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The Use of Functional Genomics in Synthetic Promoter Design [chapter]

Michael L.
<span title="2011-09-02">2011</span> <i title="InTech"> Computational Biology and Applied Bioinformatics </i> &nbsp;
On the other hand, the growth of the computational power for processing and storage has also increased the necessity for deeper knowledge in the field.  ...  Part II consists of application-oriented chapters that report case studies in which a specific biological problem is treated with bioinformatics tools.  ...  ) ABS Database of regulatory elements Blanco et al., (2006) JASPAR Database of regulatory elements Sandelin et al., (2004) HTPSELEX Database of composite regulatory elements Jagannathan et al., CisView  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/20653">doi:10.5772/20653</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cuvqdjmlojbntaepfwmnyq4sci">fatcat:cuvqdjmlojbntaepfwmnyq4sci</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725153050/https://api.intechopen.com/chapter/pdf-download/19008" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ae/0b/ae0b707570c0ee55b694703ec3d76e12f775395b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/20653"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Construction of predictive promoter models on the example of antibacterial response of human epithelial cells

Ekaterina Shelest, Edgar Wingender
<span title="2005-01-12">2005</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gdqzxgkaenh3xnqi2umstfxgva" style="color: black;">Theoretical Biology and Medical Modelling</a> </i> &nbsp;
Binding of a bacteria to a eukaryotic cell triggers a complex network of interactions in and between both cells.  ...  Applying this method, we came up with a promoter model of antibacterial response genes that consists of one TFBS pair which should be found in the whole training set and four complementary pairs.  ...  The work was financed by the Bioinformatics Competence Center "Intergenomics" using a grant of the German Ministry of Education and Research (grant no. 031U210B).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1742-4682-2-2">doi:10.1186/1742-4682-2-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15647113">pmid:15647113</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC546226/">pmcid:PMC546226</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ssqwc4bsnnhshioqgfl53q6jrq">fatcat:ssqwc4bsnnhshioqgfl53q6jrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427173426/https://tbiomed.biomedcentral.com/track/pdf/10.1186/1742-4682-2-2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/87/6b/876bf017092cedaac35555a15f66d300669ddaea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1742-4682-2-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546226" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

Alexander E Kel, Monika Niehof, Volker Matys, Rüdiger Zemlin, Jürgen Borlak
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome.  ...  The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2008/9/2/R36 Genome Biology 2008, 9:R36 http://genomebiology.com/2008/9/2/R36 Genome Biology  ...  of two and more TFs to so-called composite regulatory elements with synergistic effects on the regulation of gene expression is provided by the TRANSCompel ® database [4] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-2-r36">doi:10.1186/gb-2008-9-2-r36</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18291023">pmid:18291023</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2374721/">pmcid:PMC2374721</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2xp4hp36pbbkfl7qma47ihwvpe">fatcat:2xp4hp36pbbkfl7qma47ihwvpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170820041250/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2008-9-2-r36?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d7/43/d7435eea8e9882cd42ddb60e0f8f7c43bb427438.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-2-r36"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374721" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prediction of synergistic transcription factors by function conservation

Zihua Hu, Boyu Hu, James F Collins
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Rather than aligning the regulatory sequences from orthologous genes and then identifying conserved TF binding sites (TFBSs) in the alignment, we developed computational approaches to implement the novel  ...  Conclusion: Function conservation based on the concordance of combinatorial TFBS enrichment along with enrichment of overlapping orthologous genes has been proven to be a successful means for the identification  ...  The TRANSCompel ® database contains approximately 180 experimentally proven composite elements of two or more binding sites; of these approximately 180 composite elements, 15 are synergistic combinations  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2007-8-12-r257">doi:10.1186/gb-2007-8-12-r257</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18053230">pmid:18053230</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2246259/">pmcid:PMC2246259</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/osih4n4fi5fktelhgkwjbgktoa">fatcat:osih4n4fi5fktelhgkwjbgktoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814092011/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2007-8-12-r257?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/11/3c/113c4ac1eb98c02925998a8b32b32f67abe7def8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2007-8-12-r257"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246259" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification of interacting transcription factors regulating tissue gene expression in human

