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The differentially expressed genes (DEGs) were collected for further analysis if the expression alteration between the disease sample and normal controls was greater than 2 fold.
Multiple areas of invasive carcinoma and different histological patterns of the tumours (cribiform, mucinous, poorly-differentiated), adenomatous lesions from the same surgical sample, and normal mucosa, located far from the infiltrating tumour, were identified on corresponding haematoxylin-eosin-stained slides.
A log 2 signal ratio of zero represents the most common copy number between the sample and normal reference DNA.
The majority (86%, 36/42) of normal breast tissue sample and normal breast tissues adjacent to invasive carcinomas are negative for HECTD3 expression.
Two punch cores measuring 0.8 mm in the greatest dimension from the centre of the tumour focus were taken from each formalin-fixed, paraffin-embedded HCC sample and normal liver sample.
According to formula (6), apart from cell-free DNA from myeloid and lymphoid cells, the DNAm level difference between disease sample and normal control could also be influenced by cell-free DNA from the disease tissue cells.
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Expression differences are calculated as a p-value using a two-sample t-test for the average expression between cancer samples and normal samples.
For the classification of tumor samples and normal tissue we applied a variant of a standard methodology.
Previous histochemical studies conducted on tumor samples and normal tissues have reported three expression patterns of ENO1 gene products: cytoplasm, nuclei and both nuclei and cytoplasm [23], [27].
Analysis of variance (ANOVA) was performed using a 5% false discovery rate (FDR) threshold to identify differentially expressed miRNAs between leukaemia samples and normal bone marrow.
The dataset contains five types of tumor samples viz., primitive neuroectodermal tumors (PNETs) (8 samples), atypical teratoid/rhabdoid tumors (Rhab) (10 samples), malignant gliomas (Mglio) (10 samples), medulloblastomas (MD) (10 samples) and normal tissues (Ncer) (4 samples).
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