RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions.

Nucleic Acids Research
Maiwen Caudron-HergerSven Diederichs

Abstract

RNA-protein complexes have emerged as central players in numerous key cellular processes with significant relevance in health and disease. To further deepen our knowledge of RNA-binding proteins (RBPs), multiple proteome-wide strategies have been developed to identify RBPs in different species leading to a large number of studies contributing experimentally identified as well as predicted RBP candidate catalogs. However, the rapid evolution of the field led to an accumulation of isolated datasets, hampering the access and comparison of their valuable content. Moreover, tools to link RBPs to cellular pathways and functions were lacking. Here, to facilitate the efficient screening of the RBP resources, we provide RBP2GO (https://RBP2GO.DKFZ.de), a comprehensive database of all currently available proteome-wide datasets for RBPs across 13 species from 53 studies including 105 datasets identifying altogether 22 552 RBP candidates. These are combined with the information on RBP interaction partners and on the related biological processes, molecular functions and cellular compartments. RBP2GO offers a user-friendly web interface with an RBP scoring system and powerful advanced search tools allowing forward and reverse searches connec...Continue Reading

References

Jun 25, 2003·Molecular Cell·Justin B GreenAneel K Aggarwal
Feb 19, 2005·Current Opinion in Structural Biology·Raymond S Brown
Jan 24, 2006·Nature Structural & Molecular Biology·Florian C OberstrassFrédéric H-T Allain
Mar 24, 2007·Bioinformatics·Baris E SuzekCathy H Wu
May 3, 2007·Nature Reviews. Molecular Cell Biology·Bradley M LundeGabriele Varani
Feb 21, 2008·Cell Biochemistry and Biophysics·Kathryn J BrayerDavid J Segal
Nov 27, 2008·Bioinformatics·Seth CarbonUNKNOWN Web Presence Working Group
Nov 3, 2010·Nucleic Acids Research·Kate B CookTimothy R Hughes
Dec 4, 2010·Briefings in Functional Genomics·Shivendra KishoreMihaela Zavolan
Jun 5, 2012·Cell·Alfredo CastelloMatthias W Hentze
Jun 12, 2012·Molecular Cell·Alexander G BaltzMarkus Landthaler
Jul 13, 2013·Nature·Debashish RayTimothy R Hughes
Aug 6, 2013·Nature Structural & Molecular Biology·S Chul KwonV Narry Kim
Nov 5, 2014·Nature Reviews. Genetics·Stefanie GerstbergerThomas Tuschl
Nov 16, 2014·Bioinformatics·Baris E SuzekUNKNOWN UniProt Consortium
Nov 26, 2015·Nature Structural & Molecular Biology·Ana M Matia-GonzálezAndré P Gerber
Dec 4, 2015·Nature Communications·Benedikt M BeckmannMatthias W Hentze
Mar 19, 2016·Molecular Cell·Balaji SundararamanGene W Yeo
Apr 5, 2016·Nature Communications·Thomas ConradUlf Andersson Ørom
May 20, 2016·Genome Research·Hans-Hermann WesselsMarkus Landthaler
Jul 6, 2016·Nature Communications·Vasiliy O SysoevAnne Ephrussi
Jul 7, 2016·Genome Biology·Evelien M BunnikKarine G Le Roch
Jul 28, 2016·Molecular Cell·Alfredo CastelloMatthias W Hentze
Oct 30, 2016·Nucleic Acids Research·Lukasz P Kozlowski
Jun 10, 2017·Genome Research·Miha MilekMarkus Landthaler
Jun 27, 2017·Journal of Proteome Research·Meeli MullariMichael L Nielsen
Feb 13, 2018·Nature Methods·Xichen BaoMiguel A Esteban
Oct 26, 2018·Nucleic Acids Research·Madalina GiurgiuAndreas Ruepp
Oct 30, 2018·Nucleic Acids Research·John G TateSimon A Forbes
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Dec 12, 2018·Cell·Jakob TrendelJeroen Krijgsveld
Feb 26, 2019·Molecular Cell·Manuel Garcia-MorenoAlfredo Castello
Mar 3, 2019·Nature Communications·Erika C UrdanetaBenedikt M Beckmann
Apr 10, 2019·Molecular Systems Biology·Vadim ShchepachevDavid Tollervey
Jun 20, 2019·Nature Communications·Amol PanhaleAsifa Akhtar
Oct 31, 2019·Cell Reports·Anna L MallamKevin Drew
Jun 13, 2020·Trends in Biochemical Sciences·Erin L Sternburg, Fedor V Karginov
Jun 27, 2020·Nature Communications·Minakshi GandhiSven Diederichs

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Citations

Dec 23, 2020·Nature Microbiology·Nora SchmidtMathias Munschauer
Jun 11, 2021·Biochemical Society Transactions·Nicole J Curtis, Constance J Jeffery
Nov 5, 2021·Nature Reviews. Nephrology·Lisa SeufertRoman-Ulrich Müller

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Methods Mentioned

BETA
affinity purification

Software Mentioned

Protein Search
RBP2GO
GO Search
STRING
Advanced Search
QuickGO
CORUM
R package ‘ GO . db ’
TrEMBL

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