rubulavirus
Normalised abundance (numeric).
- Salivirus
Normalised abundance (numeric).
- Sapelovirus
Normalised abundance (numeric).
- Sclerodarnavirus
Normalised abundance (numeric).
- Senecavirus
Normalised abundance (numeric).
- Sfi1unalikevirus
Normalised abundance (numeric).
- Sfi21dtunalikevirus
Normalised abundance (numeric).
- Sicinivirus
Normalised abundance (numeric).
- Simplexvirus
Normalised abundance (numeric).
- Skunalikevirus
Normalised abundance (numeric).
- Sp6likevirus
Normalised abundance (numeric).
- Spo1virus
Normalised abundance (numeric).
- Spounalikevirus
Normalised abundance (numeric).
- T4likevirus
Normalised abundance (numeric).
- T5likevirus
Normalised abundance (numeric).
- Taupapillomavirus
Normalised abundance (numeric).
- Tenuivirus
Normalised abundance (numeric).
- Tobamovirus
Normalised abundance (numeric).
- Totivirus
Normalised abundance (numeric).
- Trichovirus
Normalised abundance (numeric).
- Tritimovirus
Normalised abundance (numeric).
- Tunalikevirus
Normalised abundance (numeric).
- Tymovirus
Normalised abundance (numeric).
- Vesivirus
Normalised abundance (numeric).
- Waikavirus
Normalised abundance (numeric).
- Whispovirus
Normalised abundance (numeric).
- Yatapoxvirus
Normalised abundance (numeric).
Source
Sourced, cleaned, and merged from Smyth et al. (2024) [doi:10.1002/cam4.70434 ], originating from cBioPortal (TCGA, PanCancer Atlas). https://www.cbioportal.org/study/summary?id=coadread_tcga_pan_can_atlas_2018