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 maintaining and updating these bioinformatics resources. We have also developed a new algorithm to simulate the gene expression regulated by two competing transcription factors. We continue to apply our software tools to various biological problems of our own and in collaboration, which yielded a few publications. We are working constantly to maintain and update the bioinformatics resources that we have developed and made available to the research community. We will continue the development of new algorithms and websites for bioinformatics needs.

Agency
National Institute of Health (NIH)
Institute
National Institute on Aging (NIA)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIAAG000702-06
Application #
8736594
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
6
Fiscal Year
2013
Total Cost
$501,343
Indirect Cost
Name
National Institute on Aging
Department
Type
DUNS #
City
State
Country
Zip Code
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 :1550019
Akiyama, Tomohiko; Xin, Li; Oda, Mayumi et al. (2015) Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res 22:307-18
Monti, Manuela; Zanoni, Mario; Calligaro, Alberto et al. (2013) Developmental arrest and mouse antral not-surrounded nucleolus oocytes. Biol Reprod 88:2
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) Top3β is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat Neurosci 16:1238-47
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 23:2233-44
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

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