understanding cancer progression in protein interaction networks

... clustering algorithms for protein-protein interaction networks BMC Bioinformatics 2006;7:488 Li X, Wu M, Kwoh CK, Ng SK Computational approaches for detecting protein complexes from protein interaction ... Detecting overlapping protein complexes in protein-protein interaction networks Nat Methods 2012;9:471–2 Macropol K, Can T, Singh AK RRW: Repeated random walks on genome-scale protein networks ... expanding a cluster of proteins by adding a protein out of the cluster, where an initial cluster is a cluster with either a single Page 52 of 81 protein or a pair of proteins sharing an interaction,

Ngày tải lên: 25/11/2020, 16:27

... parasite; [9]) In a protein-protein interaction network (PIN), a protein and an interaction between two proteins are represented as a node and a link, respectively The number of links connected ... Background: A protein-protein interaction network (PIN) was suggested to be a disassortative network, in which interactions between high- and low-degree nodes are favored while hub-hub interactions ... including S cerevisiae In their dataset, all proteins in these 19 species are classified into ortholog groups, each of which consists of the pro-teins descended from a single ancestral protein

Ngày tải lên: 01/11/2022, 09:48

... The interaction between AKAP95 and Cx43 protein was detected in Cytoplasm1 con-taining proteins of nuclear membrane In contrast, although the Cx43 protein and a small quantity of AKAP95 protein ... methylation11 AKAP95 can influence cell cycle progression by binding to cyclins D1-3/E14,12 G1/S cyclins interact with the RII subunit of PKA through AKAP95 Interestingly, the binding of cyclins to AKAP95 ... & Yongxing Zhang1 Here we show that A-kinase anchoring protein 95 (AKAP95) and connexin 43 (Cx43) dynamically interact during cell cycle progression of lung cancer A549 cells Interaction

Ngày tải lên: 24/11/2022, 17:41

... depending on their coordinates in a topological space TNMs provide new insight into networks by capturing proteins from different categories including proteins within a complex, proteins with shared ... and protein interaction networks is a valuable way to study protein complex dynamics For example, in S cerevisiae, one effective way to perturb a protein interaction network is to study protein ... for overlaps with interactions in the Biogrid database38 We found 81 interactions between proteins in the TNM 1 and 57 interactions in the TNM 2 suggesting that these proteins are important elements

Ngày tải lên: 04/12/2022, 14:56

... also called Survivin, has been shown to play a pivotal role in cancers by influencing cell div-ision and proliferation and by inhibiting apoptosis [1] Many studies using clinical specimens have ... activation of BIRC5 during carcinogen-esis in various types of cancers, treatment that targets BIRC5 has been increasingly recognized as a promising therapy for various cancers However, when the ... reported to not have binding sites for OCT4, al-though OCT4 knockdown in murine embryonic stem cells has been shown to decrease the expression level of BIRC5 protein, suggesting an indirect effect

Ngày tải lên: 05/11/2020, 07:12

... Containing 8 (TRIM8) 3 3 (3) 0 (0) Table 2 Robust controllability types of all proteins, driver proteins, and virus interacting proteins in the VIN (HIN in parenthesis) All Proteins Driver Proteins ... plotted against the classification results of IAV interacting proteins, driver proteins, and all proteins in resemble all proteins of the network, not the true inter-acting protein set, suggesting that ... One of the remaining pro-teins is two steps (two interactions and one connecting protein) from any IAV protein, and the remaining five proteins are three steps from any IAV protein The num-ber

Ngày tải lên: 25/11/2020, 12:34

... pair of genes in a link that is consistent with the regulatory nature of the link We distinguish between inhibitory and non-inhibitory links Non-inhibitory links consist of inducing links, relationships ... AGE-RAGE signaling (in diabetes) IL-17 signaling NF-kappa B signaling NOD-like receptor signaling Oxytocin signaling Rheumatoid arthritis TNF signaling Cytokine-cytokine receptor interaction CO ... particularly interested in tissue factor (TF), noting that its gene expression (F3) is upregulated In an additional experiment, they find that increased TF protein induces increased release of the cytokine

Ngày tải lên: 25/11/2020, 13:02

... method for finding molecular complexes in large protein interaction networks BMC Bioinformatics 2003;4:2 https://doi.org/10.1186/1471-2105-4-2 37 King AD, Pržulj N, Jurisica I Protein complex ... Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C STRING v10: protein-protein interaction networks, integrated ... hypergraph into a graph by replacing each multi-element interaction by a clique of pairwise interactions between all elements in this interaction The network distance over the resulting graph

Ngày tải lên: 25/11/2020, 14:16

... AccessIdentifying protein complexes based on node embeddings obtained from protein-protein interaction networks Xiaoxia Liu1, Zhihao Yang1*, Shengtian Sang1, Ziwei Zhou1, Lei Wang2*, Yin Zhang2, Hongfei Lin1, ... for new protein complexes First, node embeddings are obtained from human protein interaction network Then the protein interactions are weighted through the similarities between node embeddings After ... obtained and there were 17,203 interactions among 4930 proteins in the DIP net-work After removing the duplicated and self-linked rela-tions, we obtained 37,060 interactions and 9521 proteins

Ngày tải lên: 25/11/2020, 14:32

... structures and 6198 protein interactions forL braziliensis, and 708 protein structures and 7391 protein interactions forL infantum The predicted networks were integrated to protein interaction data already ... regions are part of protein inter-action interfaces, and therefore, they can be used to interrupt a protein interaction, and causing damage in the parasite Fig 3 Interaction Protein Networks predicted ... and interactions [6] Protein interaction networks have been used in some studies with the objective of selecting promising thera-peutic targets [29–31], and the protein interaction data contained

