From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT

Gonye, Gregory E.; Chakravarthula, Praveen; Schwaber, James S.; Vadigepalli, Rajanikanth

doi:10.1007/978-1-59745-547-3_4

Cited by 21 publications

(17 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The PAINT tool (28) offers similar functionality by integrating Match (16) in the TRANSFAC Public or Professional databases and promoter sequence retrieval for human, mouse and rat. Compared to PAINT, LASAGNA-Search contains 1726 TF models from four source databases and retrieves promoters for seven species.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

LASAGNA-Search: an Integrated Web Tool for Transcription Factor Binding Site Search and Visualization

2013

View full text Add to dashboard Cite

The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism ENCyclopedia Of DNA Elements (modENCODE) projects has significantly increased the amount of transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely use TF binding site (TFBS) search tools to scan unannotated sequences for TFBSs, particularly when searching for lesser-known TFs or TFs in organisms for which ChIP-seq data are unavailable. The sequence analysis often involves multiple steps such as TF model collection, promoter sequence retrieval, and visualization; thus, several different tools are required. We have developed a novel integrated web tool named LASAGNA-Search that allows users to perform TFBS searches without leaving the web site. LASAGNA-Search uses the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm for TFBS alignment. Important features of LASAGNA-Search include (i) acceptance of unaligned variable-length TFBSs, (ii) a collection of 1726 TF models, (iii) automatic promoter sequence retrieval, (iv) visualization in the UCSC Genome Browser, and (v) gene regulatory network inference and visualization based on binding specificities. LASAGNA-Search is freely available at http://biogrid.engr.uconn.edu/lasagna_search/.

show abstract

Section: Resultsmentioning

confidence: 99%

“…The MAPPER2 database (10) supports visualization of hits in the UCSC Genome Browser (29) for three organisms. Another useful fuction is visual representation of predicted binding specificities as a gene regulatory network (GRN) (28). Until now, there was no single web tool that incorporated all the aforementioned features.…”

mentioning

confidence: 99%

LASAGNA-Search: an Integrated Web Tool for Transcription Factor Binding Site Search and Visualization

2013

View full text Add to dashboard Cite

show abstract

“…Transcriptional Regulation Element Promotor Analysis and Interaction Network-Over-represented transcription factor response elements (TRE) were identified within promoter sequences (500 bp upstream of transcription start site(s)) of significantly up-and down-regulated genes using the PAINT version 4.0 (35,36). For the 261 genes that showed significant down-regulation, 232 corresponding unique upstream sequences were found, with 164 TREs detected based on a core similarity threshold of 1.0.…”

Section: Methodsmentioning

confidence: 99%

Expression of V3 Versican by Rat Arterial Smooth Muscle Cells Promotes Differentiated and Anti-inflammatory Phenotypes

Kang

Barth

Sproul

et al. 2015

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Arterial smooth muscle cells (ASMCs) undergo phenotypic changes during pathophysiological processes. Results: V3 expression increases contractile SMC markers while decreasing a broad range of proinflammatory chemokines and transcription factors. Conclusion: V3 expression reprograms rat ASMCs promoting differentiated and anti-inflammatory phenotypes. Significance: Modifying ECM components via V3 expression could provide a potential therapeutic intervention against vascular and other diseases.

show abstract

“…edu/dbi/tools/paint) [23]. Affymetrix probeset IDs were converted to mouse NCBI Gene IDs using NetAffx and NCBI Homologene databases.…”

Section: Bioinformaticsmentioning

confidence: 99%

Insulin-Like 3 Exposure of the Fetal Rat Gubernaculum Modulates Expression of Genes Involved in Neural Pathways1

Johnson

Robbins

Wang

et al. 2010

Biology of Reproduction

View full text Add to dashboard Cite

Insulin-like 3 (INSL3) signaling directs fetal gubernacular development and testis descent, but the actions of INSL3 in the gubernaculum are poorly understood. Using microarray gene expression profiling of fetal male rat gubernaculum explants exposed to 10 or 100 nM INSL3, significant changes in expression were identified for approximately 900 genes. Several of the genes showing the largest inductions regulate neuronal development or activity, including Pnoc (34-fold), Nptx2 (9-fold), Nfasc (4-fold), Gfra3 (3-fold), Unc5d (3-fold), and Crlf1 (3-fold). Bioinformatics analysis revealed BMP and WNT signaling pathways and several gene ontologies related to neurogenesis were altered by INSL3. Promoter response elements significantly enriched in the INSL3-regulated gene list included consensus sequences for MYB, REL, ATF2, and TEF transcription factors. Comparing in vivo gene expression profiles of male and female rat fetal gubernaculum showed expression of the Bmp, Wnt, and neurodevelopmental genes induced by INSL3 was higher in males. Using quantitative RT-PCR, the microarray data were confirmed, and the induction of Bmp3, Chrdl2, Crlf1, Nptx2, Pnoc, Wnt4, and Wnt5a mRNA levels were examined over a range of INSL3 concentrations (0.1-100 nM) in male and female gubernaculum. In both sexes, an increasing gene expression response was observed between 0.1 and 10 nM INSL3. These data suggest that INSL3 signaling in the fetal gubernaculum induces morphogenetic programs, including BMP and WNT signaling, and support other rodent data suggesting a role for these pathways in development of the gubernaculum.

show abstract

From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT

Cited by 21 publications

References 24 publications

LASAGNA-Search: an Integrated Web Tool for Transcription Factor Binding Site Search and Visualization

LASAGNA-Search: an Integrated Web Tool for Transcription Factor Binding Site Search and Visualization

Expression of V3 Versican by Rat Arterial Smooth Muscle Cells Promotes Differentiated and Anti-inflammatory Phenotypes

Insulin-Like 3 Exposure of the Fetal Rat Gubernaculum Modulates Expression of Genes Involved in Neural Pathways1

Contact Info

Product

Resources

About