Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Interplay between promoter methylation and chromosomal loss in gene silencing at 3p11-p14 in cervical cancer

ABSTRACT: The DNA copy number profiles have previously been uploaded in ArrayExpress (E-MTAB-1161). The previous study included 92 patients, and in the present study the profiles of 75 out of these patients were reused. Absolute copy numbers were calculated using the GeneCount algorithm as described (Lyng et al. 2008). Absolute gene dosages were calculated by dividing the copy numbers with ploidity. Frequency of chromosomal loss on 3p11-p14 was determined. The 3p11-p14 gene dosage data were integrated with methylation and expression data of the same region for 73 patients (integrative cohort) to explore the interplay between promoter methylation and loss in gene silencing.

ORGANISM(S): Homo sapiens

SUBMITTER: Heidi Lyng

PROVIDER: E-MTAB-3531 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts. Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts. Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts.

Dataset Information

Interplay between promoter methylation and chromosomal loss in gene silencing at 3p11-p14 in cervical cancer

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets