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AthaMap: From in silico Data to Real Transcription Factor Binding Sites
AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally v...
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| Published in: | In silico biology 2006, Vol.6 (3), p.243-252 |
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| Main Authors: | , , , , |
| Format: | Article |
| Language: | English |
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| container_end_page | 252 |
| container_issue | 3 |
| container_start_page | 243 |
| container_title | In silico biology |
| container_volume | 6 |
| creator | Bülow, Lorenz Steffens, Nils Ole Galuschka, Claudia Schindler, Martin Hehl, Reinhard |
| description | AthaMap generates a map for cis-regulatory sequences for the
whole Arabidopsis thaliana genome. AthaMap was initially developed by
matrix-based detection of putative transcription factor binding sites (TFBS)
mostly determined from random binding site selection experiments. Now, also
experimentally verified TFBS have been included for 48 different
Arabidopsis thaliana transcription factors (TF). Based on these sequences,
89,416 very similar putative TFBS were determined within the genome of A.
thaliana and annotated to AthaMap. Matrix- and single sequence-based binding
sites can be included in colocalization analysis for the identification of
combinatorial cis-regulatory elements. As an example, putative target
genes of the WRKY18 transcription factor that is involved in plant-pathogen
interaction were determined. New functions of AthaMap include descriptions for
all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR
and MIPS. Transcription factors used in the binding site determination are
linked to TAIR and TRANSFAC® databases.
AthaMap is freely available at http://www.athamap.de. |
| doi_str_mv | 10.3233/ISB-00238 |
| format | article |
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whole Arabidopsis thaliana genome. AthaMap was initially developed by
matrix-based detection of putative transcription factor binding sites (TFBS)
mostly determined from random binding site selection experiments. Now, also
experimentally verified TFBS have been included for 48 different
Arabidopsis thaliana transcription factors (TF). Based on these sequences,
89,416 very similar putative TFBS were determined within the genome of A.
thaliana and annotated to AthaMap. Matrix- and single sequence-based binding
sites can be included in colocalization analysis for the identification of
combinatorial cis-regulatory elements. As an example, putative target
genes of the WRKY18 transcription factor that is involved in plant-pathogen
interaction were determined. New functions of AthaMap include descriptions for
all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR
and MIPS. Transcription factors used in the binding site determination are
linked to TAIR and TRANSFAC® databases.
AthaMap is freely available at http://www.athamap.de.</description><identifier>ISSN: 1386-6338</identifier><identifier>EISSN: 1434-3207</identifier><identifier>DOI: 10.3233/ISB-00238</identifier><identifier>PMID: 16922688</identifier><language>eng</language><publisher>London, England: SAGE Publications</publisher><subject>Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; Arabidopsis thaliana ; Base Sequence ; Binding Sites ; Biological and medical sciences ; Databases, Genetic ; DNA, Plant - chemistry ; DNA, Plant - genetics ; Fundamental and applied biological sciences. Psychology ; Genome, Plant ; Molecular and cellular biology ; Molecular genetics ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcription. Transcription factor. Splicing. Rna processing</subject><ispartof>In silico biology, 2006, Vol.6 (3), p.243-252</ispartof><rights>IOS Press. All rights reserved</rights><rights>2006 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,4024,27923,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18103884$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16922688$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bülow, Lorenz</creatorcontrib><creatorcontrib>Steffens, Nils Ole</creatorcontrib><creatorcontrib>Galuschka, Claudia</creatorcontrib><creatorcontrib>Schindler, Martin</creatorcontrib><creatorcontrib>Hehl, Reinhard</creatorcontrib><title>AthaMap: From in silico Data to Real Transcription Factor Binding Sites</title><title>In silico biology</title><addtitle>In Silico Biol</addtitle><description>AthaMap generates a map for cis-regulatory sequences for the
whole Arabidopsis thaliana genome. AthaMap was initially developed by
matrix-based detection of putative transcription factor binding sites (TFBS)
mostly determined from random binding site selection experiments. Now, also
experimentally verified TFBS have been included for 48 different
Arabidopsis thaliana transcription factors (TF). Based on these sequences,
89,416 very similar putative TFBS were determined within the genome of A.
thaliana and annotated to AthaMap. Matrix- and single sequence-based binding
sites can be included in colocalization analysis for the identification of
combinatorial cis-regulatory elements. As an example, putative target
genes of the WRKY18 transcription factor that is involved in plant-pathogen
interaction were determined. New functions of AthaMap include descriptions for
all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR
and MIPS. Transcription factors used in the binding site determination are
linked to TAIR and TRANSFAC® databases.
