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Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms

T. Heinemeyer, X. Chen, H. Karas, A. E. Kel, O. V. Kel, I. Liebich, T. Meinhardt, I. Reuter, F. Schacherer, E. Wingender
1999 Nucleic Acids Research  
Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously  ...  The databases are available on the WWW at  ...  ACKNOWLEDGEMENTS The authors are indebted to H. Hermjakob (EBI, Hinxton, UK) for his support in establishing TRANSFAC-links to the EMBL data library and to the SwissProt database, and to M.  ... 
doi:10.1093/nar/27.1.318 pmid:9847216 pmcid:PMC148171 fatcat:fjpblo3scrcv7fhpt75ttmc7vy

PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes

Logan Everett, Antony Vo, Sridhar Hannenhalli
2008 Nucleic Acids Research  
The PTM-Switchboard database meets this need by cataloging such instances in the model system Saccharomyces cerevisiae.  ...  In the future, the database will be expanded to mammalian organisms, and will also include triplets predicted from computational approaches. The database can be accessed at  ...  For the computational biologist, the entirety of the database (or a subset filtered by an appropriate evidence code) can serve as an ideal gold set for training and testing models of three-way regulatory  ... 
doi:10.1093/nar/gkn731 pmid:18927104 pmcid:PMC2686453 fatcat:ro2ojp3jifh5fihifgehprnw2y

Conformational and physicochemical DNA features specific for transcription factor binding sites

J. V. Ponomarenko, M. P. Ponomarenko, A. S. Frolov, D. G. Vorobyev, G. C. Overton, N. A. Kolchanov
1999 Bioinformatics  
Motivation: A reliable recognition of transcription factor binding sites is essential for analysis of regulatory genomic sequences.  ...  Results: We suggest an approach for revealing significant conformational and physicochemical properties of functional sites implemented in the database B-DNA-VIDEO.  ...  Acknowledgements The work was supported by the Russian Foundation for Basic Research, the Russian Human Genome Program, Russian State Committee on Science and Technology, Integrated Program of Siberian  ... 
doi:10.1093/bioinformatics/15.7.654 pmid:10487873 fatcat:lgtc7oupyzgmrejpybw3rsk6hq

Complex evolution of the inositol-1-phosphate synthase gene among archaea and eubacteria

Nandita Bachhawat, Shekkar C. Mande
2000 Trends in Genetics  
The tree was constructed after 100 cycles of bootstrapping using programs PROTDIST, SEQBOOT and CONSENSUS, available in the PHYLIP suite 5 .  ...  The multiple sequence alignments used for generating the phylogenetic tree were constructed by excluding highly variable N-terminal and C-terminal amino acid stretches of the sequences.  ...  Development 124, 1851-1864 10 Heinemeyer, T. et al. (1999) Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.  ... 
doi:10.1016/s0168-9525(99)01966-6 pmid:10689351 fatcat:tpouqoapejfw7i364pifotwk3a

A Systems' Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks

Xin Lai, Animesh Bhattacharya, Ulf Schmitz, Manfred Kunz, Julio Vera, Olaf Wolkenhauer
2013 BioMed Research International  
We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions.  ...  For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments.  ...  Acknowledgments The authors would like to acknowledge the funding from the German Federal Ministry of Education and Research (BMBF): eBio-miRSys (0316175A to Xin Lai and Julio Vera), eBio-SysMet (0316171  ... 
doi:10.1155/2013/703849 pmid:24350286 pmcid:PMC3848080 fatcat:y4ef36vwg5hh5cvdpddyguijbe

Page 1092 of None Vol. 42, Issue 5 [page]

2000 None  
Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nuclete Acids Res 27: 318 322, 1999 Heller R, Stoffers D, Hussain M, Miller CP, and Habener J.  ...  The pancreatic istet tactor STF-1 binds cooperatively with Pbx to a regulatory element in the somatostatin promoter: im portance of the FPWMK motif and of the homeodomain.  ... 

A Glimpse to Background and Characteristics of Major Molecular Biological Networks

Md. Altaf-Ul-Amin, Tetsuo Katsuragi, Tetsuo Sato, Shigehiko Kanaya
2015 BioMed Research International  
These huge datasets have paved the way for system-level analysis of the processes and subprocesses of the cell.  ...  For system-level understanding, initially the elements of a system are connected based on their mutual relations and a network is formed.  ...  Conflict of Interests The authors declare that there is no conflict of interests regarding the publication of this paper.  ... 
doi:10.1155/2015/540297 pmid:26491677 pmcid:PMC4605226 fatcat:lwzn2z7nzrh7np6at6twisrvem

Evolution and applications of plant pathway resources and databases

Y. Sucaet, T. Deva
2011 Briefings in Bioinformatics  
We also discuss how progress in non-plant communities can serve as an example for the improvement of the plant pathway database landscape and thereby allow quantitative modeling of plant biosystems.  ...  Study of plant biological pathways, the interconnection between these pathways and plant systems biology on the whole has in general lagged behind human systems biology.  ...  Eve Syrkin Wurtele and Dr Julie Dickerson at Iowa State University, who supported us in a number of ways with encouragement, sound advice, guidance and lots of good ideas.  ... 
doi:10.1093/bib/bbq083 pmid:21949268 fatcat:v4w7i5b47zhj7idwb7k5wrpdgi

