Abstract

In our previous work, we developed four major bioinformatics tools/databases: (1) the web-based ANOVA-FDR software to provide user-friendly microarray data analysis (http://lgsun.grc.nia.nih.gov/ANOVA/);(2) an algorithm and a fully-automated computational pipeline for transcript assembly from expressed sequences aligned to the mouse genome;(3) a web-based browser to visualize all transcripts and alternative spliced forms of mouse genes (NIA Mouse Gene Index: http://lgsun.grc.nia.nih.gov/geneindex/mm9/);(4) a web-based database and tool to visualize and map the transcription factor binding sites of the mouse genome (CisView: http://lgsun.grc.nia.nih.gov/geneindex/mm6/cisview.html);and (5) a web-based tool to identify consensus sequence motifs based on the genome-wide chromatin-immunoprecipitation coupled with sequencing (ChIP-Seq) method (CisFinder: http: http://lgsun.grc.nia.nih.gov/CisFinder/). During the last year, we have been working on the maintaining and updating these bioinformatics resources.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute on Aging (NIA)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIAAG000702-04
Application #
8335896
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2011
Total Cost
$360,093
Indirect Cost

  Institution

Name
National Institute on Aging
Department
Type
DUNS #
City
State
Country
Zip Code

  Publications

Sharov, Alexei A; Schlessinger, David; Ko, Minoru S H (2015) ExAtlas: An interactive online tool for meta-analysis of gene expression data. J Bioinform Comput Biol 13:1550019
Amano, Tomokazu; Hirata, Tetsuya; Falco, Geppino et al. (2013) Zscan4 restores the developmental potency of embryonic stem cells. Nat Commun 4:1966
Monti, Manuela; Zanoni, Mario; Calligaro, Alberto et al. (2013) Developmental arrest and mouse antral not-surrounded nucleolus oocytes. Biol Reprod 88:2
Livigni, Alessandra; Peradziryi, Hanna; Sharov, Alexei A et al. (2013) A conserved Oct4/POUV-dependent network links adhesion and migration to progenitor maintenance. Curr Biol 23:2233-2244
Hung, Sandy S C; Wong, Raymond C B; Sharov, Alexei A et al. (2013) Repression of global protein synthesis by eif1a-like genes that are expressed specifically in the two-cell embryos and the transient zscan4-positive state of embryonic stem cells. DNA Res 20:391-402
Nishiyama, Akira; Sharov, Alexei A; Piao, Yulan et al. (2013) Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci Rep 3:1390
Morgani, Sophie M; Canham, Maurice A; Nichols, Jennifer et al. (2013) Totipotent embryonic stem cells arise in ground-state culture conditions. Cell Rep 3:1945-57
Xu, Dongyi; Shen, Weiping; Guo, Rong et al. (2013) Top3? is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat Neurosci 16:1238-47
Yang, Hsih-Te; Ko, Minoru S H (2012) Stochastic modeling for the expression of a gene regulated by competing transcription factors. PLoS One 7:e32376
Sharov, Alexei A; Nishiyama, Akira; Piao, Yulan et al. (2011) Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. BMC Genomics 12:102

Showing the most recent 10 out of 16 publications