Systems Biology Tools for Integrated Omics Analysis

2015 ◽  
Vol 35 (3) ◽  
pp. 18-19 ◽  
Author(s):  
Mark Hughes
Keyword(s):  
Systems Biology ◽  
Omics Analysis ◽  
Integrated Omics

scholarly journals Onco-Multi-OMICS Approach: A New Frontier in Cancer Research

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Sajib Chakraborty ◽  
Md. Ismail Hosen ◽  
Musaddeque Ahmed ◽  
Hossain Uddin Shekhar
Keyword(s):  
Cancer Research ◽  
Systems Biology ◽  
Cancer Cells ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Resolving Power ◽  
Cancer Hallmarks ◽  
Molecular Alterations ◽  
Integrated Omics

The acquisition of cancer hallmarks requires molecular alterations at multiple levels including genome, epigenome, transcriptome, proteome, and metabolome. In the past decade, numerous attempts have been made to untangle the molecular mechanisms of carcinogenesis involving single OMICS approaches such as scanning the genome for cancer-specific mutations and identifying altered epigenetic-landscapes within cancer cells or by exploring the differential expression of mRNA and protein through transcriptomics and proteomics techniques, respectively. While these single-level OMICS approaches have contributed towards the identification of cancer-specific mutations, epigenetic alterations, and molecular subtyping of tumors based on gene/protein-expression, they lack the resolving-power to establish the casual relationship between molecular signatures and the phenotypic manifestation of cancer hallmarks. In contrast, the multi-OMICS approaches involving the interrogation of the cancer cells/tissues in multiple dimensions have the potential to uncover the intricate molecular mechanism underlying different phenotypic manifestations of cancer hallmarks such as metastasis and angiogenesis. Moreover, multi-OMICS approaches can be used to dissect the cellular response to chemo- or immunotherapy as well as discover molecular candidates with diagnostic/prognostic value. In this review, we focused on the applications of different multi-OMICS approaches in the field of cancer research and discussed how these approaches are shaping the field of personalized oncomedicine. We have highlighted pioneering studies from “The Cancer Genome Atlas (TCGA)” consortium encompassing integrated OMICS analysis of over 11,000 tumors from 33 most prevalent forms of cancer. Accumulation of huge cancer-specific multi-OMICS data in repositories like TCGA provides a unique opportunity for the systems biology approach to tackle the complexity of cancer cells through the unification of experimental data and computational/mathematical models. In future, systems biology based approach is likely to predict the phenotypic changes of cancer cells upon chemo-/immunotherapy treatment. This review is sought to encourage investigators to bring these different approaches together for interrogating cancer at molecular, cellular, and systems levels.

scholarly journals Integrated ‘omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes

2018 ◽  
Vol 289 ◽  
pp. 1-13 ◽  
Author(s):  
Jarno E.J. Wolters ◽  
Simone G.J. van Breda ◽  
Jonas Grossmann ◽  
Claudia Fortes ◽  
Florian Caiment ◽  
...  
Keyword(s):  
Human Hepatocytes ◽  
Drug Induced ◽  
New Drug ◽  
Omics Analysis ◽  
Integrated Omics

scholarly journals Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA

PLoS ONE ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. e0210910 ◽  
Author(s):  
Bobak D. Kechavarzi ◽  
Huanmei Wu ◽  
Thompson N. Doman
Keyword(s):  
Breast Cancer ◽  
Bottom Up ◽  
Omics Analysis ◽  
Integrated Omics

scholarly journals Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology

2015 ◽  
Author(s):  
Marco Fondi ◽  
Pietro Liò
Keyword(s):  
Systems Biology ◽  
Large Scale ◽  
Biological Information ◽  
Special Focus ◽  
Metabolic Modelling ◽  
Microbial Life ◽  
Multi Scale ◽  
Integrated Omics ◽  
Molecular Components ◽  
Omics Data Integration

Integrated -omics approaches are quickly spreading across microbiology research labs, leading to i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organisation and ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from -omics experiments. In this work, we present opportunities and challenges of multi –omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists.

scholarly journals Integrated omics analysis of sweat reveals an aberrant amino acid metabolism pathway in Vogt–Koyanagi–Harada disease

2020 ◽  
Vol 200 (3) ◽  
pp. 250-259
Author(s):  
X. Cui ◽  
G. Su ◽  
L. Zhang ◽  
S. Yi ◽  
Q. Cao ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Metabolism Pathway ◽  
Omics Analysis ◽  
Integrated Omics

Integrated omics approaches in plant systems biology

2009 ◽  
Vol 13 (5-6) ◽  
pp. 532-538 ◽  
Author(s):  
Atsushi Fukushima ◽  
Miyako Kusano ◽  
Henning Redestig ◽  
Masanori Arita ◽  
Kazuki Saito
Keyword(s):  
Systems Biology ◽  
Integrated Omics ◽  
Plant Systems Biology

scholarly journals Integrated omics-analysis reveals Wnt-mediated NAD+ metabolic reprogramming in cancer stem-like cells

Oncotarget ◽  
2016 ◽  
Vol 7 (30) ◽  
pp. 48562-48576 ◽  
Author(s):  
Jueun Lee ◽  
Hyun Jung Kee ◽  
Soonki Min ◽  
Ki Cheong Park ◽  
Sunho Park ◽  
...  
Keyword(s):  
Metabolic Reprogramming ◽  
Omics Analysis ◽  
Integrated Omics

scholarly journals Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Victor Mataigne ◽  
Nathan Vannier ◽  
Philippe Vandenkoornhuyse ◽  
Stéphane Hacquard
Keyword(s):  
Microbial Community ◽  
Systems Biology ◽  
Microbial Communities ◽  
Molecular Mechanisms ◽  
Microbial Community Composition ◽  
Systems Ecology ◽  
New Concepts ◽  
Integrated Omics ◽  
Genome Scale ◽  
Microbial Systems

Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.

scholarly journals Identification of miR-145 targets through an integrated omics analysis

2015 ◽  
Vol 11 (1) ◽  
pp. 197-207 ◽  
Author(s):  
Tai-Chung Huang ◽  
Santosh Renuse ◽  
Sneha Pinto ◽  
Praveen Kumar ◽  
Yi Yang ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Tumor Suppressor ◽  
Proteomics Analysis ◽  
Omics Analysis ◽  
Integrated Omics ◽  
Novel Targets

The integration of transcriptomics and proteomics analysis identifies novel targets of a tumor suppressor miRNA, miR-145, in pancreatic cancer.

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