OncoLnc

OncoLnc enables analysis of molecular changes associated with bladder cancer by using next-generation sequencing data to profile mRNA, miRNA, and lncRNA expression and correlate these profiles with TCGA survival information.

Key Features:

• Data integration and analysis: Integrates mRNA, miRNA, and lncRNA expression from clinical specimens and links expression data with TCGA survival information and protein-expression datasets.
• Functional enrichment analyses: Performs Gene Ontology (GO) functional analysis and KEGG pathway enrichment using the Database for Annotation, Visualization, and Integrated Discovery (DAVID).
• Network analysis: Constructs gene interaction networks in Cytoscape and detects modules with Molecular Complex Detection (MCODE) to identify hub genes.
• Survival analysis: Applies Cox regression to associate gene expression with overall survival and identifies prognostic genes such as CCNB1, ESPL1, CENPM, BLM, and ASPM.

Scientific Applications:

• Pan-cancer and bladder cancer profiling: Enables molecular profiling across cancers with focused analyses on bladder cancer (BC) development and recurrence.
• Differential expression analyses (SC and CR): Compares surrounding tissue versus cancer tissue (SC analysis) and cancer tissue versus recurrent tissue cluster (CR analysis), identifying 4211 DEGs in SC analysis and 410 DEGs in CR analysis.
• Pathway and functional interpretation: Identifies enrichment of DEGs in cytoplasmic and nucleoplasmic functions and involvement of the PI3K-Akt signaling pathway.
• Hub gene and prognostic marker identification: Detects hub genes within interaction networks and links specific genes to patient prognosis.

Methodology:

Gene expression and protein-expression data are acquired from sources including ONCOMINE and integrated with survival data on OncoLnc; differential expression analysis is performed between tissue types; GO and KEGG enrichment are conducted via DAVID; network construction and module detection use Cytoscape and MCODE; Cox regression is used for survival correlation.