Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping

2007 ◽  
Vol 4 (8) ◽  
pp. 659-664 ◽  
Author(s):  
Vanessa Vermeirssen ◽  
Bart Deplancke ◽  
M Inmaculada Barrasa ◽  
John S Reece-Hoyes ◽  
H Efsun Arda ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Triple System ◽  
High Performance ◽  
Steiner Triple System ◽  
Transcription Regulatory Network ◽  
Network Mapping

scholarly journals Characterisation Results for Steiner Triple Systems and Their Application to Edge-Colourings of Cubic Graphs

2010 ◽  
Vol 62 (2) ◽  
pp. 355-381 ◽  
Author(s):  
Daniel Král’ ◽  
Edita Máčajov´ ◽  
Attila Pór ◽  
Jean-Sébastien Sereni
Keyword(s):  
Triple System ◽  
Steiner Triple System ◽  
Cubic Graphs ◽  
Steiner Triple Systems ◽  
Cubic Graph ◽  
Triple Systems ◽  
Forbidden Configurations ◽  
Edge Colourings

AbstractIt is known that a Steiner triple system is projective if and only if it does not contain the four-triple configuration C14. We find three configurations such that a Steiner triple system is affine if and only if it does not contain one of these configurations. Similarly, we characterise Hall triple systems using two forbidden configurations.Our characterisations have several interesting corollaries in the area of edge-colourings of graphs. A cubic graph G is S-edge-colourable for a Steiner triple system S if its edges can be coloured with points of S in such a way that the points assigned to three edges sharing a vertex form a triple in S. Among others, we show that all cubic graphs are S-edge-colourable for every non-projective nonaffine point-transitive Steiner triple system S.

A High-Performance and Low-Power On-Chip Network with Reconfigurable Topology

2010 ◽  
pp. 309-329
Author(s):  
Mehdi Modarressi ◽  
Hamid Sarbazi-Azad
Keyword(s):  
High Performance ◽  
Chip Multiprocessors ◽  
Optimization Methods ◽  
Critical Feature ◽  
Design Constraints ◽  
Core System ◽  
Traffic Pattern ◽  
On Chip ◽  
Network Mapping ◽  
Application Specific

In this chapter, we present a reconfigurable architecture for network-on-chips (NoC) on which arbitrary application-specific topologies can be implemented. The proposed NoC can dynamically tailor its topology to the traffic pattern of different applications, aiming to address one of the main drawbacks of existing application-specific NoC optimization methods, i.e. optimizing NoCs based on the traffic pattern of a single application. Supporting multiple applications is a critical feature of an NoC as several different applications are integrated into the modern and complex multi-core system-on-chips and chip multiprocessors and an NoC that is designed to run exactly one application does not necessarily meet the design constraints of other applications. The proposed NoC supports multiple applications by configuring as a topology which matches the traffic pattern of the currently running application in the best way. In this chapter, we first introduce the proposed reconfigurable topology and then address the two problems of core to network mapping and topology exploration. Experimental results show that this architecture effectively improves the performance of NoCs and reduces power consumption.

Direct Product of Derived Steiner Systems Using Inversive Planes

1981 ◽  
Vol 33 (6) ◽  
pp. 1365-1369 ◽  
Author(s):  
K. T. Phelps
Keyword(s):  
Direct Product ◽  
Triple System ◽  
Steiner Triple System ◽  
Steiner System ◽  
Steiner Systems

A Steiner system S(t, k, v) is a pair (P, B) where P is a v-set and B is a collection of k-subsets of P (usually called blocks) such that every t-subset of P is contained in exactly one block of B. As is well known, associated with each point x ∈ P is a S(t � 1, k � 1, v � 1) defined on the set Px = P\{x} with blocksB(x) = {b\{x}|x ∈ b and b ∈ B}.The Steiner system (Px, B(x)) is said to be derived from (P, B) and is called (obviously) a derived Steiner (t – 1, k – 1)-system. Very little is known about derived Steiner systems despite much effort (cf. [11]). It is not even known whether every Steiner triple system is derived.Steiner systems are closely connected to equational classes of algebras (see [7]) for certain values of k.

