Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Insights into cancer severity from biomolecular interaction mechanisms.

ABSTRACT: To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or -nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes. Over half of these interfaces involve protein-small-molecule interactions highlighting their overall importance in cancer. We found distinct differences in the predominance of perturbed interfaces between cancers and histological subtypes and presence or absence of certain interfaces appears to correlate with cancer severity.

SUBMITTER: Raimondi F

PROVIDER: S-EPMC5048291 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Insights into cancer severity from biomolecular interaction mechanisms.

Raimondi Francesco F Singh Gurdeep G Betts Matthew J MJ Apic Gordana G Vukotic Ranka R Andreone Pietro P Stein Lincoln L Russell Robert B RB Russell Robert B RB

Scientific reports 20161004

To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or -nuclei ...[more]

PMID: 27698488

Similar Datasets

Biomolecular mechanisms for signal differentiation.

Project description:Cells can sense temporal changes of molecular signals, allowing them to predict environmental variations and modulate their behavior. This paper elucidates biomolecular mechanisms of time derivative computation, facilitating the design of reliable synthetic differentiator devices for a variety of applications, ultimately expanding our understanding of cell behavior. In particular, we describe and analyze three alternative biomolecular topologies that are able to work as signal differentiators to input signals around their nominal operation. We propose strategies to preserve their performance even in the presence of high-frequency input signal components which are detrimental to the performance of most differentiators. We find that the core of the proposed topologies appears in natural regulatory networks and we further discuss their biological relevance. The simple structure of our designs makes them promising tools for realizing derivative control action in synthetic biology.

| S-EPMC8649740 | biostudies-literature

BIND--The Biomolecular Interaction Network Database.

Project description:The Biomolecular Interaction Network Database (BIND; http://binddb. org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes can also be described. Everything from small molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for kinetic simulations. BIND anticipates the coming large influx of interaction information from high-throughput proteomics efforts including detailed information about post-translational modifications from mass spectrometry. Version 2.0 of the BIND data model is discussed as well as implementation, content and the open nature of the BIND project. The BIND data specification is available as ASN.1 and XML DTD.

| S-EPMC29820 | biostudies-literature

BIND: the Biomolecular Interaction Network Database.

Project description:The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions. An interaction network clustering tool has also been developed to help focus on regions of interest. Continued input from users has helped further mature the BIND data specification, which now includes the ability to store detailed information about genetic interactions. The BIND data specification is available as ASN.1 and XML DTD.

| S-EPMC165503 | biostudies-literature

Biomolecular Interaction, Anti-Cancer and Anti-Angiogenic Properties of Cobalt(III) Schiff Base Complexes.

Project description:Two cobalt(III) Schiff base complexes, trans-[Co(salen)(DA)2](ClO4) (1) and trans-[Co(salophen)(DA)2](ClO4) (2) (where salen: N,N'-bis(salicylidene)ethylenediamine, salopen: N,N'-bis(salicylidene)-1,2-phenylenediamine, DA: dodecylamine) were synthesised and characterised using various spectroscopic and analytical techniques. The binding affinity of both the complexes with CT-DNA was explored adopting UV-visible, fluorescence, circular dichroism spectroscopy and cyclic voltammetry techniques. The results revealed that both the complexes interacted with DNA via intercalation as well as notable groove binding. Protein (BSA) binding ability of these complexes was investigated by absorption and emission spectroscopy which indicate that these complexes engage in strong hydrophobic interaction with BSA. The mode of interaction between these complexes and CT-DNA/BSA was studied by molecular docking analysis. The in vitro cytotoxic property of the complexes was evaluated in A549 (human small cell lung carcinoma) and VERO (African green monkey kidney cells). The results revealed that the complexes affect viability of the cells. AO and EB staining and cell cycle analysis revealed that the mode of cell death is apoptosis. Both the complexes showed profound inhibition of angiogenesis as revealed in in-vivo chicken chorioallantoic membrane (CAM) assay. Of the two complexes, the complex 2 proved to be much more efficient in affecting the viability of lung cancer cells than complex 1. These results indicate that the cobalt(III) Schiff base complexes in this study can be potentially used for cancer chemotherapy and as inhibitor of angiogenesis, in general, and lung cancer in particular, for which there is need for substantiation at the level of signalling mechanisms and gene expressions.

| S-EPMC6389928 | biostudies-literature

POPSCOMP: an automated interaction analysis of biomolecular complexes.

Project description:Large-scale analysis of biomolecular complexes reveals the functional network within the cell. Computational methods are required to extract the essential information from the available data. The POPSCOMP server is designed to calculate the interaction surface between all components of a given complex structure consisting of proteins, DNA or RNA molecules. The server returns matrices and graphs of surface area burial that can be used to automatically annotate components and residues that are involved in complex formation, to pinpoint conformational changes and to estimate molecular interaction energies. The analysis can be performed on a per-atom level or alternatively on a per-residue level for low-resolution structures. Here, we present an analysis of ribosomal structures in complex with various antibiotics to exemplify the potential and limitations of automated complex analysis. The POPSCOMP server is accessible at http://ibivu.cs.vu.nl/programs/popscompwww/.

| S-EPMC1160130 | biostudies-literature

Comparison of methods for quantitative biomolecular interaction analysis.

