Literature DB >> 22702248

WikiCell: a unified resource platform for human transcriptomics research.

Dongyu Zhao1, Jiayan Wu, Yuanyuan Zhou, Wei Gong, Jingfa Xiao, Jun Yu.   

Abstract

Here we present a database, WikiCell, as a portal for a unified view of the human transcriptome. At present, WikiCell consists of Expressed Sequenced Tags (ESTs), and users can access, curate, and submit database data by interactive mode, and also can browse, query, upload, and download sequences. Researchers can utilize the transcriptome model based on a human taxonomy graph. The sequences in each model are sorted by attributes such as physiological and pathological samples. The Genbank EST data format are conserved. Gene information is provided, including housekeeping genes, taxonomy location, and gene ontology (GO) description. We believe that WikiCell provides a useful resource for defining expression pattern and tissue differentiation based on human taxonomy mode. It can be accessed at http://www.wikicell.org/.

Entities:  

Mesh:

Year:  2012        PMID: 22702248      PMCID: PMC3369277          DOI: 10.1089/omi.2011.0139

Source DB:  PubMed          Journal:  OMICS        ISSN: 1536-2310


  21 in total

1.  On the nature of human housekeeping genes.

Authors:  Jiang Zhu; Fuhong He; Songnian Hu; Jun Yu
Journal:  Trends Genet       Date:  2008-09-09       Impact factor: 11.639

2.  DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Authors:  Likun Wang; Zhixing Feng; Xi Wang; Xiaowo Wang; Xuegong Zhang
Journal:  Bioinformatics       Date:  2009-10-24       Impact factor: 6.937

3.  Identification of novel transcripts in annotated genomes using RNA-Seq.

Authors:  Adam Roberts; Harold Pimentel; Cole Trapnell; Lior Pachter
Journal:  Bioinformatics       Date:  2011-06-21       Impact factor: 6.937

Review 4.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

5.  MOPED: Model Organism Protein Expression Database.

Authors:  Eugene Kolker; Roger Higdon; Winston Haynes; Dean Welch; William Broomall; Doron Lancet; Larissa Stanberry; Natali Kolker
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

6.  Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules.

Authors:  Eran Hodis; Jaime Prilusky; Eric Martz; Israel Silman; John Moult; Joel L Sussman
Journal:  Genome Biol       Date:  2008-08-03       Impact factor: 13.583

7.  Mining biological pathways using WikiPathways web services.

Authors:  Thomas Kelder; Alexander R Pico; Kristina Hanspers; Martijn P van Iersel; Chris Evelo; Bruce R Conklin
Journal:  PLoS One       Date:  2009-07-30       Impact factor: 3.240

8.  TopHat: discovering splice junctions with RNA-Seq.

Authors:  Cole Trapnell; Lior Pachter; Steven L Salzberg
Journal:  Bioinformatics       Date:  2009-03-16       Impact factor: 6.937

9.  How many human genes can be defined as housekeeping with current expression data?

Authors:  Jiang Zhu; Fuhong He; Shuhui Song; Jing Wang; Jun Yu
Journal:  BMC Genomics       Date:  2008-04-16       Impact factor: 3.969

10.  WikiPathways: pathway editing for the people.

Authors:  Alexander R Pico; Thomas Kelder; Martijn P van Iersel; Kristina Hanspers; Bruce R Conklin; Chris Evelo
Journal:  PLoS Biol       Date:  2008-07-22       Impact factor: 8.029

View more
  9 in total

1.  MOPED enables discoveries through consistently processed proteomics data.

Authors:  Roger Higdon; Elizabeth Stewart; Larissa Stanberry; Winston Haynes; John Choiniere; Elizabeth Montague; Nathaniel Anderson; Gregory Yandl; Imre Janko; William Broomall; Simon Fishilevich; Doron Lancet; Natali Kolker; Eugene Kolker
Journal:  J Proteome Res       Date:  2013-12-18       Impact factor: 4.466

2.  On bioinformatic resources.

Authors:  Runsheng Chen
Journal:  Genomics Proteomics Bioinformatics       Date:  2015-03-02       Impact factor: 7.691

Review 3.  Biological databases for human research.

Authors:  Dong Zou; Lina Ma; Jun Yu; Zhang Zhang
Journal:  Genomics Proteomics Bioinformatics       Date:  2015-02-21       Impact factor: 7.691

4.  Ribogenomics: the science and knowledge of RNA.

Authors:  Jiayan Wu; Jingfa Xiao; Zhang Zhang; Xumin Wang; Songnian Hu; Jun Yu
Journal:  Genomics Proteomics Bioinformatics       Date:  2014-04-24       Impact factor: 7.691

5.  Database Resources of the BIG Data Center in 2018.

Authors: 
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

6.  Community intelligence in knowledge curation: an application to managing scientific nomenclature.

Authors:  Lin Dai; Chao Xu; Ming Tian; Jian Sang; Dong Zou; Ang Li; Guocheng Liu; Fei Chen; Jiayan Wu; Jingfa Xiao; Xumin Wang; Jun Yu; Zhang Zhang
Journal:  PLoS One       Date:  2013-02-25       Impact factor: 3.240

7.  RiceWiki: a wiki-based database for community curation of rice genes.

Authors:  Zhang Zhang; Jian Sang; Lina Ma; Gang Wu; Hao Wu; Dawei Huang; Dong Zou; Siqi Liu; Ang Li; Lili Hao; Ming Tian; Chao Xu; Xumin Wang; Jiayan Wu; Jingfa Xiao; Lin Dai; Ling-Ling Chen; Songnian Hu; Jun Yu
Journal:  Nucleic Acids Res       Date:  2013-10-16       Impact factor: 16.971

8.  MTD: a mammalian transcriptomic database to explore gene expression and regulation.

Authors:  Xin Sheng; Jiayan Wu; Qianqian Sun; Xue Li; Feng Xian; Manman Sun; Wan Fang; Meili Chen; Jun Yu; Jingfa Xiao
Journal:  Brief Bioinform       Date:  2016-01-27       Impact factor: 11.622

9.  Database Resources of the BIG Data Center in 2019.

Authors: 
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.