Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning
In a large-scale gene expression screen 1765 randomly picked cDNAs were analyzed by whole-mount in situ hybridization in Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 204 of which are novel in Xenopus. Partial DNA sequences and expression patt...
Gespeichert in:
| Veröffentlicht in: | Mechanisms of development 1998-10, Vol.77 (2), p.95-141 |
|---|---|
| Hauptverfasser: | , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 141 |
|---|---|
| container_issue | 2 |
| container_start_page | 95 |
| container_title | Mechanisms of development |
| container_volume | 77 |
| creator | Gawantka, Volker Pollet, Nicolas Delius, Hajo Vingron, Martin Pfister, Ralf Nitsch, Rebecca Blumenstock, Claudia Niehrs, Christof |
| description | In a large-scale gene expression screen 1765 randomly picked cDNAs were analyzed by whole-mount in situ hybridization in
Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 204 of which are novel in
Xenopus. Partial DNA sequences and expression patterns were documented and assembled into a database, `AXelDB'. Approximately 30% of cDNAs analyzed represent differentially expressed genes and about 5% show highly regionalized expression. Novel marker genes and potential developmental regulators were found. Differential expression of mitochondrial genes was observed. Marker genes were used to study regionalization of the entire gastrula as well as the tail forming region and the epidermis of the tailbud embryo. Four `synexpression' groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation were identified. According to their probable functional significance these groups are designated as Delta1, Bmp4, ER-import and Chromatin group. Within synexpression groups, a likely function of genes without sequence similarity can be predicted. The results indicate that synexpression groups have strong prognostic value. A cluster analysis was made by comparing gene expression patterns to derive a novel parameter, `tissue relatedness'. In conclusion, this study describes a semi-functional approach to investigate genes expressed during early development and provides global insight into embryonic patterning. |
| doi_str_mv | 10.1016/S0925-4773(98)00115-4 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_70082150</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0925477398001154</els_id><sourcerecordid>70082150</sourcerecordid><originalsourceid>FETCH-LOGICAL-c426t-55bd08b67107576a6bf56aaeb567929755f2203cb0c84e7998c532235f4c69e13</originalsourceid><addsrcrecordid>eNqFUc1qFTEYDaLUa_URClmJglOTzCSZrKQUrULBRRXchUzmm2tkJrnmm2l7H6LvbKb30q2rEM5fcg4hZ5ydc8bVxxtmhKwaret3pn3PGOfl9oxseKtFpWqpnpPNE-UleYX4h60sxU_IiWlrrhq2IQ9XEIHC_S4DYkiRos8AMcQtDZH-gph2C9LQQ5zDEADplEbwy-gy3bn5953b4wdaxH3wM9LtajYs0c-rlYt9gdJtUSN1dDumzo30NsAdTQOFqcv7FINfjWbIa-Zr8mJwI8Kb43lKfn75_OPya3X9_erb5cV15Ruh5krKrmdtpzRnWmrlVDdI5Rx0UmkjjJZyEILVvmO-bUAb03pZC1HLofHKAK9PyduDb3ne3wVwtlNAD-PoIqQFrWasFVyyQpQHos8JMcNgdzlMLu8tZ3adwT7OYNeOrWnt4wy2KbqzY8DSTdA_qY69F_zTAYfyy9JItugDRF96zOBn26fwn4R_b4OZ8A</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>70082150</pqid></control><display><type>article</type><title>Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning</title><source>MEDLINE</source><source>Elsevier ScienceDirect Journals Complete</source><source>EZB Electronic Journals Library</source><creator>Gawantka, Volker ; Pollet, Nicolas ; Delius, Hajo ; Vingron, Martin ; Pfister, Ralf ; Nitsch, Rebecca ; Blumenstock, Claudia ; Niehrs, Christof</creator><creatorcontrib>Gawantka, Volker ; Pollet, Nicolas ; Delius, Hajo ; Vingron, Martin ; Pfister, Ralf ; Nitsch, Rebecca ; Blumenstock, Claudia ; Niehrs, Christof</creatorcontrib><description>In a large-scale gene expression screen 1765 randomly picked cDNAs were analyzed by whole-mount in situ hybridization in
Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 204 of which are novel in
