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Pipeline publication

[…] significant in univariate analysis to determine the prognostic effect., Brier score was used to assess the prediction error in the model. Pec from the R package was used for Brier score prediction. All the statistical analyses were performed using R package and p < 0.05 was considered as significant. We considered the lncRNA as a potential prognostic marker, if they showed significant survival difference in log-rank test and had a statistically significant hazard value in coxph regression analysis either in dichotomization or in continuous scale. Survival analysis and coxph regression analyses were performed using Survival package in R., The reads were cleaned for adapter sequence using Trimmomatic (v 0.32) and the alignment of cleaned reads was done with hg19 reference genome using HISAT aligner (mode: --sensitive --qc-filter). We used Gencode v19 annotation to quantify the read abundance using HTSeq-count. The differential gene expression between knockdown (KD) and control cells was analyzed using bioconductor package edgeR. Genes were tested for differential expression only if expression (CPM) is greater than 1 in at least two samples of comparison groups. The significant candidates were filtered with log-fold change > ± 1 and FDR ≤ 0.05., The significantly deregulated genes from siRNA knockdown samples were tested for pathway enrichment using tool GeneSCF v1.1. The parameters for GeneSCF were set to database Reactome with background genes 20,345 (all protein-coding genes from Gencode v19 annotation used in this study). The enriched functions were filtered based on p < 0.05 and minimum of 10 genes involved in corresponding process., We assayed the proliferation capacity of transiently transfected cells 48 h post-transfection using CellTiter 96® Non-Radioactive Proliferation Assay kit (Promega, USA) with some modifications to the manufacturer's protocol. The media were aspirated and cells were washed once with PBS, and 425 µl of fresh medium plus 75 µl of MTT dye were added and incubated at 37 °C in dark for 4 h. Then, each reaction was terminated using 500 µl of st […]

Pipeline specifications

Software tools Trimmomatic, HISAT, HTSeq, edgeR, GeneSCF
Organisms Homo sapiens, Homo sapiens/Mus musculus xenograft
Diseases Neoplasms