Ngày tải lên: 25/11/2020, 15:22

... amounts of protein-protein interaction (PPI) data In general, a PPI data set can be represented as a protein-protein interaction network(PIN) where nodes are proteins and edges signifies the interactions ... both small and large protein complexes Keywords: Small protein complex, Large protein complex, Protein-protein interaction, Protein complex prediction Background Most proteins perform biological ... overlapping protein complexes in protein-protein interaction networks Nat Methods 2012;9(5):471–2. 12 Chen B, Wu FX Identifying protein complexes based on multiple topological structures in PPI networks

Ngày tải lên: 25/11/2020, 16:07

... techniques Keywords: Protein-protein interactions, Protein docking, Structural bioinformatics, Machine learning, Gene Ontology filters, eFindSitePPI, eRankPPI Background Protein-protein interactions ... organism Protein interaction data for E coli consisting of 13,374 known interactions formed by 2,994 bacterial proteins were downloaded from the Database of Interacting Proteins (DIP) [31] in March ... modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks Surabhi Maheshwari1and Michal Brylinski1,2* Abstract Background: Deciphering complete networks of interactions

Ngày tải lên: 25/11/2020, 17:45

... positive; GO, Gene ontology; PC, Protein complex; PDC, Partial dense cover; PPI, Protein protein interaction; PPIN, Protein protein interaction network; TAP-MS,Tandem affinity purification coupled ... analyze these networks are clustering algorithms We concentrate here on the specific task of predicting protein complexes (PC) in large protein-protein interaction networks (PPIN) Currently, ... to compile large maps of protein interactions, which are usually denoted as protein-protein interaction networks (PPIN) How-ever, extracting useful knowledge from such networks is not straightforward

Ngày tải lên: 04/12/2022, 16:05

... without investigation into the links between biological molecules, inparticular, protein-protein interactions (PPI) Protein-protein interactions are physical contacts between two or more proteins ... plant’scellular machinery In PPI networks, nodes are proteins and edges are protein-protein interactions.Usually, a PPI network represents a collection of protein-protein interaction data in an organism ... andstudy interaction data of different types in cellular systems, such as protein-proteininteraction, metabolic and gene regulation [9] By investigating the interactions at a network level, new insights

Ngày tải lên: 10/09/2015, 09:24

... feedback loopin the extrinsic pathway through further activation of the initiatorcaspases-8 and -10 Smac/DIABLO proteinsinactivate the IAP (inhibitors of apoptosis proteins) proteinfamily, which ... cytochrome c; DISC, death-inducing signaling complex; IAPs, inhibition of apoptosis proteins; Smac/DIABLO, second mitochondria-derived activator of caspases/direct IAP-binding protein with low pI APOPTOSIS ... with LCM in Tumor Tissues ……… ….79 3.6 Sequencing of CC3 exon 3 in colorectal cancer tissues, cell lines and breast cancer cell lines ……… ……… 80 3.7 Expression CC3 in 13 colorectal cell lines ………

Ngày tải lên: 14/09/2015, 08:50

... regions of the protein involved in interaction with Cdk2 and cyclin A: 1, domain interacting with cyclin A; 2, a linker helix involved in binding both cyclin A and Cdk2; 3, domain interacting with ... biological protein protein interaction networks maintain a scale-free nature throughout full interactomes remains to be verified Secondly, experimental protein protein interaction data contains a significant ... identifying and cataloguing ID regions in hub proteins could provide a useful approach for organizing protein protein interaction subnetworks into larger networks We have presented evidence that ID proteins...

Ngày tải lên: 07/03/2014, 21:20

... 1.2 Intrinsic Protein Disorder in Protein- Protein Interactions Many proteins execute their biological functions through protein- protein interactions By binding to interacting partners, proteins ... thus leading to extremely complicated protein- protein interaction networks 1.7 Importance of MoRF Mechanisms in Hub Proteins Independent of their roles in hub protein interactions, intrinsically ... sets of protein- protein interactions over entire proteomes Mapping protein- protein interactions leads to networks that are far from random While most proteins have only a few interacting partners,...

Ngày tải lên: 24/08/2014, 09:56

... approach by comparing proteins and associated links within such interaction networks to identify the combined set of network interactions as well those interactions that are unique to individual species ... K12 Figure Complete protein- protein interaction network for two organisms Complete protein- protein interaction network for two organisms (a) Taxonomy of the organisms examined in this study (b,c) ... of complete protein interaction networks for two of the organisms evaluated here These figures enable the examination of the size distribution of protein- protein interaction networks in different...

Ngày tải lên: 14/08/2014, 08:20

... screening protein interactions Broad classification of affinity scoring schemes for reliability estimation of protein interactions Protein interaction ... Techniques for inferring protein interactions All mass is interaction - Richard Feynman statement titled “Principles” (c 1950), as quoted in [21] Proteins interact with each other in a highly specific ... relatively few interactions for proteins involved in transport and sensing (transmembrane proteins), while Y2H being targeted in the nucleus fail to cover extracellular proteins [26] 2.3.2 Estimating the...

Ngày tải lên: 16/09/2015, 12:17

... clustered W12 W2 Module reviews Proteins Proteins Proteins Module Proteins comment Species Module Proteins Poyatos and Hurst R93.3 (b) Interaction matrix Proteins Proteins (a) Genome Biology 2004, ... of networks [9-11] To this end, it is helpful to represent networks as graphs, with proteins playing the role of nodes and protein- protein interactions playing the role of edges between nodes In ... motif constituents in the yeast protein interaction network Nat Genet 2003, 35:176-179 Jansen R, Greenbaum D, Gerstein M: Relating whole-genome expression data with protein- protein interactions Genome...

Ngày tải lên: 14/08/2014, 14:21