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Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
1999
Nucleic Acids Research
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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 http://transfac.gbf.de/ ...
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
2008
Nucleic Acids Research
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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
1999
Bioinformatics
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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
2000
Trends in Genetics
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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
2013
BioMed Research International
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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
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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
2015
BioMed Research International
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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
2011
Briefings in Bioinformatics
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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
2008
IET Systems Biology
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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
2009
PLoS Computational Biology
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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
2021
Biomolecules
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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]
2008
Msphere
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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
2014
PLoS ONE
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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
2012
Circulation Research
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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
2015
Progress in Biophysics and Molecular Biology
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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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