Computational protocol: Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia

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Protocol publication

[…] Agilent's background subtracted signals (gIsWellAboveBG; rIsWellAboveBG) were used to filter spots lower than background intensity in both channels and intra-array normalization was carried out using lowess []. Genes with more than 30% missing values were removed and the remaining missing values were estimated using LSimpute []. The samples were divided into three groups: before, early (2–4 hours) and late (18–24 hours) after start of treatment and the mRNA expression levels of the treated samples were compared to the untreated ones. The Rank product method [] was used to identify genes consistently up- or down-regulated. Gene ontology (GO) analysis was applied for functional studies using iterative group analysis (iGA) [] utilizing the Source database http://source.stanford.edu[]. False discovery rates for GO-terms were estimated by performing 100 permutations.In the ex vivo experiment cell samples were treated with different doses (0, 1.6, and 8 μM) of anthracycline (daunorubicin). The untreated sample was kept as a control. Subsequently, the mRNA expression levels of the untreated sample were compared to the treated. To study if there was a general trend of up- or downregulation of genes in the treated compared to the untreated sample, the difference in expression levels was calculated for each gene. The genes were ranked according to expression difference for each of the three comparisons, e.g. three different rankings of the genes were produced, and these rankings were analyzed together using the rank product test []. The genes were then ordered by p-value for up- and downregulation in the treated samples relative to the untreated sample. On top of the rank product derived gene lists, we performed an iterative group analysis using GO terms as groups [].The gene expression profile of patients with FLT3 length mutation/internal tandem mutation (ITD) (2/7) was analyzed against patients harboring FLT3 wildtype (5/7) using Significant Analysis of Microarray (SAM) and Analysis of Variance (ANOVA) performed in J-Express http://www.molmine.com[]. […]

Pipeline specifications

Software tools LSImpute, iGA, J-Express
Application scRNA-seq analysis
Organisms Homo sapiens
Diseases Leukemia, Neoplasms, Leukemia, Myeloid, Acute
Chemicals Cytarabine