Project description:In order to perform good kinetic experiments, not only the experimental conditions have to be optimized, but the evaluation procedure as well. The focus of this work is the in-depth comparison of different approaches and algorithms to determine kinetic rate constants for biomolecular interaction analysis (BIA). The different algorithms are applied not only to flawless simulated data, but also to real-world measurements. We compare five mathematical approaches for the evaluation of binding curves following pseudo-first-order kinetics with different noise levels. In addition, reflectometric interference spectroscopy (RIfS) measurements of two antibodies are evaluated to determine their binding kinetics. The advantages and disadvantages of the individual approach will be investigated and discussed in detail. In summary, we will raise awareness on how to evaluate and judge results from BIA by using different approaches rather than having to rely on "black box" closed (commercial) software packages.

| S-EPMC8748344 | biostudies-literature

Study of Biomolecular Interactions of Mitochondrial Proteins Related to Alzheimer's Disease: Toward Multi-Interaction Biomolecular Processes.

Project description:Progressive mitochondrial dysfunction due to the accumulation of amyloid beta (A?) peptide within the mitochondrial matrix represents one of the key characteristics of Alzheimer's disease (AD) and appears already in its early stages. Inside the mitochondria, A? interacts with a number of biomolecules, including cyclophilin D (cypD) and 17?-hydroxysteroid dehydrogenase type 10 (17?-HSD10), and affects their physiological functions. However, despite intensive ongoing research, the exact mechanisms through which A? impairs mitochondrial functions remain to be explained. In this work, we studied the interactions of A? with cypD and 17?-HSD10 in vitro using the surface plasmon resonance (SPR) method and determined the kinetic parameters (association and dissociation rates) of these interactions. This is the first work which determines all these parameters under the same conditions, thus, enabling direct comparison of relative affinities of A? to its mitochondrial binding partners. Moreover, we used the determined characteristics of the individual interactions to simulate the concurrent interactions of A? with cypD and 17?-HSD10 in different model situations associated with the progression of AD. This study not only advances the understanding of A?-induced processes in mitochondria during AD, but it also provides a new perspective on research into complex multi-interaction biomolecular processes in general.

| S-EPMC7563123 | biostudies-literature

The Biomolecular Interaction Network Database in PSI-MI 2.5.

Project description:The Biomolecular Interaction Network Database (BIND) is a major source of curated biomolecular interactions, which has been unmaintained for the last few years, a trend which will eventually result in the loss of a significant amount of unique biomolecular interaction information, mostly as database identifiers become out of date. To help reverse this trend, we converted BIND to a standard format, Proteomics Standard Initiative-Molecular Interaction 2.5, starting from the last curated data release (from 2005) available in a custom XML format and made the core components (interactions and complexes) plus additional valuable curated information available for download (http://download.baderlab.org/BINDTranslation/). Major work during the conversion process was required to update out of date molecule identifiers resulting in a more comprehensive conversion of BIND, by measures including number of species and interactor types covered, than what is currently accessible elsewhere. This work also highlights issues of data modeling, controlled vocabulary adoption and data cleaning that can serve as a general case study on the future compatibility of interaction databases. Database URL: http://download.baderlab.org/BINDTranslation/

| S-EPMC3021793 | biostudies-literature

Insights Into Mechanisms of Tumor and Immune System Interaction: Association With Wound Healing.

Project description:A large number of studies have presented a great deal of information about tumor and immune system interaction. Nevertheless, the problem of tumor evasion from the immune reaction is still difficult to resolve. Understanding the ways in which immunosuppressive tumor microenvironment develops and maintains its potential is of utmost importance to ensure the best use of the suppressed immune functions. The study presents a review covering the data on tumor-associated antigens, mechanisms of tumor evasion from the immune reactions, and search for common immunosuppressive processes of tumor growth and normal wound healing. The study discusses the important role of monocytes/macrophages in the regulation of immune system reactions. We suggest that the simultaneous actions of growth factors and pro-inflammatory cytokines may result in the suppression of the immune system. The study describes intracellular signaling molecules that take part in the regulation of the myeloid cell functions. If the hypothesis is proved correct, the indicated interaction of cytokines could be regarded as a prospective target for antitumor therapy.

| S-EPMC6823879 | biostudies-literature

RSV disease severity: Insights into Protective Immune Responses

Project description:This was a prospective observational cohort study involving a convenience sample of previously healthy children <2 years of age with acute RSV infection as well as healthy non-infected age matched controls. The study was conducted at Nationwide Children’s Hospital (NCH; Columbus, OH) during four respiratory seasons, from 2011 to 2015. Children were enrolled at the NCH urgent care clinics, the emergency department or in the inpatient ward or intensive care unit (PICU). For the inpatients enrolled at ward or PICU the median time from admission to sample collection was 21.3h (interquartile range [IQR] 16.7 -37.6h). The majority of children had a confirmatory RSV test (either rapid antigen testing or PCR based) at enrollment per standard of care. In addition, the presence of RSV was confirmed by quantitative real time (qRT)-PCR in all study subjects. Healthy age-matched controls were enrolled during well-child visits or minor elective surgical procedures not involving the respiratory tract as described [Mejias 2013]. Exclusion criteria were as follows: documented bacterial co-infections, premature birth (<36 weeks of gestation), chronic or congenital medical conditions, and immunodeficiency. For healthy controls, additional exclusion criteria included: presence of fever or symptoms of respiratory tract infection within two weeks of enrollment.

2020-04-22 | GSE105450 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data