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Related Concept Videos

Censoring Survival Data01:09

Censoring Survival Data

Survival analysis is a statistical method used to analyze time-to-event data, often employed in fields such as medicine, engineering, and social sciences. One of the key challenges in survival analysis is dealing with incomplete data, a phenomenon known as "censoring." Censoring occurs when the event of interest (such as death, relapse, or system failure) has not occurred for some individuals by the end of the study period or is otherwise unobservable, and it might have many different reasons...
Encoding01:19

Encoding

Information enters the brain through encoding, which is the input of information into the memory system. Once sensory information is received from the environment, the brain labels or codes it. The information is then organized with similar information and connected to existing concepts. Encoding occurs through automatic processing and effortful processing.
Automatic processing involves the encoding of details like time, space, frequency, and the meaning of words, usually done without conscious...
DNA-only Transposons02:57

DNA-only Transposons

DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

modMine: flexible access to modENCODE data.

Sergio Contrino1, Richard N Smith, Daniela Butano

  • 1Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.

Nucleic Acids Research
|November 15, 2011
PubMed
Summary
This summary is machine-generated.

The modENCODE project provides a rich database for researchers studying Drosophila melanogaster and Caenorhabditis elegans genomes. The modMine database enables easy access and analysis of extensive genomic data, facilitating biological discovery.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Model Organism Research

Background:

  • The NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium aimed to characterize functional genomic elements.
  • Extensive genomic data was generated for Drosophila melanogaster and Caenorhabditis elegans.

Purpose of the Study:

  • To build the modMine database for accessing and analyzing modENCODE data.
  • To integrate modENCODE data with other datasets for comprehensive analysis.
  • To provide tools for biologists and bioinformaticians to explore genomic information.

Main Methods:

  • Development of the modMine database by the modENCODE Data Coordination Center.
  • Collection of extensive experimental metadata.
  • Creation of sophisticated search and data access interfaces.

Main Results:

  • Thousands of modENCODE datasets are available for search and download.
  • Integrated access to modENCODE and non-modENCODE data.
  • Facilitation of fine-grained analysis of genomic data.

Conclusions:

  • The modMine database provides a valuable resource for the research community.
  • Enhanced accessibility and analysis capabilities for model organism genomic data.
  • Supports further research into functional elements of Drosophila and C. elegans genomes.