Computational protocol: Knockdown of spindle pole body component 25 homolog inhibits cell proliferation and cycle progression in prostate cancer

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Protocol publication

[…] The detailed SPC25 expression data of 490 patients with PCa were downloaded from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) database by using the Firebrowse dataset (http://firebrowse.org/) (,). The RNA expression data (level 3) were generated from the HiSeq 2000 sequencing platform (Illumina Inc., San Diego, CA, USA) by RNASeqV2 post-processing pipelines and were presented as RNA-Seq by Expectation-Maximization normalized count data. Patient clinical features, including age at diagnosis, days to last follow-up, pathological tumor (T) stage and node (N) stage, were retrospectively obtained from patient records. All the patients were staged using the 2009 Tumor-Node-Metastasis (TNM) classification of the American Joint Committee on Cancer/International Union Against Cancer (). The Gleason grading system was also used to evaluate the prognosis of men with prostate cancer using samples from a prostate biopsy. The Gleason scores range from 2 to 10, with higher number indicating greater risks and higher mortality (). In order to further investigate the prognostic value of SPC25 in PCa, the overall survival rates of patients with high or low SPC25 expression were assessed using the Kaplan-Meier method by using GSE21032 dataset, which was reported by Taylor et al. The upper 75% SPC25 mRNA expression in all PCa tissues was used as the cut-off point to divide all cases into high (n=36, ≥75% SPC25 expression), and low (n=105, <75% SPC25 expression), groups and clinicopathological characteristics, including the Gleason score. […]

Pipeline specifications

Software tools Firebrowse, RSEM
Databases TCGA Data Portal
Application RNA-seq analysis
Organisms Homo sapiens