PathGen: a transitive gene pathway generator

Clement, Kendell; Gustafson, Nathaniel; Berbert, Amanda; Carroll, Hyrum; Merris, Christopher; Olsen, Ammon; Clement, Mark J.; Snell, Quinn; Allen, Jared; Roper, Randall J.

doi:10.1093/bioinformatics/btp661

Cited by 7 publications

(11 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The NMG vacuum (σ = const) sector contains two propagating (massive) degrees of freedom (the "graviton" polarizations) and as a result it admits a variety of physically interesting classical solutionsgravitational waves, black holes, etc. [5]. When matter is added the only known exact solutions [6] are certain asymptotically dS 3 geometries that describe Bounce-like evolutions of 3D Universe.…”

Section: Introductionmentioning

confidence: 99%

New massive gravity domain walls

Sotkov

2010

Physics Letters B

View full text Add to dashboard Cite

The properties of the asymptotic AdS 3 space-times representing flat domain walls (DW's) solutions of the New Massive 3D Gravity with scalar matter are studied. Our analysis is based on I st order BPS-like equations involving an appropriate superpotential. The Brown-York boundary stress-tensor is used for the calculation of DW's tensions as well as of the CF T 2 central charges. The holographic renormalization group flows and the phase transitions in specific deformed CF T 2 dual to 3D massive gravity model with quadratic superpotential are discussed.1 Although the NMG action (1) involves up to fourth order derivatives of 3D metrics g µν , the corresponding equations for the DW's (2) are of second order:σ +σφ − V ′ (σ) = 0 3 although there exist controversy claims concerning its super-renormalizability [4].

show abstract

Section: Introductionmentioning

confidence: 99%

New massive gravity domain walls

Sotkov

2010

Physics Letters B

View full text Add to dashboard Cite

show abstract

“…Based on the literature implicating TGFb as an important signaling pathway associated with MSC differentiation (Roelen and Duke, 2003) and on pathway analysis by PathGen (Clement et al, 2010), we hypothesized that TGFb1 may follow the expression patterns of our significant differentiation gene sets. TGFb1 expression was determined by RT-qPCR, and our results suggest that TGFb1 expression ( Figure 7A) mirrors differentiation-specific patterns for adipogenesis, osteogenesis, and chondrogenesis (Figs.…”

Section: Changes In Transforming Growth Factor Beta (Tgfb) Associatedmentioning

confidence: 99%

In Vivo Exposure to Inorganic Arsenic Alters Differentiation-Specific Gene Expression of Adipose-Derived Mesenchymal Stem/Stromal Cells in C57BL/6J Mouse Model

Shearer

Neto

Umbaugh

et al. 2017

Toxicological Sciences

View full text Add to dashboard Cite

The number of mesenchymal stem cell (MSC) therapeutic modalities has grown in recent years. Adipose-derived mesenchymal stem/stromal cells (ASCs) can be isolated and expanded relatively easily as compared with their bonemarrow counterparts, making them a particularly promising source of MSCs. And although the biological mechanisms surrounding ASCs are actively being investigated, little is known about the effects that in vivo environmental exposures might have on their ability to properly differentiate. Therefore, we hypothesized that ASCs isolated from mice exposed to inorganic arsenic (iAs) would have an altered response towards adipogenic, osteogenic, and/or chondrogenic differentiation. To test this hypothesis, C57BL/6J male mice were provided drinking water containing 0, 300, or 1000 ppb iAs. ASCs were then isolated and differentiated, which was assessed by immunocytochemistry and real-time quantitative PCR (RT-qPCR). Our results showed that total urinary arsenic equilibrated within 1 week of exposure to iAs and was maintained throughout the study. ASCs isolated from each exposure group maintained differentiation capabilities for each lineage. The magnitude of differentiation-specific gene expression, however, appeared to be concentration dependent. For osteogenesis and chondrogenesis, differentiation-specific gene expression decreased, whereas adipogenesis showed a biphasic response with an initial decrease followed by an increase in adipogenic-related gene expression following iAs exposure. These results suggest that the level in which differentiation-specific genes are induced within these stromal cells might be sensitive to environmental contaminants. These findings highlight the need to take into account potential environmental exposures prior to selecting stromal cell donors, so ASCs can achieve optimal efficiency in regenerative therapy applications.

show abstract

“…Domain specific information is used to include possible missing links thus identifying a potential signaling pathway. PathGen incorporates data from several sources to create transitive connections that span multiple gene interaction databases [6].…”

Section: Related Workmentioning

confidence: 99%

“…A few of the aforementioned database extensions provide some functionality that can be used to extract paths between molecules [9,2,6] or answer some biological related connectivity queries [20,9,29,23]. These tools attempt to provide generic systems for analyzing biological data.…”

Section: Related Workmentioning

confidence: 99%

Relational operators for prioritizing candidate biomarkers in high-throughput differential expression data

Onsongo

Xie²,

Griffin³

et al. 2010

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology

View full text Add to dashboard Cite

Recent developments in high-throughput proteomics technologies have made it possible to detect and identify low abundance proteins. These technologies provide a new window through which proteomes can be analyzed. Despite holding great promise, the contribution of mass spectrometry based proteomics in identifying novel diagnostic biomarkers has been disappointing. This failure has, in part, been attributed to the lack of effective strategies for determining candidate biomarkers that justify more expensive and timeconsuming validation studies. An approach that bridges the gap between unbiased experimental paradigm emphasizing comprehensive characterizations of proteins and a candidatedriven paradigm would overcome this limitation [38]. To this end, we have developed database operators that extend the database management systems to analyze highthroughput proteomics and genomics data. By analyzing differentially expressed genes and proteins using pathway databases, these operators take advantage of established expert domain knowledge in pathway annotation to prioritize candidate biomarkers. They provide a systematic way of bridging the gap between unbiased experimental paradigm and candidate-driven paradigm. To test the operators, we analyzed a dataset of salivary proteins differentially expressed between pre-malignant and malignant oral lesions. Six proteins are identified as candidate biomarkers worth of validation studies. A literature search reveals these high priority * Accompanying software and supplementary data available at candidate biomarkers interact with proteins implicated in cancer development highlighting their potential utility as biomarkers demonstrating the effectiveness of our operators. The developed operators will help overcome one of the main challenges of high-throughput computational techniques; provide a systematic way of bridging the gap between unbiased data driven approach and hypothesis driven approach to prioritize candidate biomarkers worth of more expensive and time consuming validation studies.

show abstract

PathGen: a transitive gene pathway generator

Abstract: Supplementary data are available at Bioinformatics online. Further information is available at http://dna.cs.byu.edu/pathgen/PathGenSupplemental.pdf.

Cited by 7 publications

References 8 publications

New massive gravity domain walls

New massive gravity domain walls

In Vivo Exposure to Inorganic Arsenic Alters Differentiation-Specific Gene Expression of Adipose-Derived Mesenchymal Stem/Stromal Cells in C57BL/6J Mouse Model

Relational operators for prioritizing candidate biomarkers in high-throughput differential expression data

Contact Info

Product

Resources

About