Zihua Hu, Steven M Gallo
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Results: We have integrated a function conservation approach, which is based on evolutionary conservation of biological function, and genes with highest expression level in human tissues to predict TF  ...  To find interacting TFs controlling tissue gene expression in a broad spatial and temporal manner, we looked for TF pairs common to the same type of tissues and identified 379 such TF pairs, based on which  ...  The TRANSCompel® database contains 180 experimentally proven composite elements of two or more binding sites which were previously identified by individual wet lab studies from others.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-11-49">doi:10.1186/1471-2164-11-49</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20955586">pmid:20955586</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3091724/">pmcid:PMC3091724</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/apsxofjzdngrjjqsvi5uctejra">fatcat:apsxofjzdngrjjqsvi5uctejra</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830101836/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-11-49?site=http://bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9f/33/9f3307bafa0c44c4b88ed8e80e8ba1205a7ef361.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-11-49"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091724" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery

Siwen Hu-Lieskovan, Srabani Bhaumik, Kavita Dhodapkar, Jean-Charles J B Grivel, Sumati Gupta, Brent A Hanks, Sylvia Janetzki, Thomas O Kleen, Yoshinobu Koguchi, Amanda W Lund, Cristina Maccalli, Yolanda D Mahnke (+5 others)
<span title="">2020</span> <i title="BMJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tcu4zb76ybaefkex5wp4pzcq3u" style="color: black;">Journal for ImmunoTherapy of Cancer</a> </i> &nbsp;
However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint  ...  In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker  ...  . 584 ► TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. 585 ► JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/jitc-2020-000705">doi:10.1136/jitc-2020-000705</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33268350">pmid:33268350</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iuqgiddv4ra63bz7ge3rq2ppk4">fatcat:iuqgiddv4ra63bz7ge3rq2ppk4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427215730/https://jitc.bmj.com/content/jitc/8/2/e000705.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/ce/6bcea67199ae7c2fede20e580cdbcad04e519910.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/jitc-2020-000705"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> bmj.org </button> </a>

A bioinformatics approach to the study of the transcriptional regulation of AMPA Glutamate receptors (GRIAs) and genes whose expression are co-regulated with GRIAs

Allen Chong, Vladimir Bajic Ii K E Y W O R D S
<span title="">2009</span> <span class="release-stage">unpublished</span>
It was postulated that each gene has three main sets of transcriptional elements: one which is gene-specific, one which is family-specific, and a third which is tissue-specific.  ...  elements that were present in the AMPA receptor gene promoters but were not so common in the general population of gene promoters.  ...  The collection of composite elements in these databases are manually curated and are based on proven composite elements described in the literature.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7gaa6wqyvjeprh2urhbk5wdjdm">fatcat:7gaa6wqyvjeprh2urhbk5wdjdm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180518124041/http://etd.uwc.ac.za/xmlui/bitstream/handle/11394/3175/Chong_PHD_2009.pdf;jsessionid=4CB059A1F4CF09B8A5E2896792CA0909?sequence=3" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/22/4e/224eaacab379a57817cca83c60317a816c440eea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Co-occurrence of transcription factor binding sites [article]

Holger Klein, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
<span title="2010-06-08">2010</span>
of a large fraction of genes in a large variety of cell types and conditions.  ...  In metazoan organisms completely different cell types, like a liver and a brain cell, are encoded in the same genome. However, the set of genes needed in both cases differs.  ...  Using a window size of 100bps also captures most of the binding site distances from composite elements of the TransCOMPEL database [219] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17169/refubium-15330">doi:10.17169/refubium-15330</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wdlikk4ds5dapmaksddexqzg3u">fatcat:wdlikk4ds5dapmaksddexqzg3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220123054419/https://refubium.fu-berlin.de/bitstream/handle/fub188/11132/diss_klein_gesamt.pdf;jsessionid=7BE814B98AF64255F609CE87EAD2467E?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ae/07/ae075987f714aefc7259296c8ddae57a649b7358.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17169/refubium-15330"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Expression and regulation of sialic acid biosynthesis and sialyltransferase genes in the mammary gland

Jovana Maksimovic
<span title="2017-01-31">2017</span>
This study describes the expression of sialic acid biosynthesis and sialyltransferase genes in the lactating eutherian and marsupial mammary gland and the role of lactogenic hormones in their regulation  ...  Sialic acids are a family of nine-carbon, acidic monosaccharides.  ...  This program uses a library of experimentally identified composite elements collected in the TRANSCOMPEL database, as well as mononucleotide position weight matrices for individual TFBS collected in TRANSFAC  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4225/03/58901c6014743">doi:10.4225/03/58901c6014743</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nclaz6hmp5hihgxfcz56txalba">fatcat:nclaz6hmp5hihgxfcz56txalba</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209081224/https://au-east.erc.monash.edu.au/fpfiles/16448741/4597669_monash_80942.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/30/26/3026874c3f8b928d27b50f2c5d2ba3edcf8ab059.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4225/03/58901c6014743"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>