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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
TLDR
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Integrated Genomic Analyses of Ovarian Carcinoma
TLDR
It is reported that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1,BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes.
Somatic mutations affect key pathways in lung adenocarcinoma
TLDR
Somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B are found.
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
TLDR
The interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated gliobeasts, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.
The ENCODE (ENCyclopedia Of DNA Elements) Project
TLDR
The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function.
An integrated encyclopedia of DNA elements in the human genome
TLDR
The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
TLDR
Two studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized.
A comparative encyclopedia of DNA elements in the mouse genome
TLDR
By comparing with the human genome, this work not only confirms substantial conservation in the newly annotated potential functional sequences, but also finds a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
TLDR
An overview of the project and the resources it is generating and the application of ENCODE data to interpret the human genome are provided.
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
TLDR
These studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized, providing insights into the organization, structure, and function of the two genomes.
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