Computational protocol: LncRNA MT1JP functions as a ceRNA in regulating FBXW7 through competitively binding to miR-92a-3p in gastric cancer

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Protocol publication

[…] Coding Potential Assessment Tool (CPAT, http://lilab.research.bcm.edu/cpat/) was used to assess the coding capacity of lncRNA MT1JP. The CPAT conducted a logistic regression model by using the sequence features of open reading frame coverage, open reading frame size, hexamer usage bias and Fickett TESTCODE statistic. The CPAT chose 0.364 as a cutoff as human coding probability (CP). CP < 0.364 suggests noncoding sequence, whereas CP ≥ 0.364 indicates coding sequence []. […]

Pipeline specifications

Software tools CPAT, BCM
Application Transcription analysis
Organisms Homo sapiens
Diseases Neoplasms, Stomach Neoplasms, Tuberculosis, Lymph Node