Non-coding RNAs occupy a significant fraction of the human genome. Their biological significance is backed up by a plethora of emerging evidence. One of the most robust approaches to demonstrate
non-coding RNA's biological relevance is through their prognostic value. Using the rich gene expression data from The
Cancer Genome Altas (TCGA), we designed Advanced Expression Survival Analysis (AESA), a web tool which provides several novel survival analysis approaches not offered by previous tools. In addition to the common single-gene approach, AESA computes the gene expression composite score of a set of genes for survival analysis and utilizes permutation test or cross-validation to assess the significance of log-rank statistic and the degree of over-fitting. AESA offers survival feature selection with post-selection inference and utilizes expanded TCGA clinical data including overall, disease-specific, disease-free, and progression-free survival information. Users can analyse either
protein-coding or non-coding regions of the transcriptome. We demonstrated the effectiveness of AESA using several empirical examples. Our analyses showed that non-coding RNAs perform as well as messenger RNAs in predicting survival of
cancer patients. These results reinforce the potential prognostic value of non-coding RNAs. AESA is developed as a module in the freely accessible analysis suite MutEx. Abbreviation: ACC:
Adrenocortical Carcinoma (n = 92); BLCA: Bladder Urothelial
Carcinoma (n = 412); BRCA: Breast Invasive
Carcinoma (n = 1098); CESC: Cervical
Squamous Cell Carcinoma and Endocervical
Adenocarcinoma (n = 307); CHOL:
Cholangiocarcinoma (n = 51);
COAD:
Colon Adenocarcinoma (n = 461); DLBC: Lymphoid
Neoplasm Diffuse Large B-cell Lymphoma (n = 58); ESCA: Oesophageal
Carcinoma (n = 185); GBM:
Glioblastoma Multiforme (n = 617); HNSC:
Head and Neck Squamous Cell Carcinoma (n = 528); KICH: Kidney Chromophobe (n = 113); KIRC: Kidney Renal Clear Cell
Carcinoma (n = 537); KIRP: Kidney Renal Papillary Cell
Carcinoma (n = 291); LAML: Acute Myeloid Leukaemia (n = 200); LGG: Brain Lower Grade
Glioma (n = 516); LIHC: Liver
Hepatocellular Carcinoma (n = 377); LUAD:
Lung Adenocarcinoma (n = 585); LUSC: Lung
Squamous Cell Carcinoma (n = 504); MESO:
Mesothelioma (n = 87); OV: Ovarian
Serous Cystadenocarcinoma (n = 608) PAAD: Pancreatic
Adenocarcinoma (n = 185);
PCPG:
Pheochromocytoma and
Paraganglioma (n = 179); PRAD: Prostate
Adenocarcinoma (n = 500); READ: Rectum
Adenocarcinoma (n = 172); SARC:
Sarcoma (n = 261); SKCM: Skin Cutaneous
Melanoma (n = 470); STAD: Stomach
Adenocarcinoma (n = 443); TGCT: Testicular Germ Cell Tumours (n = 150); THCA:
Thyroid Carcinoma (n = 507) THYM:
Thymoma (n = 124); UCEC: Uterine Corpus
Endometrial Carcinoma (n = 560); UCS: Uterine
Carcinosarcoma (n = 57); UVM:
Uveal Melanoma (n = 80).