Xenopus. Partial DNA sequences and expression patterns were documented and assembled into a database, `AXelDB'. Approximately 30% of cDNAs analyzed represent differentially expressed genes and about 5% show highly regionalized expression. Novel marker genes and potential developmental regulators were found. Differential expression of mitochondrial genes was observed. Marker genes were used to study regionalization of the entire gastrula as well as the tail forming region and the epidermis of the tailbud embryo. Four `synexpression' groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation were identified. According to their probable functional significance these groups are designated as Delta1, Bmp4, ER-import and Chromatin group. Within synexpression groups, a likely function of genes without sequence similarity can be predicted. The results indicate that synexpression groups have strong prognostic value. A cluster analysis was made by comparing gene expression patterns to derive a novel parameter, `tissue relatedness'. In conclusion, this study describes a semi-functional approach to investigate genes expressed during early development and provides global insight into embryonic patterning.</description><identifier>ISSN: 0925-4773</identifier><identifier>EISSN: 1872-6356</identifier><identifier>DOI: 10.1016/S0925-4773(98)00115-4</identifier><identifier>PMID: 9831640</identifier><language>eng</language><publisher>Ireland: Elsevier Ireland Ltd</publisher><subject>Amphibian ; Animals ; Bmp4 ; Body Patterning - genetics ; cDNA sequencing ; Chromatin ; Databases, Factual ; Delta ; Developmental biology ; Differentiation ; Early development ; Ectoderm ; Embryo, Nonmammalian ; Embryology ; Embryonic Induction - genetics ; Endoderm ; Endoplasmic reticulum ; Epidermis ; Epidermis - embryology ; Expressed sequence tags ; Expression profiles ; Functional genomics ; Gastrula ; Gastrulation ; Gene expression ; Gene Expression Regulation, Developmental ; Genetic Techniques ; Genome ; In situ hybridization ; In Situ Hybridization - methods ; Mesoderm ; Mitochondria ; Neurula ; Partial cDNA sequencing ; Pattern formation ; Regionalization ; Screening ; Synexpression ; Tail - embryology ; Tailbud ; Tissue relatedness ; Transcriptional regulation ; Xenopus - embryology ; Xenopus - genetics ; Xenopus laevis</subject><ispartof>Mechanisms of development, 1998-10, Vol.77 (2), p.95-141</ispartof><rights>1998 Elsevier Science Ireland Ltd</rights><rights>Copyright 1998 Elsevier Science Ireland Ltd. All Rights Reserved</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c426t-55bd08b67107576a6bf56aaeb567929755f2203cb0c84e7998c532235f4c69e13</citedby><cites>FETCH-LOGICAL-c426t-55bd08b67107576a6bf56aaeb567929755f2203cb0c84e7998c532235f4c69e13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/S0925-4773(98)00115-4$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,777,781,3537,27905,27906,45976</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9831640$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gawantka, Volker</creatorcontrib><creatorcontrib>Pollet, Nicolas</creatorcontrib><creatorcontrib>Delius, Hajo</creatorcontrib><creatorcontrib>Vingron, Martin</creatorcontrib><creatorcontrib>Pfister, Ralf</creatorcontrib><creatorcontrib>Nitsch, Rebecca</creatorcontrib><creatorcontrib>Blumenstock, Claudia</creatorcontrib><creatorcontrib>Niehrs, Christof</creatorcontrib><title>Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning</title><title>Mechanisms of development</title><addtitle>Mech Dev</addtitle><description>In a large-scale gene expression screen 1765 randomly picked cDNAs were analyzed by whole-mount in situ hybridization in
Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 204 of which are novel in
Xenopus. Partial DNA sequences and expression patterns were documented and assembled into a database, `AXelDB'. Approximately 30% of cDNAs analyzed represent differentially expressed genes and about 5% show highly regionalized expression. Novel marker genes and potential developmental regulators were found. Differential expression of mitochondrial genes was observed. Marker genes were used to study regionalization of the entire gastrula as well as the tail forming region and the epidermis of the tailbud embryo. Four `synexpression' groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation were identified. According to their probable functional significance these groups are designated as Delta1, Bmp4, ER-import and Chromatin group. Within synexpression groups, a likely function of genes without sequence similarity can be predicted. The results indicate that synexpression groups have strong prognostic value. A cluster analysis was made by comparing gene expression patterns to derive a novel parameter, `tissue relatedness'. In conclusion, this study describes a semi-functional approach to investigate genes expressed during early development and provides global insight into embryonic patterning.