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Related Concept Videos

Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Polytene Chromosomes02:04

Polytene Chromosomes

Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly...
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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...
Genomic DNA in Prokaryotes00:46

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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Full-length transcriptome-based H-InvDB throws a new light on chromosome-centric proteomics.

Tadashi Imanishi1, Yoko Nagai, Takuya Habara

  • 1Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. t.imanishi@aist.go.jp

Journal of Proteome Research
|December 19, 2012
PubMed
Summary

The H-Inv Extended Protein Database (H-EPD) expands human protein data from H-InvDB. This resource aids in discovering novel human proteins and advancing proteome research.

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • The H-Invitational Database (H-InvDB) is a comprehensive resource for human genes and transcripts.
  • H-InvDB contains extensive information on both characterized and uncharacterized human transcripts.
  • Identifying novel and uncharacterized human proteins (missing proteins) is crucial for understanding the human proteome.

Purpose of the Study:

  • To develop an extended protein database (H-EPD) by augmenting predicted protein data in H-InvDB.
  • To facilitate database-driven proteome research for advancing discoveries within the current and future Chromosome-centric Human Proteome Project (C-HPP).
  • To integrate genome, transcriptome, and proteome databases and develop a knowledge discovery system using data mining tools.

Main Methods:

  • Extension of predicted protein data from the H-Invitational Database (H-InvDB).
  • Development of the H-Inv Extended Protein Database (H-EPD).
  • Utilizing a unique tool for connecting distributed databases and incorporating data mining tools.

Main Results:

  • The creation of the H-Inv Extended Protein Database (H-EPD).
  • H-EPD serves as a valuable resource for identifying novel and uncharacterized human proteins.
  • The foundation for database-driven proteome research and integration of multi-omics data.

Conclusions:

  • H-EPD enhances the utility of H-InvDB for proteome research.
  • The developed resources and methods will drive discoveries in human protein identification and functional annotation.
  • Future integration of multi-omics data will enable advanced knowledge discovery in human biology.