Last rolls of the yoyo: Assessing the human canonical protein count

F1000Research
Christopher Southan

Abstract

In 2004, when the protein estimate from the finished human genome was only 24,000, the surprise was compounded as reviewed estimates fell to 19,000 by 2014. However, variability in the total canonical protein counts (i.e. excluding alternative splice forms) of open reading frames (ORFs) in different annotation portals persists. This work assesses these differences and possible causes. A 16-year analysis of Ensembl and UniProtKB/Swiss-Prot shows convergence to a protein number of ~20,000. The former had shown some yo-yoing, but both have now plateaued. Nine major annotation portals, reviewed at the beginning of 2017, gave a spread of counts from 21,819 down to 18,891. The 4-way cross-reference concordance (within UniProt) between Ensembl, Swiss-Prot, Entrez Gene and the Human Gene Nomenclature Committee (HGNC) drops to 18,690, indicating methodological differences in protein definitions and experimental existence support between sources. The Swiss-Prot and neXtProt evidence criteria include mass spectrometry peptide verification and also cross-references for antibody detection from the Human Protein Atlas. Notwithstanding, hundreds of Swiss-Prot entries are classified as non-coding biotypes by HGNC. The only inference that prote...Continue Reading

References

Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Jan 1, 1952·Advances in Protein Chemistry·F SANGER
Oct 22, 2004·Nature·UNKNOWN International Human Genome Sequencing Consortium
Dec 31, 2005·Nucleic Acids Research·Frank DesiereRuedi Aebersold
Nov 28, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michele ClampEric S Lander
May 6, 2010·Genome Biology·Mihaela Pertea, Steven L Salzberg
Jun 19, 2014·Human Molecular Genetics·Iakes EzkurdiaMichael L Tress
Apr 22, 2015·Nucleic Acids Research·Damian SmedleyArek Kasprzyk
Nov 29, 2015·Biochemical Society Transactions·Muhammad Ali S Mumtaz, Juan Pablo Couso
Apr 7, 2016·Database : the Journal of Biological Databases and Curation·Simon FishilevichDoron Lancet
Jun 5, 2016·Trends in Biochemical Sciences·Jose I PueyoJuan P Couso
Sep 7, 2016·Nature Methods·Mathias UhlenTadashi Yamamoto
Oct 8, 2016·Trends in Biochemical Sciences·Michael L TressAlfonso Valencia
Nov 1, 2016·Nature Reviews. Genetics·Jonathan M Mudge, Jennifer Harrow
Nov 26, 2016·Expert Review of Proteomics·Victor SeguraFernando J Corrales
Dec 3, 2016·Nucleic Acids Research·UNKNOWN NCBI Resource Coordinators
Dec 3, 2016·Nucleic Acids Research·Bronwen L AkenPaul Flicek
Dec 3, 2016·Nucleic Acids Research·Pascale GaudetAmos Bairoch
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium
Feb 28, 2017·Nature·Chung-Chau HonAlistair R R Forrest
Mar 1, 2017·Nature Methods·Yasset Perez-Riverol, Juan Antonio Vizcaíno

❮ Previous
Next ❯

Citations

Oct 6, 2017·Nature Reviews. Rheumatology·Yuanjia TangNan Shen

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
NMR
Edman
APLEA
RNA-seq

Software Mentioned

HNGC
neXtProt
IUPHAR Guide
ProteinAtlas
Swiss
neXprot
GeneCards
PeptideAtlas
APELA
GtoPdb

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.