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Transcription Regulatory Regions Database (TRRD): its status in 2002

N. A. Kolchanov
2002 Nucleic Acids Research  
Transcription Regulatory Regions Database (TRRD) is an informational resource containing an integrated description of the gene transcription regulation.  ...  The visualization tool, TRRD Viewer, provides the information representation in a form of maps of gene regulatory regions.  ...  TRRD is a unique database as it contains simultaneously the information obtained while studying extended regulatory regions, transcription factor binding sites and specific expression patterns of various  ... 
doi:10.1093/nar/30.1.312 pmid:11752324 pmcid:PMC99088 fatcat:i56couva6jexrfzupox6aiki6m

NPRD: Nucleosome Positioning Region Database

V. G. Levitsky
2004 Nucleic Acids Research  
The object of the database is a single NFS described in an individual entry.  ...  At present, the NPRD database contains 438 entries and integrates the data described in 124 original papers. The database URL: http://srs6.bionet.nsc.ru/srs6/.  ...  An NFS in the human hepatocyte nuclear factor 4-alpha gene promoter is crucial for determining expression status.  ... 
doi:10.1093/nar/gki049 pmid:15608285 pmcid:PMC540003 fatcat:wvmukhbrwvfpjbwabnxu3aupry

The Molecular Biology Database Collection: 2002 update

A. D. Baxevanis
2002 Nucleic Acids Research  
As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research.  ...  The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches.  ...  in eukaryotic genes Transterm http://uther.otago.ac.nz/Transterm.html Codon usage, start and stop signals TRRD http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/ Transcription regulatory regions of  ... 
doi:10.1093/nar/30.1.1 pmid:11752241 pmcid:PMC99169 fatcat:n46iu5l6oreapd5yxswe7pmg5m

Eukaryotic Promoter Recognition

James W. Fickett, Artemis G. Hatzigeorgiou
1997 Genome Research  
Currently maintained collections include TRANSFAC (Wingender et al. 1996) and the Transcription Regulatory Region Database (TRRD; Kel et al. 1994 ).  ...  regulatory regions.  ... 
doi:10.1101/gr.7.9.861 pmid:9314492 fatcat:ygnlf7m4m5hxhlfio76s2gsqni

Benchmark and integration of resources for the estimation of human transcription factor activities

Luz Garcia-Alonso, Christian H. Holland, Mahmoud M. Ibrahim, Denes Turei, Julio Saez-Rodriguez
2019 Genome Research  
The prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach to characterize the functional status of transcriptional  ...  regulatory circuits.  ...  Because of their ability to interact with specific DNA regulatory regions, transcription factors (TFs) are key proteins in linking signaling transduction networks to gene-specific transcriptional regulation  ... 
doi:10.1101/gr.240663.118 pmid:31340985 pmcid:PMC6673718 fatcat:oc2fyvmaf5et5gubbqgr35syae

Baicalin inhibits recruitment of GATA1 to the HSD3B2 promoter and reverses hyperandrogenism of PCOS

Jin Yu, Yuhuan Liu, Danying Zhang, Dongxia Zhai, Linyi Song, Zailong Cai, Chaoqin Yu
2019 Journal of Endocrinology  
In summary , our data revealed that GATA1 is an important transcription factor activating the HSD3B2 promoter in steroidogenesis, and baicalin potentially be an effective therapeutic agent for hyperandrogenism  ...  Hyperandrogenic PCOS model rats treated with baicalin significantly reversed the high androgen levels of serum and the abnormal ovarian status, restored the estrous cyclicity, and decreased the expression  ...  NCI-H295R cells were transfected with luciferase reporter plasmids containing fragments of the upstream regulatory region of HSD3B2.  ... 
doi:10.1530/joe-18-0678 fatcat:h4jvsj3tbrgjhgwaqup4xoy5ie

Gene network analysis leads to functional validation of pathways linked to cancer cell growth and survival