Network integration and graph analysis in mammalian molecular systems biology

A. Ma'ayan
2008 IET Systems Biology  
Besides synaptic vesicles, the molecular organisation of macro-molecular complexes is still mostly unknown.  ...  A first step towards assembling this 3D puzzle is identifying protein-protein interactions, their localisation and the functional relationship among the components [5] .  ...  [67] , MAPPER [68] , TRANSCompel [69] , TRRD [70, 71] and SWISS-REGULON [72] are web-based tools providing a user interface for an underlying gene-regulatory network database.  ... 
doi:10.1049/iet-syb:20070075 pmid:19045817 pmcid:PMC2745214 fatcat:t55zchkczrfflpdeolrf7wxn2y

Biomedical Discovery Acceleration, with Applications to Craniofacial Development

Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner, Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter, Satoru Miyano
2009 PLoS Computational Biology  
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher  ...  An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development.  ...  Structured knowledge, in the form of molecular biology relevant databases, has also been growing at an impressive rate.  ... 
doi:10.1371/journal.pcbi.1000215 pmid:19325874 pmcid:PMC2653649 fatcat:pd3cyfntdzcv3ggtgpl7kk7fz4

Omics Technologies to Decipher Regulatory Networks in Granulocytic Cell Differentiation

Svetlana Novikova, Olga Tikhonova, Leonid Kurbatov, Tatiana Farafonova, Igor Vakhrushev, Alexey Lupatov, Konstantin Yarygin, Victor Zgoda
2021 Biomolecules  
Obtained results indicate that the omics data reflect involvement of the DNA repair system and the MAPK kinase cascade as well as show the balance between the processes of the cell survival and apoptosis  ...  Using data on differentially expressed transcripts and proteins we have applied upstream regulator search and obtained transcriptome- and proteome-based regulatory networks of induced granulocytic differentiation  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biom11060907 pmid:34207065 pmcid:PMC8233756 fatcat:da6qzfykazgi5epbap5fvzxzsm

Prediction of Regulatory Elements [chapter]

Albin Sandelin
2008 Msphere  
Experimental efforts towards understanding the regulation of genes is laborious and expensive, but can be substantially accelerated with the use of computational predictions.  ...  one of the most fundamental processes for all life forms, transcriptional regulation remains an intriguing and challenging subject for biomedical research.  ...  Input promoter sequences are either entered by the user or retrieved semi-automatically using a novel expert system based on the Genelynx databases 96 .  ... 
doi:10.1007/978-1-60327-429-6_11 pmid:18712306 fatcat:ku3wqjcnmjaw5ncqdaszcpzpj4

Integrative Identification of Deregulated MiRNA/TF-Mediated Gene Regulatory Loops and Networks in Prostate Cancer

Ali Sobhi Afshar, Joseph Xu, John Goutsias, Sebastien Pfeffer
2014 PLoS ONE  
TFs available in existing databases, certain molecular structures identified to be statistically over-represented in gene regulatory networks, available molecular subtyping information, and state-of-the-art  ...  Our findings show that the proposed computational method can be used to effectively achieve notable insights into the poorly understood molecular mechanisms of miRNA-mediated interactions and dissect their  ...  A natural approach towards this goal is to first identify the most relevant molecular species to build an initial network and subsequently expand this network with additional species.  ... 
doi:10.1371/journal.pone.0100806 pmid:24968068 pmcid:PMC4072696 fatcat:rk37ktzuizazxafy3wtcvi3k3a

The Emerging Paradigm of Network Medicine in the Study of Human Disease

S. Y. Chan, J. Loscalzo
2012 Circulation Research  
The molecular pathways that govern human disease consist of molecular circuits that coalesce into complex, overlapping networks.  ...  (eg, the unique flux of information through the network) to understand better the pathogenic behavior of complex molecular interconnections that traditional methods fail to recognize.  ...  Sources of Funding This work was supported in part by the NIH, the Pulmonary Hypertension Association, Gilead Sciences, and the Lerner, Harris, and Watkins funds (S.Y.C.); and NIH grants HL061795, HL48743  ... 
doi:10.1161/circresaha.111.258541 pmid:22821909 pmcid:PMC3425394 fatcat:m4zwmfv42vejrpd3kkbpx2k4h4

Identifying functional gene regulatory network phenotypes underlying single cell transcriptional variability

James Park, Babatunde Ogunnaike, James Schwaber, Rajanikanth Vadigepalli
2015 Progress in Biophysics and Molecular Biology  
Simulations of the inferred gene regulatory network response to experimentally observed stimuli levels mirrored the pattern and quantitative range of gene expression across individual neurons remarkably  ...  In addition, the network identification results revealed that distinct regulatory interactions, coupled with differences in the regulatory network stimuli, drive the variable gene expression patterns observed  ...  Daniel Lees for his critical review of the paper and Mr. Hiren Makadia for facilitating the computational analyses.  ... 
doi:10.1016/j.pbiomolbio.2014.11.004 pmid:25433230 pmcid:PMC4366310 fatcat:eqmznll56ngpzdwlpk7kavmfnq
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