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Mammalian Promoter Database
The Mammalian Promoter Database (MPromDb) is a curated database of gene promoters identified from ChIP-seq. The proximal promoter region (upstream of the core-promoter region) contains the cis-regulatory elements of most of the transcription factors (TFs). Recently, a better approach to annotate active promoters has been demonstrated with a combination of ChIP-seq and computational technique. This technique has been used to find the target genes of TFs in mammalian systems. The MPromDb is based on this technology. Curated promoter sequences for eukaryotic organisms are provided by an EPD database; however, promoter activity information at tissue/ cell centric level is not offered. The MPromDb data base added active RNAP-II promoters identified after analyzing ten different mouse cell/tissue ChIP-seq experiments performed with RNAP-II antibodies An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to ident ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computation
Computation is any type of arithmetic or non-arithmetic calculation that follows a well-defined model (e.g., an algorithm). Mechanical or electronic devices (or, historically, people) that perform computations are known as '' computers''. An especially well-known discipline of the study of computation is computer science. Physical process of Computation Computation can be seen as a purely physical process occurring inside a closed physical system called a computer. Examples of such physical systems are digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, microfluidics-based computers, analog computers, and wetware computers. This point of view has been adopted by the physics of computation, a branch of theoretical physics, as well as the field of natural computing. An even more radical point of view, pancomputationalism (inaudible word), is the postulate of digital physics that argues that the evolution of the universe is itself ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics Databases
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g. dominance), and within the contex ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rna Pol II
RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription. Discovery Early studies suggested a minimum of two RNAPs: one which synthesized rRNA in the nucleolus, and one which synthesized other RNA in the nucleoplasm, part of the nucleus but outside the nucleolus. In 1969, science experimentalists Robert Roeder and William Rutter definitively discovered an additional RNAP that was responsible for transcription of some kind of RNA in the nucleoplasm. The finding was obtained by the use of ion-exchange chromatography via DEAE coated Sephadex beads. The technique separated the enzymes ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Human Cell
There are many different types of cells in the human body. Cells derived primarily from endoderm Exocrine secretory epithelial cells *Brunner's gland cell in duodenum ( enzymes and alkaline mucus) *Insulated goblet cell of respiratory and digestive tracts (mucus secretion) *Stomach ** Foveolar cell (mucus secretion) ** Chief cell (pepsinogen secretion) ** Parietal cell ( hydrochloric acid secretion) * Pancreatic acinar cell ( bicarbonate and digestive enzyme secretion) * Paneth cell of small intestine ( lysozyme secretion) *Type II pneumocyte of lung (surfactant secretion) * Club cell of lung Barrier cells *Type I pneumocyte (lung) * Gall bladder epithelial cell *Centroacinar cell (pancreas) * Intercalated duct cell (pancreas) *Intestinal brush border cell (with microvilli) Hormone-secreting cells * Enteroendocrine cell **K cell (secretes gastric inhibitory peptide) **L cell (secretes glucagon-like peptide-1, peptide YY3-36, oxyntomodulin, and glucagon-like pept ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Antibody
An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and Viral disease, viruses. The antibody recognizes a unique molecule of the pathogen, called an antigen. Each tip of the "Y" of an antibody contains a paratope (analogous to a lock) that is specific for one particular epitope (analogous to a key) on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can ''tag'' a microbe or an infected cell for attack by other parts of the immune system, or can neutralize it directly (for example, by blocking a part of a virus that is essential for its invasion). To allow the immune system to recognize millions of different antigens, the antigen-binding sites at both tips of the antibody come in an equally wide variety. In contrast, the remainder of the antibody is relatively constant. It only occurs ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChIP
Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites, and possibly define cistromes. ChIP also aims to determine the specific location in the genome that various histone modifications are associated with, indicating the target of the histone modifiers. ChIP is crucial for the advancements in the field of epigenomics and learning more about epigenetic phenomena. Briefly, the conventional method is as follows: # DNA and associated proteins on chromatin in living cells or tissues are crosslinked (this step is omitted in Native ChIP). # The DNA-protein complexes (chromatin-protein) are then sheared into ~500 bp DNA fragments by sonication or nuclease digestion. # Cross-linked DNA fragments associated with the pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNAP II
RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription. Discovery Early studies suggested a minimum of two RNAPs: one which synthesized rRNA in the nucleolus, and one which synthesized other RNA in the nucleoplasm, part of the nucleus but outside the nucleolus. In 1969, science experimentalists Robert Roeder and William Rutter definitively discovered an additional RNAP that was responsible for transcription of some kind of RNA in the nucleoplasm. The finding was obtained by the use of ion-exchange chromatography via DEAE coated Sephadex beads. The technique separated the enzyme ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell (biology)
The cell is the basic structural and functional unit of life forms. Every cell consists of a cytoplasm enclosed within a membrane, and contains many biomolecules such as proteins, DNA and RNA, as well as many small molecules of nutrients and metabolites.Cell Movements and the Shaping of the Vertebrate Body in Chapter 21 of Molecular Biology of the Cell '' fourth edition, edited by Bruce Alberts (2002) published by Garland Science. The Alberts text discusses how the "cellular building blocks" move to shape developing s. It is also common ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tissue (biology)
In biology, tissue is a biological organizational level between cells and a complete organ. A tissue is an ensemble of similar cells and their extracellular matrix from the same origin that together carry out a specific function. Organs are then formed by the functional grouping together of multiple tissues. The English word "tissue" derives from the French word "tissu", the past participle of the verb tisser, "to weave". The study of tissues is known as histology or, in connection with disease, as histopathology. Xavier Bichat is considered as the "Father of Histology". Plant histology is studied in both plant anatomy and physiology. The classical tools for studying tissues are the paraffin block in which tissue is embedded and then sectioned, the histological stain, and the optical microscope. Developments in electron microscopy, immunofluorescence, and the use of frozen tissue-sections have enhanced the detail that can be observed in tissues. With these tools, th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Eukaryotic
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacteria and Archaea (both prokaryotes) make up the other two domains. The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the Asgard archaea. This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among archaea. Eukaryotes represent a small minority of the number of organisms, but, due to their generally much larger size, their collective global biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.3–1.8 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs. Their name comes from the Greek εὖ (''eu'', "well" or "good") and κάρυον (''karyon'', "nut" or "kernel"). E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Curator
A curator (from la, cura, meaning "to take care") is a manager or overseer. When working with cultural organizations, a curator is typically a "collections curator" or an "exhibitions curator", and has multifaceted tasks dependent on the particular institution and its mission. In recent years the role of curator has evolved alongside the changing role of museums, and the term "curator" may designate the head of any given division. More recently, new kinds of curators have started to emerge: "community curators", "literary curators", " digital curators" and " biocurators". Collections curator A "collections curator", a "museum curator" or a "keeper" of a cultural heritage institution (e.g., gallery, museum, library or archive) is a content specialist charged with an institution's collections and involved with the interpretation of heritage material including historical artifacts. A collections curator's concern necessarily involves tangible objects of some sort—artwork, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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