Human Proteinpedia, which is closely associated with Institute of Bioinformatics (IOB),

Bangalore Bangalore (), officially Bengaluru (), is the capital and largest city of the Indian state of Karnataka. It has a population of more than and a metropolitan population of around , making it the third most populous city and fifth most ...

and

Johns Hopkins University Johns Hopkins University (Johns Hopkins, Hopkins, or JHU) is a private university, private research university in Baltimore, Maryland. Founded in 1876, Johns Hopkins is the oldest research university in the United States and in the western hem ...

, is a portal for sharing and integration of human proteomic data. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database (

HPRD The Human Protein Reference Database (HPRD) is a protein database accessible through the Internet. It is closely associated with the premier Indian Non-Profit research organisation Institute of Bioinformatics (IOB), Bangalore. This database is a c ...

) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information at the context of an individual protein. In essence, researchers can add new data to HPRD by registering to Human Proteinpedia. The data deposited in Human Proteinpedia is freely available for download. Emphasizing the importance of

proteomics Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

data disposition to public repositories, ''Nature Methods'' recommends Human Proteinpedia in their editorial.Editorial. Thou shalt share your data. Nat Methods. 2008 Mar;5:209 More than 70 labs participate in this effort.

Data types

Data pertaining to

post-translational modifications Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes ...

, protein–protein interactions, tissue expression, expression in

cell lines An immortalised cell line is a population of cells from a multicellular organism which would normally not proliferate indefinitely but, due to mutation, have evaded normal cellular senescence and instead can keep undergoing division. The cells ...

subcellular localization The cells of eukaryotic organisms are elaborately subdivided into functionally-distinct membrane-bound compartments. Some major constituents of eukaryotic cells are: extracellular space, plasma membrane, cytoplasm, nucleus, mitochondria, Golgi ap ...

and

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

substrate relationships can be submitted to Human Proteinpedia.

Experimental platforms

Protein annotations present in Human Proteinpedia are derived from a number of platforms such as #

Co-immunoprecipitation Immunoprecipitation (IP) is the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a samp ...

and

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is use ...

-based protein–protein interaction #

and Western blotting based protein–protein interaction #

Fluorescence Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, tha ...

based experiments #

Immunohistochemistry Immunohistochemistry (IHC) is the most common application of immunostaining. It involves the process of selectively identifying antigens (proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to an ...

# Mass spectrometric analysis #

Protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

and

peptide microarray A peptide microarray (also commonly known as peptide chip or peptide epitope microarray) is a collection of peptides displayed on a solid surface, usually a glass or plastic chip. Peptide chips are used by scientists in biology, medicine and pharm ...

s #

Western blot The western blot (sometimes called the protein immunoblot), or western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract. Besides detect ...

ting #

Yeast two-hybrid Two-hybrid screening (originally known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein–protein interactions (PPIs) and protein–DNA interactions by testing for physical interactions (such as bindi ...

based protein–protein interaction This portal that allows adding of protein information was developed as a collaborative effort between the laboratory of Dr. Akhilesh Pandey at

and the Institute of Bioinformatics.

FAQs

* What are the criteria for contributing data? Any investigator who fulfills the following criteria can contribute data: i) provides experimentally derived data, and, ii) is willing to share data, and, iii) is willing to be listed as the 'contributor' of the data * Can I contribute data anonymously? Anonymous contributions are not allowed. Contributor details should be clearly presented while contributing data. * Can bioinformatically predicted data be shared through Human Proteinpedia? Predictions of any type are not allowed. Contributed data should be derived experimentally and should be accompanied with experimental evidence. * Is the contributed data subjected to peer review? The data are not subjected to peer review and the actual experimental data (raw or processed) should be provided. * What will happen to conflicting results from different laboratories? In cases where a given entry is documented as erroneous, we will consult with the contributing group(s) about deleting the entry.

External links

humanproteinpedia.orgwww.hprd.org

References

{{reflist Bioinformatics Proteomics