Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.

By Esti Yeger-Lotem, Shmuel Sattath, Nadav Kashtan, Shalev Itzkovitz, Ron Milo, R. Pinter, Uri Alon, Hanah Margalit. Proceedings of the National Academy of Sciences of the United States of America, 2004

579 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ee8146f7801c8d6858b4b632f80c172b1fb723d7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Analysis of Biological Networks (2008, background): “Recent studies also take into account the effect of weighted edges [74].”
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. (2004, methodology): “The capabilities of the FunCat as a controlled (structured) vocabulary and classification scheme are not only limited to the functional annotation of genomes but also provide a powerful tool to analyse genome- and proteome-wide data which have been generated by large-scale transcriptome/ proteome ex”
Introduction to systems biology. (2007, background): “Most noticeably are small world organization [57, 58], modularity [59, 60], motifs [61–63], fl ux balance analysis, extreme pathway and elementary mode analysis [6, 64–67].”
Cancer: a Systems Biology disease. (2006, background): “The identification of the structure and the intrinsic properties of frequently occurring regulatory motifs (sometimes referred to as ‘network motifs’) is a challenge and may give us a functional view on the organization of signaling networks rather than a molecular view (Yeger-Lotem et al., 2004).”
Protein-to-protein interactions: Technologies, databases, and algorithms (2010, background): “…and reconstruction of metabolic networks; (ii) determination of evolution of networks; (iii) pathway analysis (e.g., comparison or alignment); and (iv) integration of genomic and proteomic data [Schuster et al. 2002; Yeger-Lotem et al. 2004; Holme et al. 2003; Xiong et al. 2004; Przulj et al.”
Feedback regulation of EGFR signalling: decision making by early and delayed loops (2011, background): “It is pertinent to note that the combination of covalent modifications, subcellular translocations and the recurring patterns of transcription regulation and protein–protein interaction”
Scale-free networks in cell biology (2005, background): “Yeger-Lotem et al. have identified frequent composite transcription/protein interaction motifs, such as interacting transcription factors coregulating a gene or interacting proteins being coregulated by the same transcription factor (Yeger-Lotem et al., 2004).”
Graph theory and networks in Biology. (2006, result): “Similar findings have been reported for genetic networks in [177], where a network of approximately 1000 genes and 4000 interactions was found to have a characteristic path length of 3.3, and for protein interaction networks in [187, 201, 200].”
Integrative approaches for finding modular structure in biological networks (2013, background): “In early work along these lines, composite ‘motifs’ comprised of regulatory and protein–protein interactions among 2, 3 or 4 proteins were mapped and classified into distinct feed-forward loops, interacting transcriptional hubs and other logical circuits 152 .”
Functional Motifs in Biochemical Reaction Networks (2010, methodology): “Using bioinformatic methods, Alon and colleagues (49, 50) have shown that FFLs are unusually common (i.”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, unknown): “We compared the number (NY2H) of interactions in loop motifs in the Y2H and the randomized networks; then, Z score values (Z score = (NY2H �N rand)/SD) were calculated as a qualitative measure of statistical significance ( Yeger-Lotem et al., 2004 ).”
Analyzing and modeling real-world phenomena with complex networks: a survey of applications (2007, background): “The feed-forward loop motif often occurs when a n external signal causes a rapid response to many systems and networks characterized by mult iple feed-forward motifs tend to be stable instead of transient [247].”