POSTAR2: deciphering the post-transcriptional regulatory logics

Nucleic Acids Research
Yumin ZhuPengyuan Wang

Abstract

Post-transcriptional regulation of RNAs is critical to the diverse range of cellular processes. The volume of functional genomic data focusing on post-transcriptional regulation logics continues to grow in recent years. In the current database version, POSTAR2 (http://lulab.life.tsinghua.edu.cn/postar), we included the following new features and data: updated ∼500 CLIP-seq datasets (∼1200 CLIP-seq datasets in total) from six species, including human, mouse, fly, worm, Arabidopsis and yeast; added a new module 'Translatome', which is derived from Ribo-seq datasets and contains ∼36 million open reading frames (ORFs) in the genomes from the six species; updated and unified post-transcriptional regulation and variation data. Finally, we improved web interfaces for searching and visualizing protein-RNA interactions with multi-layer information. Meanwhile, we also merged our CLIPdb database into POSTAR2. POSTAR2 will help researchers investigate the post-transcriptional regulatory logics coordinated by RNA-binding proteins and translational landscape of cellular RNAs.

References

Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Apr 18, 2007·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Patricia M McGowanMichael J Duffy
Sep 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Michal RabaniEran Segal
Nov 27, 2008·Bioinformatics·Seth CarbonUNKNOWN Web Presence Working Group
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Apr 24, 2009·Annual Review of Microbiology·Paul BabitzkeTony Romeo
Nov 17, 2009·Nucleic Acids Research·Todd W HarrisPaul W Sternberg
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
Aug 20, 2011·Genome Biology·David L CorcoranUwe Ohler
Nov 24, 2011·Nucleic Acids Research·J Michael CherryEdith D Wong
Jan 19, 2012·Nature Reviews. Genetics·Julian KönigJernej Ule
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
Oct 2, 2012·Bioinformatics·Philip J UrenAndrew D Smith
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Dec 27, 2013·Science China. Life Sciences·Yucheng YangZhi John Lu
Nov 6, 2014·Genome Research·Han-Qing ZhaoLiping Wei
Feb 6, 2015·BMC Genomics·Yu-Cheng T YangZhi John Lu
Nov 21, 2015·Nucleic Acids Research·Yi ZhaoRunsheng Chen
Dec 15, 2015·Nature Methods·Lorenzo CalvielloUwe Ohler
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Jul 19, 2017·Trends in Cancer·Bruno PereiraRaquel Almeida
Sep 10, 2017·Trends in Genetics : TIG·Lorenzo Calviello, Uwe Ohler
Oct 19, 2017·Nucleic Acids Research·Jia-Jia XuanJian-Hua Yang
Nov 8, 2017·Frontiers in Molecular Biosciences·Sofía M García-MauriñoIrene Díaz-Moreno
Nov 11, 2017·Nucleic Acids Research·Carrie A DavisJ Michael Cherry
Nov 23, 2017·Nucleic Acids Research·Irene PapatheodorouRobert Petryszak
Jan 18, 2018·Nature Reviews. Molecular Cell Biology·Matthias W HentzeThomas Preiss
Jan 18, 2018·Wiley Interdisciplinary Reviews. RNA·Robert F HarveyAnne E Willis
Feb 6, 2018·Molecular Cell·Flora C Y Lee, Jernej Ule
Mar 30, 2018·Cell Systems·Kyle EllrottUNKNOWN Cancer Genome Atlas Research Network

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Citations

May 31, 2019·Nucleic Acids Research·Qi Liu, Richard I Gregory
Jun 20, 2019·Protein and Peptide Letters·Amit Sagar, Bin Xue
Oct 9, 2019·The Journal of Clinical Investigation·Changhao ChenTianxin Lin
Sep 12, 2019·RNA·Muhammad IdrisDavid M Virshup
Sep 23, 2020·Nucleic Acids Research·Yuhui DouTorben Heick Jensen
Jul 17, 2020·Nature Machine Intelligence·Shinya TasakiYanling Wang
Jan 24, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Richard Virgen-SlaneCarl F Ware
Jun 20, 2020·Nucleic Acids Research·Alexander Gulliver Bjørnholt GrønningBrage Storstein Andresen
Feb 23, 2020·Frontiers in Genetics·Lihong PengLiqian Zhou
Jun 5, 2020·Nature Communications·Nuria Casas-VilaFalk Butter
Nov 30, 2019·Frontiers in Pharmacology·Julia A FilippovaGrigory A Stepanov
Jul 18, 2020·Communications Biology·Juan XieShiyong Liu
Jan 8, 2020·Nucleic Acids Research·Yunqing LinDong Wang
Jun 23, 2020·Evolutionary Bioinformatics Online·Bowen SongZhen Wei
Oct 7, 2020·Nucleic Acids Research·Xiaotong LuoZhixiang Zuo
Dec 4, 2020·Nucleic Acids Research·Jen-Hao YangMyriam Gorospe
Dec 12, 2019·Cell Reports·Toshiaki ShigeokaChristine E Holt
Mar 7, 2021·Non-coding RNA·Elena López-Jiménez, Eduardo Andrés-León
Mar 12, 2021·Methods : a Companion to Methods in Enzymology·Jiani MaHui Liu
Mar 19, 2021·Frontiers in Genetics·Yiqian Zhang, Michiaki Hamada
Mar 27, 2021·EMBO Reports·Shengjie WangHong-Tao Zhang
Apr 28, 2021·Nucleic Acids Research·Lorenzo CalvielloStephen N Floor
May 30, 2021·Nucleic Acids Research·Yuwei ZhangYi Zhao
Jul 3, 2021·Nature Genetics·Xushen XiongManolis Kellis
Aug 28, 2021·Biomolecules·Fotis A BaltoumasGeorgios A Pavlopoulos
Sep 23, 2021·Nucleic Acids Research·Jing FengChunjiang He

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Methods Mentioned

BETA
immunoprecipitation
CLIP-seq
Ribo-seq
eCLIP-seq
eCLIP
PIP-seq
CLIP
PAR-CLIP
iCLIP
HITS-CLIP

Software Mentioned

Cufflinks
CLIP
RNAcontext
NovoAlign
RNApromo
RiboWave
TopHat
CLIPdb
Piranha
AmiGO

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