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Using Biological Networks in Protein Function Prediction and Gene Expression Analysis

Limsoon Wong
2011 Internet Mathematics  
This paper presents a review on biological network databases and on approaches to protein function prediction and gene expression profile analysis that are based on biological networks.  ...  While sequence homology search has been the main work horse in protein function prediction, it is not applicable to a significant portion of novel proteins that do not have informative homologs in sequence  ...  The third type of networks are used in many types of analysis, e.g., protein function prediction [12] and disease-gene association studies [30, 54] .  ... 
doi:10.1080/15427951.2011.604561 fatcat:fauz3fw44fbxnm7vggstqlqgky

Putting microarrays in a context: Integrated analysis of diverse biological data

O. G. Troyanskaya
2005 Briefings in Bioinformatics  
The focus of this review is on the use of such methods for gene function prediction, understanding of protein regulation and modelling of biological networks.  ...  Gene expression microarrays are the most commonly available source of such data.  ...  Integrated genomic data can be used to predict gene function and regulation and in modelling of biological networks Figure 1 : Overview of integrated analysis of genomic data.  ... 
doi:10.1093/bib/6.1.34 pmid:15826355 fatcat:pjhdv2r3enehhhu23wj6moxojm

Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of Ews/Ewsr1 KO mice

Chai-Jin Lee, Hongryul Ahn, Sean Bong Lee, Jong-Yeon Shin, Woong-Yang Park, Jong-Il Kim, Junghee Lee, Hoon Ryu, Sun Kim
2016 BMC Medical Genomics  
On the biological side, we report that EWS regulates G-protein, Gnai1, in the spinal cord of Ews/Ewsr1 KO mice using the two biological network integrated analysis method.  ...  Conclusions: Our integrated analysis of miRNA-transcriptome network and PPI network combined with qRT-PCR verifies that Gnai1 function is impaired in the spinal cord of Ews/Ewsr1 KO mice.  ...  Protein-protein interaction network analysis Input: Key genes identified in Step 2 Output: G protein complex genes and regulators After selecting the key gene in Step 2, we investigated the biological  ... 
doi:10.1186/s12920-016-0195-4 pmid:27534535 pmcid:PMC4989891 fatcat:3ypbhfrm3rfplkrvbqtxugmeaq

A comparison of the functional modules identified from time course and static PPI network data

Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen, Yi Pan
2011 BMC Bioinformatics  
Results: In this paper, Time Course Protein Interaction Networks (TC-PINs) are reconstructed by incorporating time series gene expression into PPI networks.  ...  A protein-protein interaction (PPI) network with static connectivity is dynamic in the sense that the nodes implement so-called functional activities that evolve in time.  ...  Computational analysis of these networks has great potential in aiding our understanding of gene function, biological pathways and cellular organization.  ... 
doi:10.1186/1471-2105-12-339 pmid:21849017 pmcid:PMC3174950 fatcat:tz4hhurihfbp3i24of67aohipy

Predicting new molecular targets for rhein using network pharmacology

Aihua Zhang, Hui Sun, Bo Yang, Xijun Wang
2012 BMC Systems Biology  
Currently, network pharmacology has used in identifying potential drug targets to predicting the spread of drug activity and greatly contributed toward the analysis of biological systems on a much larger  ...  We have implemented a computational platform that integrates pathway, protein-protein interaction, differentially expressed genome and literature mining data to result in comprehensive networks for drug-target  ...  Nodes: specific proteins or genes. Central nodes (Yellow) of the interaction network were used to illustrate the gene expression obtained and represents significant change in expression.  ... 
doi:10.1186/1752-0509-6-20 pmid:22433437 pmcid:PMC3338090 fatcat:gjm2fkchvfa2fps5bukxuul5wq

Gene module level analysis: identification to networks and dynamics

Xuewei Wang, Ertugrul Dalkic, Ming Wu, Christina Chan
2008 Current Opinion in Biotechnology  
Gene-module level analysis is based on this module concept, aiming to understand biological network design and systems behavior in disease and development by emphasizing on modules of genes rather than  ...  Module-level analysis has been extensively applied in genome wide level analysis, exploring the organization of biological systems from identifying modules to reconstructing module networks and analyzing  ...  ED is supported in part by the Quantitative Biology and Modeling Initiative.  ... 
doi:10.1016/j.copbio.2008.07.011 pmid:18725293 pmcid:PMC2615490 fatcat:yvp5cmaq5zamncy3fcykkc2coe

Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis

Younghee Lee, Xinan Yang, Yong Huang, Hanli Fan, Qingbei Zhang, Youngfei Wu, Jianrong Li, Rifat Hasina, Chao Cheng, Mark W. Lingen, Mark B. Gerstein, Ralph R. Weichselbaum (+3 others)
2010 PLoS Computational Biology  
Restoration of miR-204 function in HNSCC cell lines inhibits the expression of its functionally related gene targets, leads to the reduced adhesion, migration and invasion in vitro and attenuates experimental  ...  Using this approach we characterize miR-204 as a tumor suppressor microRNA and uncover previously unknown connections between microRNA regulation, network topology, and expression dynamics.  ...  Through enrichment analysis and network modeling using mRNA gene expression profile, we identified a set of functionally related miR-204 targets that showed increased mRNA expression in HNSCC upon miR-  ... 
doi:10.1371/journal.pcbi.1000730 pmid:20369013 pmcid:PMC2848541 fatcat:m2xgzzhpv5hvdjes2dab25baqa