Emmanuelle Berger, Nathalie Vega, Hubert Vidal, Alain Geloën
2012 Biotechnology Journal  
PPARA is highly expressed in liver where it is a key regulator of lipid metabolism and its regulatory activity on fatty acid oxidation has been established in HepG2 cells [41] [42] [43] .  ...  for transcription factors having putative binding sites in the promoter regions of these 2 sets of genes by using Fatigo+ software.  ... 
doi:10.1002/biot.201200188 pmid:22930530 fatcat:hc332hegvfchrm6jaqhntl6jke

XWRAPComposer

Ling Liu, Jianjun Zhang, Wei Han, Carlton Pu, James Caverlee, Sungkeun Park, Terence Critchlow, David Buttler, Matthew Coleman
2006 International Journal of Web Services Research  
We illustrate the problems and challenges of multipage data extraction in the context of bioinformatics applications and evaluate the design and development of XWRAPComposer through our experiences of  ...  Any opinions, findings, and conclusions or recommendations expressed in the project material are those of the authors and do not necessarily reflect the views of the sponsors.  ...  In Step (5), these promoter sequences are identified and analyzed using specific tools, such as Mat-Inspector (Peterson, 2002) , TRANSFAC, TRRD, or COMPEL (Quandt et al., 1995) to find the common transcription  ... 
doi:10.4018/jwsr.2006040102 fatcat:osamptynhjas3nz7y2fnhnxcgy

Benchmark and integration of resources for the estimation of human transcription factor activities

Luz Garcia-Alonso, Christian H. Holland, Mahmoud Ibrahim, Dénes Türei, Julio Sáez Rodríguez
2020
The prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach to characterize the functional status of transcriptional  ...  regulatory circuits.  ...  Because of their ability to interact with specific DNA regulatory regions, transcription factors (TFs) are key proteins in linking signaling transduction networks to gene-specific transcriptional regulation  ... 
doi:10.18154/rwth-2020-03288 fatcat:i44byepu4rhazc7apcgeankjg4

On computational strategies for regulatory element and regulatory polymorphism detection

Stephen Blair Montgomery
2006
It is here where computational approaches are required to prioritize candidate regulatory variants.  ...  New experimental approaches offer the opportunity to effectively identify markers of disease susceptibility in gene regulatory regions but the discovery of the molecular mechanism of dysregulation remains  ...  Transcriptional Regulatory Regions Database (TRRD) [132] Contains information on structural and functional organization of transcription regulatory regions of eukaryotic genes.  ... 
doi:10.14288/1.0093020 fatcat:tl6tplfc2zbsvbefqb3olizea4

Human trophoblast survival and invasion in the developing placenta: autocrine regulation by hbegf HUMAN TROPHOBLAST SURVIVAL AND INVASION IN THE DEVELOPING PLACENTA: AUTOCRINE REGULATION BY HBEGF

Philip Jessmon, Philip Dissertation
unpublished
Databases on Transcriptional Regulation: TRANSFAC, TRRD, and COMPEL. . Nucleic Acids Res. 26:364--370. Higashiyama, S., R. Iwamoto, K. Goishi, G. Raab, N. Taniguchi, M. Klagsbrun, and E.  ...  Given the lack of transcriptional regulation, it was hypothesized that HBEGF translation could be regulated by regions in its large 3'UTR.  ...  TUNEL assays indicate that HBEGF signals through the MAPK14 pathway to inhibit apoptosis in CTBs induced by 2% O 2 or reoxygenation injury. Previous studies  ... 
fatcat:h7d5tz36pnetvb2hkaholgkxnq

Functional studies of PPP2R2A in breast cancer

Qianli Ma
2015
We hypothesized that the high frequency deletion of PPP2R2A, as well as its correlation with ER expression status, implies its functional roles in breast cancer development.  ...  SPDEF was particularly up regulated and recruited in ER transcriptional machinery.  ...  to its own transcriptional regulatory site with ER.  ... 
doi:10.14288/1.0166260 fatcat:czd327dcdrhdrok6qax4y7xtru