AthaMap is freely available at http://www.athamap.de.</description><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis Proteins - metabolism</subject><subject>Arabidopsis thaliana</subject><subject>Base Sequence</subject><subject>Binding Sites</subject><subject>Biological and medical sciences</subject><subject>Databases, Genetic</subject><subject>DNA, Plant - chemistry</subject><subject>DNA, Plant - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genome, Plant</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><subject>Transcription. Transcription factor. Splicing. Rna processing</subject><issn>1386-6338</issn><issn>1434-3207</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><recordid>eNqFkT1PwzAQhi0EoqUw8AeQF9gCPttxbba20FKpCImW2XISp7jKF3Yy8O8JUNSR6W549N7peRG6BHLLKGN3y_U0IoQyeYSGwBmPGCXj435nUkSCMTlAZyHsCCGSU36KBiAUpULKIVpM2nfzbJp7PPd1iV2FgytcWuMH0xrc1vjVmgJvvKlC6l3TurrCc5O2tcdTV2Wu2uK1a204Rye5KYK92M8Reps_bmZP0eplsZxNVlFDQbT9MxllWSrjnJIcVBILmWdZAgSyxCQ2USJXAriKE2FpnI8NA54BSEggF0oINkI3v7mNrz86G1pdupDaojCVrbughaTxGDj9FwQVc8WY6sGrPdglpc10411p_Kf-c9QD13vAhNQUee8ideHASSBMSn64GMzW6l3d-ao3oYHo75J0X5L-KYl9AXwafoE</recordid><startdate>2006</startdate><enddate>2006</enddate><creator>Bülow, Lorenz</creator><creator>Steffens, Nils Ole</creator><creator>Galuschka, Claudia</creator><creator>Schindler, Martin</creator><creator>Hehl, Reinhard</creator><general>SAGE Publications</general><general>IOS Press</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>2006</creationdate><title>AthaMap: From in silico Data to Real Transcription Factor Binding Sites</title><author>Bülow, Lorenz ; Steffens, Nils Ole ; Galuschka, Claudia ; Schindler, Martin ; Hehl, Reinhard</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p216t-63d23dc85f20f19b568fddb101dbabeb96f961495b6e25f7a314d1181b1f69663</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Arabidopsis - genetics</topic><topic>Arabidopsis Proteins - genetics</topic><topic>Arabidopsis Proteins - metabolism</topic><topic>Arabidopsis thaliana</topic><topic>Base Sequence</topic><topic>Binding Sites</topic><topic>Biological and medical sciences</topic><topic>Databases, Genetic</topic><topic>DNA, Plant - chemistry</topic><topic>DNA, Plant - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genome, Plant</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Transcription Factors - genetics</topic><topic>Transcription Factors - metabolism</topic><topic>Transcription. Transcription factor. Splicing. Rna processing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bülow, Lorenz</creatorcontrib><creatorcontrib>Steffens, Nils Ole</creatorcontrib><creatorcontrib>Galuschka, Claudia</creatorcontrib><creatorcontrib>Schindler, Martin</creatorcontrib><creatorcontrib>Hehl, Reinhard</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>In silico biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bülow, Lorenz</au><au>Steffens, Nils Ole</au><au>Galuschka, Claudia</au><au>Schindler, Martin</au><au>Hehl, Reinhard</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>AthaMap: From in silico Data to Real Transcription Factor Binding Sites</atitle><jtitle>In silico biology</jtitle><addtitle>In Silico Biol</addtitle><date>2006</date><risdate>2006</risdate><volume>6</volume><issue>3</issue><spage>243</spage><epage>252</epage><pages>243-252</pages><issn>1386-6338</issn><eissn>1434-3207</eissn><abstract>AthaMap generates a map for cis-regulatory sequences for the
whole Arabidopsis thaliana genome. AthaMap was initially developed by
matrix-based detection of putative transcription factor binding sites (TFBS)
mostly determined from random binding site selection experiments. Now, also
experimentally verified TFBS have been included for 48 different
Arabidopsis thaliana transcription factors (TF). Based on these sequences,
89,416 very similar putative TFBS were determined within the genome of A.
thaliana and annotated to AthaMap. Matrix- and single sequence-based binding
sites can be included in colocalization analysis for the identification of
combinatorial cis-regulatory elements. As an example, putative target
genes of the WRKY18 transcription factor that is involved in plant-pathogen
interaction were determined. New functions of AthaMap include descriptions for
all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR
and MIPS. Transcription factors used in the binding site determination are
linked to TAIR and TRANSFAC® databases.
AthaMap is freely available at http://www.athamap.de.</abstract><cop>London, England</cop><pub>SAGE Publications</pub><pmid>16922688</pmid><doi>10.3233/ISB-00238</doi><tpages>10</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1386-6338 |
| ispartof | In silico biology, 2006, Vol.6 (3), p.243-252 |
| issn | 1386-6338 1434-3207 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_68257142 |
| source | Full-Text Journals in Chemistry (Open access) |
| subjects | Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Arabidopsis thaliana Base Sequence Binding Sites Biological and medical sciences Databases, Genetic DNA, Plant - chemistry DNA, Plant - genetics Fundamental and applied biological sciences. Psychology Genome, Plant Molecular and cellular biology Molecular genetics Transcription Factors - genetics Transcription Factors - metabolism Transcription. Transcription factor. Splicing. Rna processing |
| title | AthaMap: From in silico Data to Real Transcription Factor Binding Sites |
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