The dataset additionally demonstrated over-representation of CpA and UpG dinucleotides at the 3 1 position; these are typically created by the (methylation-associated) C->T transition upstream of G (fifth and 14th main columns in Figure 1A) and of CpC and CpU (Simmen, 2008).
We began by confirming previous karyotypic results demonstrating over-representation of part or all of chromosome 22 in cells selected for resistance in vitro or in vivo (recurrent tumor) using whole chromosome paint (WCP) for chromosome 22.
These studies have demonstrated an over-representation of radiation-associated meningioma (RAM) and other radiation-associated cancers in specific families.
Genes up-regulated in MPNST (cluster C9) demonstrated significant over-representation of gene orthologues activated in migrating neural crest cells.
Methylation analysis at PLAGL1, MEST and IGF2R ICs demonstrated an over-representation of patients with abnormally low methylation (8.5%, 12% and 6% respectively).
PANTHER/DAVID pathway analyses demonstrated significant over-representation of genes coding for nucleic acid binding in normal and tumour tissues, and for p53, EGF, and FGF signalling pathways in tumour tissue.
To demonstrate how over-representation analysis and the visualization methods are complementary, and enhance the analysis of ChIP-Seq data, we applied the TFBS-landscape view and the Dinucleotide-environment view to two case studies.
The superiority of the auditory cortical representations has been demonstrated over the conventional MFCCs and chroma features in the three music classification tasks studied as well.
This demonstrated a significant over-representation of haplogroup J1 in the "isolated" nephropathy group [p = 0.018, OR = 2.3 (1.15–4.7)] and in the "isolated" retinopathy group [p = 0.017, OR = 3.1 (1.2 7.8)].
The ΨEs also demonstrate species-specific over-representation of GO functional categories relative to duplicated exons in general; for example, in human, GO functional categories for 'ion-binding' and 'nucleic acid binding' are significantly over-represented, compared to duplicated exons generally.
Accordingly, our experiments do not exhibit the over-representation of the foveal region as it has been demonstrated electrophysiologically in the pigeon [52] and the zebra finch [53].
