Literature DB >> 16030070

PACdb: PolyA Cleavage Site and 3'-UTR Database.

J Michael Brockman1, Priyam Singh, Donglin Liu, Sean Quinlan, Jesse Salisbury, Joel H Graber.   

Abstract

UNLABELLED: The PolyA Cleavage Site and 3'-UTR Database (PACdb) is a web-accessible database that catalogs putative 3'-processing sites and 3'-UTR sequences for multiple organisms. Sites have been identified primarily via expressed sequence tag-genome alignments, enabling delineation of both the specificities and heterogeneity of 3'-processing events. AVAILABILITY: By web browser or CGI: PACdb: http://harlequin.jax.org/pacdb/; AtPACdb: http://harlequin.jax.org/atpacdb/. SUPPLEMENTARY INFORMATION: Available online at http://harlequin.jax.org/pacdb/supplemental.php.

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Year:  2005        PMID： 16030070     DOI： 10.1093/bioinformatics/bti589

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  37 in total

1.  Identification of gene 3' ends by automated EST cluster analysis.

Authors:  Enrique M Muro; Robert Herrington; Salima Janmohamed; Catherine Frelin; Miguel A Andrade-Navarro; Norman N Iscove
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-18       Impact factor: 11.205

2.  Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier.

Authors:  Sarah Sheppard; Nathan D Lawson; Lihua Julie Zhu
Journal:  Bioinformatics       Date:  2013-08-20       Impact factor: 6.937

Review 3.  Signals for pre-mRNA cleavage and polyadenylation.

Authors:  Bin Tian; Joel H Graber
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-10-19       Impact factor: 9.957

4.  Characterization and prediction of mRNA polyadenylation sites in human genes.

Authors:  Tzu-Hao Chang; Li-Ching Wu; Yu-Ting Chen; Hsien-Da Huang; Baw-Jhiune Liu; Kuang-Fu Cheng; Jorng-Tzong Horng
Journal:  Med Biol Eng Comput       Date:  2011-02-01       Impact factor: 2.602

5.  mRNA isoform diversity can obscure detection of miRNA-mediated control of translation.

Authors:  Jennifer L Clancy; Grace H Wei; Nicole Echner; David T Humphreys; Traude H Beilharz; Thomas Preiss
Journal:  RNA       Date:  2011-04-05       Impact factor: 4.942

Review 6.  Ending the message: poly(A) signals then and now.

Authors:  Nick J Proudfoot
Journal:  Genes Dev       Date:  2011-09-01       Impact factor: 11.361

Review 7.  Current approaches to micro-RNA analysis and target gene prediction.

Authors:  Tenzin W Lhakhang; M Ahmad Chaudhry
Journal:  J Appl Genet       Date:  2011-09-03       Impact factor: 3.240

8.  In silico method for systematic analysis of feature importance in microRNA-mRNA interactions.

Authors:  Jiamin Xiao; Yizhou Li; Kelong Wang; Zhining Wen; Menglong Li; Lifang Zhang; Xuanmin Guang
Journal:  BMC Bioinformatics       Date:  2009-12-16       Impact factor: 3.169

9.  Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation.

Authors:  Jesse Salisbury; Keith W Hutchison; Karen Wigglesworth; John J Eppig; Joel H Graber
Journal:  PLoS One       Date:  2009-10-16       Impact factor: 3.240

10.  The relationship between the evolution of microRNA targets and the length of their UTRs.

Authors:  Chao Cheng; Nitin Bhardwaj; Mark Gerstein
Journal:  BMC Genomics       Date:  2009-09-14       Impact factor: 3.969
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