Combinatorial Transcription Regulatory Network

2013 ◽  
pp. 441-444
Author(s):  
Yong Wang
Keyword(s):  
Regulatory Network ◽  
Transcription Regulatory Network

scholarly journals Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing

Diagnostics ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 98
Author(s):  
Chia-Chun Tseng ◽  
Ling-Yu Wu ◽  
Wen-Chan Tsai ◽  
Tsan-Teng Ou ◽  
Cheng-Chin Wu ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Differential Expression ◽  
Regulatory Network ◽  
Functional Annotation ◽  
Interaction Analysis ◽  
Expression Profiles ◽  
Synovial Fibroblasts ◽  
Rna Seq ◽  
Network Mapping ◽  
Generation Sequencing

Using next-generation sequencing to decipher the molecular mechanisms underlying aberrant rheumatoid arthritis synovial fibroblasts (RASF) activation, we performed transcriptome-wide RNA-seq and small RNA-seq on synovial fibroblasts from rheumatoid arthritis (RA) subject and normal donor. Differential expression of mRNA and miRNA was integrated with interaction analysis, functional annotation, regulatory network mapping and experimentally verified miRNA–target interaction data, further validated with microarray expression profiles. In this study, 3049 upregulated mRNA and 3552 downregulated mRNA, together with 50 upregulated miRNA and 35 downregulated miRNA in RASF were identified. Interaction analysis highlighted contribution of miRNA to altered transcriptome. Functional annotation revealed metabolic deregulation and oncogenic signatures of RASF. Regulatory network mapping identified downregulated FOXO1 as master transcription factor resulting in altered transcriptome of RASF. Differential expression in three miRNA and corresponding targets (hsa-miR-31-5p:WASF3, hsa-miR-132-3p:RB1, hsa-miR-29c-3p:COL1A1) were also validated. The interactions of these three miRNA–target genes were experimentally validated with past literature. Our transcriptomic and miRNA interactomic investigation identified gene signatures associated with RASF and revealed the involvement of transcription factors and miRNA in an altered transcriptome. These findings help facilitate our understanding of RA with the hope of serving as a springboard for further discoveries relating to the disease.

scholarly journals C-LOOPS: EXTENSIONS AND CONSTRUCTIONS

2007 ◽  
Vol 06 (01) ◽  
pp. 1-20 ◽  
Author(s):  
MICHAEL K. KINYON ◽  
J. D. PHILLIPS ◽  
PETR VOJTĚCHOVSKÝ
Keyword(s):  
Abelian Group ◽  
Triple System ◽  
Abelian Groups ◽  
Steiner Triple System

C-loops are loops satisfying the identity x(y · yz) = (xy · y)z. We develop the theory of extensions of C-loops, and characterize all nuclear extensions provided the nucleus is an abelian group. C-loops with central squares have very transparent extensions; they can be built from small blocks arising from the underlying Steiner triple system. Using these extensions, we decide for which abelian groups K and Steiner loops Q there is a nonflexible C-loop C with center K such that C/K is isomorphic to Q. We discuss possible orders of associators in C-loops. Finally, we show that the loops of signed basis elements in the standard real Cayley–Dickson algebras are C-loops.

HNF1, a homeoprotein member of the hepatic transcription regulatory network

BioEssays ◽  
1992 ◽  
Vol 14 (9) ◽  
pp. 579-587 ◽  
Author(s):  
Fran�lois Tronche ◽  
Moshe Yaniv
Keyword(s):  
Regulatory Network ◽  
Transcription Regulatory Network

Steiner triple systems of order 19 constructed from the Steiner triple system of order 9

1983 ◽  
Vol 94 (1-2) ◽  
pp. 89-92 ◽  
Author(s):  
Alan R. Prince
Keyword(s):  
Standard Method ◽  
Triple System ◽  
Isomorphism Class ◽  
Automorphism Groups ◽  
Steiner Triple System ◽  
Steiner Triple Systems ◽  
Triple Systems ◽  
Isomorphism Classes

SynopsisA standard method of constructing Steiner triple systems of order 19 from the Steiner triple system of order 9 gives rise to 212 different such systems. It is shown that there are just three isomorphism classes amongst these systems. Representatives of each isomorphism class are described and the orders of their automorphism groups are determined.

scholarly journals Yeast one-hybrid assays for gene-centered human gene regulatory network mapping

2011 ◽  
Vol 8 (12) ◽  
pp. 1050-1052 ◽  
Author(s):  
John S Reece-Hoyes ◽  
A Rasim Barutcu ◽  
Rachel Patton McCord ◽  
Jun Seop Jeong ◽  
Lizhi Jiang ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Human Gene ◽  
Gene Regulatory ◽  
Network Mapping
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