Computational identification of cellular networks and pathways

Florian Markowetz, Olga G. Troyanskaya
2007 Molecular Biosystems  
In this article we highlight recent developments in computational functional genomics to identify networks of functionally related genes and proteins based on diverse sources of genomic data.  ...  We discuss integrated analysis of microarray datasets, methods to combine heterogeneous data sources, the analysis of highdimensional phenotyping screens and describe efforts to establish a reliable and  ...  biological molecules, with functional data from perturbation screens that carry only indirect information of gene and protein interactions.  ... 
doi:10.1039/b617014p pmid:17579773 fatcat:4vo2qkodsjhyflapkq7v3o23oy

Biological process annotation of proteins across the plant kingdom

Joachim W. Bargsten, Edouard I. Severing, Jan-Peter Nap, Gabino F. Sanchez-Perez, Aalt D.J. van Dijk
2014 Current Plant Biology  
We here demonstrate the combination of a method for protein function annotation that uses network information to predict the biological processes a protein is involved in, with a sequence-based prediction  ...  The combined function prediction is based on co-expression networks and combines the network-based prediction method BMRF with the sequencebased prediction method Argot2.  ...  This work was supported by the FP7 "Infrastructures" project Trans-PLANT Award 283496 and by the BioRange program of the Netherlands Bioinformatics Centre (NBIC), which is supported by a BSIK grant through  ... 
doi:10.1016/j.cpb.2014.07.001 fatcat:zab2335dbbhdziihrskrfb73ye

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network

Batool Hosseinpour, Mohammad Reza Bakhtiarizadeh, Pegah Khosravi, Esmaeil Ebrahimie
2013 Gene  
were predicted in the network.  ...  Additionally, a protein interaction network of hESC genes was constructed based on biological processes, and interestingly, 126 downregulated genes along with upregulated ones identified by promoter analysis  ...  PI network analysis Using the genes listed in Tables 1 and 2 (Supplementary material 3) and 328 genes predicted by promoter analysis (Supplementary material 4) , two PI networks based on the biological  ... 
doi:10.1016/j.gene.2013.09.011 pmid:24042128 fatcat:fdteqw6ggjh6znqfttbhnpiydy

The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses

M. Lin, X. Zhou, X. Shen, C. Mao, X. Chen
2011 The Plant Cell  
These inferred interactions can nicely power several network topology-based systems biology analyses, such as gene set linkage analysis, protein function prediction, and identification of regulatory genes  ...  of genes and gene networks.  ...  The analyses discussed above, gene set linkage analysis, functional prediction, and identification of expressionally insignificant regulators, are examples of these network topology-based systems biology  ... 
doi:10.1105/tpc.110.082529 pmid:21441435 pmcid:PMC3082272 fatcat:f7durtcgt5bebg7mzkl4666guu

Survey of Network-Based Approaches to Research of Cardiovascular Diseases

Anida Sarajlić, Nataša Pržulj
2014 BioMed Research International  
Consequently, topology of biological networks has successfully been used for identifying genes, pathways, and modules that govern molecular actions underlying various complex diseases.  ...  Here, we review approaches that explore and use relationships between topological properties of biological networks and mechanisms underlying CVDs.  ...  The gene correlation network was constructed using statistical analysis of gene expression data.  ... 
doi:10.1155/2014/527029 pmid:24772427 pmcid:PMC3977459 fatcat:pu2qrjtgg5hm7j6htwcm3koi2u

Protein Interaction Network of Arabidopsis thaliana Female Gametophyte Development Identifies Novel Proteins and Relations

Batool Hosseinpour, Vahid HajiHoseini, Rafieh Kashfi, Esmaeil Ebrahimie, Farhid Hemmatzadeh, Francisco José Esteban
2012 PLoS ONE  
Seventy-four and 24 upregulated genes as well as 171 and 3 downregulated genes were identified in subtracted networks based on biological processes and molecular function respectively, including novel  ...  including proteome map based on biological processes and molecular functions of proteins.  ...  In this investigation, novel upregulated and downregulated genes were identified in the networks and their predicted functions were discussed.  ... 
doi:10.1371/journal.pone.0049931 pmid:23239973 pmcid:PMC3519845 fatcat:rvcasocuvvgszje47yoz3pjpo4

Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data

Ahmad Firoz, Adeel Malik, Sanjay Kumar Singh, Vivekanand Jha, Amjad Ali
2014 International Journal of Genomics  
DAVID functional analysis suggested inflammatory response, glycosaminoglycan metabolic process, and protein maturation as the enriched biological processes in BvL579, BvM501, and LvM442, respectively.  ...  Further studies are required to confirm the role of predicted hub genes as well as the significance of biological processes.  ...  , India); and School of Biotechnology, Yeungnam University (Gyeongsan, South Korea) for providing lab facilities to conduct this research.  ... 
doi:10.1155/2014/837365 pmid:25121089 pmcid:PMC4121153 fatcat:jcj6j5344fhivhgoecnoi2zhae

Construction of polycythemia vera protein interaction network and prediction of related biological functions

L.-J. Liu, X.-J. Cao, C. Zhou, Y. Sun, Q.-L. Lv, F.-B. Feng, Y.-Y. Zhang, C.-G. Sun
2016 Genetics and Molecular Research  
Various molecular complexes were detected using the Clustervize plugin and a gene ontologyenrichment analysis of the biological pathways, molecular functions, and cellular components of the selected molecular  ...  Fifty-four PV-related genes were identified in OMIM. The protein-protein interaction network contains 5 molecular complexes with correlation integral values >4.  ...  GO develops effective bioinformatic methods to realize the targets of genetic network analysis and the functional prediction of unknown genes using previously existing biological architecture and knowledge  ... 
doi:10.4238/gmr.15017169 pmid:26909922 fatcat:qqp7olakr5eyvhljxrmmo76qca
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