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Transcription Regulatory Regions Database (TRRD): its status in 2002
2002
Nucleic Acids Research
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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
2004
Nucleic Acids Research
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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
2002
Nucleic Acids Research
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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
1997
Genome Research
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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
2019
Genome Research
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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
2019
Journal of Endocrinology
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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
2012
Biotechnology Journal
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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
2006
International Journal of Web Services Research
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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
2020
Preserved Fulltext
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The file type is application/pdf.
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
2006
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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
unpublished
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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
2015
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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