Literature DB >> 19900953

hPDI: a database of experimental human protein-DNA interactions.

Zhi Xie1, Shaohui Hu, Seth Blackshaw, Heng Zhu, Jiang Qian.   

Abstract

UNLABELLED: The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for >500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes. AVAILABILITY: http://bioinfo.wilmer.jhu.edu/PDI/.

Entities:  

Mesh：

Substances：

Year:  2009        PMID： 19900953      PMCID： PMC2804296          DOI： 10.1093/bioinformatics/btp631

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


  13 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Authors:  Albin Sandelin; Wynand Alkema; Pär Engström; Wyeth W Wasserman; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  WebLogo: a sequence logo generator.

Authors:  Gavin E Crooks; Gary Hon; John-Marc Chandonia; Steven E Brenner
Journal:  Genome Res       Date:  2004-06       Impact factor: 9.043

4.  A gene-centered C. elegans protein-DNA interaction network.

Authors:  Bart Deplancke; Arnab Mukhopadhyay; Wanyuan Ao; Ahmed M Elewa; Christian A Grove; Natalia J Martinez; Reynaldo Sequerra; Lynn Doucette-Stamm; John S Reece-Hoyes; Ian A Hope; Heidi A Tissenbaum; Susan E Mango; Albertha J M Walhout
Journal:  Cell       Date:  2006-06-16       Impact factor: 41.582

5.  Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.

Authors:  Marcus B Noyes; Ryan G Christensen; Atsuya Wakabayashi; Gary D Stormo; Michael H Brodsky; Scot A Wolfe
Journal:  Cell       Date:  2008-06-27       Impact factor: 41.582

6.  Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling.

Authors:  Shaohui Hu; Zhi Xie; Akishi Onishi; Xueping Yu; Lizhi Jiang; Jimmy Lin; Hee-sool Rho; Crystal Woodard; Hong Wang; Jun-Seop Jeong; Shunyou Long; Xiaofei He; Herschel Wade; Seth Blackshaw; Jiang Qian; Heng Zhu
Journal:  Cell       Date:  2009-10-30       Impact factor: 41.582

7.  TRANSFAC: a database on transcription factors and their DNA binding sites.

Authors:  E Wingender; P Dietze; H Karas; R Knüppel
Journal:  Nucleic Acids Res       Date:  1996-01-01       Impact factor: 16.971

8.  An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression.

Authors:  David N Messina; Jarret Glasscock; Warren Gish; Michael Lovett
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

9.  A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Authors:  Gwenael Badis; Esther T Chan; Harm van Bakel; Lourdes Pena-Castillo; Desiree Tillo; Kyle Tsui; Clayton D Carlson; Andrea J Gossett; Michael J Hasinoff; Christopher L Warren; Marinella Gebbia; Shaheynoor Talukder; Ally Yang; Sanie Mnaimneh; Dimitri Terterov; David Coburn; Ai Li Yeo; Zhen Xuan Yeo; Neil D Clarke; Jason D Lieb; Aseem Z Ansari; Corey Nislow; Timothy R Hughes
Journal:  Mol Cell       Date:  2008-12-26       Impact factor: 17.970

10.  UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.

Authors:  Daniel E Newburger; Martha L Bulyk
Journal:  Nucleic Acids Res       Date:  2008-10-08       Impact factor: 16.971
View more
  46 in total

Review 1.  Systematic characterization of protein-DNA interactions.

Authors:  Zhi Xie; Shaohui Hu; Jiang Qian; Seth Blackshaw; Heng Zhu
Journal:  Cell Mol Life Sci       Date:  2011-01-05       Impact factor: 9.261

2.  Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Authors:  Lingyun Song; Zhancheng Zhang; Linda L Grasfeder; Alan P Boyle; Paul G Giresi; Bum-Kyu Lee; Nathan C Sheffield; Stefan Gräf; Mikael Huss; Damian Keefe; Zheng Liu; Darin London; Ryan M McDaniell; Yoichiro Shibata; Kimberly A Showers; Jeremy M Simon; Teresa Vales; Tianyuan Wang; Deborah Winter; Zhuzhu Zhang; Neil D Clarke; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Jason D Lieb; Terrence S Furey
Journal:  Genome Res       Date:  2011-07-12       Impact factor: 9.043

Review 3.  DNA-protein interaction: identification, prediction and data analysis.

Authors:  Abbasali Emamjomeh; Darush Choobineh; Behzad Hajieghrari; Nafiseh MahdiNezhad; Amir Khodavirdipour
Journal:  Mol Biol Rep       Date:  2019-03-26       Impact factor: 2.316

4.  Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data.

Authors:  Xin Zhou; Zhibin Chen; Xiaodong Cai
Journal:  Epigenetics       Date:  2018-08-07       Impact factor: 4.528

5.  Computational methodology for ChIP-seq analysis.

Authors:  Hyunjin Shin; Tao Liu; Xikun Duan; Yong Zhang; X Shirley Liu
Journal:  Quant Biol       Date:  2013-03-01

Review 6.  Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges.

Authors:  Weiqiang Zhou; Ben Sherwood; Hongkai Ji
Journal:  Hum Hered       Date:  2017-01-12       Impact factor: 0.444

7.  RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

Authors:  Jaime Abraham Castro-Mondragon; Sébastien Jaeger; Denis Thieffry; Morgane Thomas-Chollier; Jacques van Helden
Journal:  Nucleic Acids Res       Date:  2017-07-27       Impact factor: 16.971

8.  Characterization of protein-DNA interactions using protein microarrays.

Authors:  Shaohui Hu; Zhi Xie; Seth Blackshaw; Jiang Qian; Heng Zhu
Journal:  Cold Spring Harb Protoc       Date:  2011-05-01

9.  Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter.

Authors:  Michal Mikula; Pawel Gaj; Karolina Dzwonek; Tymon Rubel; Jakub Karczmarski; Agnieszka Paziewska; Artur Dzwonek; Piotr Bragoszewski; Michal Dadlez; Jerzy Ostrowski
Journal:  DNA Res       Date:  2010-06-29       Impact factor: 4.458

10.  Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons.

Authors:  Simona Lodato; Bradley J Molyneaux; Emanuela Zuccaro; Loyal A Goff; Hsu-Hsin Chen; Wen Yuan; Alyssa Meleski; Emi Takahashi; Shaun Mahony; John L Rinn; David K Gifford; Paola Arlotta
Journal:  Nat Neurosci       Date:  2014-07-06       Impact factor: 24.884
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.