</description><subject>Amphibian</subject><subject>Animals</subject><subject>Bmp4</subject><subject>Body Patterning - genetics</subject><subject>cDNA sequencing</subject><subject>Chromatin</subject><subject>Databases, Factual</subject><subject>Delta</subject><subject>Developmental biology</subject><subject>Differentiation</subject><subject>Early development</subject><subject>Ectoderm</subject><subject>Embryo, Nonmammalian</subject><subject>Embryology</subject><subject>Embryonic Induction - genetics</subject><subject>Endoderm</subject><subject>Endoplasmic reticulum</subject><subject>Epidermis</subject><subject>Epidermis - embryology</subject><subject>Expressed sequence tags</subject><subject>Expression profiles</subject><subject>Functional genomics</subject><subject>Gastrula</subject><subject>Gastrulation</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Genetic Techniques</subject><subject>Genome</subject><subject>In situ hybridization</subject><subject>In Situ Hybridization - methods</subject><subject>Mesoderm</subject><subject>Mitochondria</subject><subject>Neurula</subject><subject>Partial cDNA sequencing</subject><subject>Pattern formation</subject><subject>Regionalization</subject><subject>Screening</subject><subject>Synexpression</subject><subject>Tail - embryology</subject><subject>Tailbud</subject><subject>Tissue relatedness</subject><subject>Transcriptional regulation</subject><subject>Xenopus - embryology</subject><subject>Xenopus - genetics</subject><subject>Xenopus laevis</subject><issn>0925-4773</issn><issn>1872-6356</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1998</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUc1qFTEYDaLUa_URClmJglOTzCSZrKQUrULBRRXchUzmm2tkJrnmm2l7H6LvbKb30q2rEM5fcg4hZ5ydc8bVxxtmhKwaret3pn3PGOfl9oxseKtFpWqpnpPNE-UleYX4h60sxU_IiWlrrhq2IQ9XEIHC_S4DYkiRos8AMcQtDZH-gph2C9LQQ5zDEADplEbwy-gy3bn5953b4wdaxH3wM9LtajYs0c-rlYt9gdJtUSN1dDumzo30NsAdTQOFqcv7FINfjWbIa-Zr8mJwI8Kb43lKfn75_OPya3X9_erb5cV15Ruh5krKrmdtpzRnWmrlVDdI5Rx0UmkjjJZyEILVvmO-bUAb03pZC1HLofHKAK9PyduDb3ne3wVwtlNAD-PoIqQFrWasFVyyQpQHos8JMcNgdzlMLu8tZ3adwT7OYNeOrWnt4wy2KbqzY8DSTdA_qY69F_zTAYfyy9JItugDRF96zOBn26fwn4R_b4OZ8A</recordid><startdate>19981001</startdate><enddate>19981001</enddate><creator>Gawantka, Volker</creator><creator>Pollet, Nicolas</creator><creator>Delius, Hajo</creator><creator>Vingron, Martin</creator><creator>Pfister, Ralf</creator><creator>Nitsch, Rebecca</creator><creator>Blumenstock, Claudia</creator><creator>Niehrs, Christof</creator><general>Elsevier Ireland Ltd</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>19981001</creationdate><title>Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning</title><author>Gawantka, Volker ; Pollet, Nicolas ; Delius, Hajo ; Vingron, Martin ; Pfister, Ralf ; Nitsch, Rebecca ; Blumenstock, Claudia ; Niehrs, Christof</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c426t-55bd08b67107576a6bf56aaeb567929755f2203cb0c84e7998c532235f4c69e13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1998</creationdate><topic>Amphibian</topic><topic>Animals</topic><topic>Bmp4</topic><topic>Body Patterning - genetics</topic><topic>cDNA sequencing</topic><topic>Chromatin</topic><topic>Databases, Factual</topic><topic>Delta</topic><topic>Developmental biology</topic><topic>Differentiation</topic><topic>Early development</topic><topic>Ectoderm</topic><topic>Embryo, Nonmammalian</topic><topic>Embryology</topic><topic>Embryonic Induction - genetics</topic><topic>Endoderm</topic><topic>Endoplasmic reticulum</topic><topic>Epidermis</topic><topic>Epidermis - embryology</topic><topic>Expressed sequence tags</topic><topic>Expression profiles</topic><topic>Functional genomics</topic><topic>Gastrula</topic><topic>Gastrulation</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Genetic Techniques</topic><topic>Genome</topic><topic>In situ hybridization</topic><topic>In Situ Hybridization - methods</topic><topic>Mesoderm</topic><topic>Mitochondria</topic><topic>Neurula</topic><topic>Partial cDNA sequencing</topic><topic>Pattern formation</topic><topic>Regionalization</topic><topic>Screening</topic><topic>Synexpression</topic><topic>Tail - embryology</topic><topic>Tailbud</topic><topic>Tissue relatedness</topic><topic>Transcriptional regulation</topic><topic>Xenopus - embryology</topic><topic>Xenopus - genetics</topic><topic>Xenopus laevis</topic><toplevel>online_resources</toplevel><creatorcontrib>Gawantka, Volker</creatorcontrib><creatorcontrib>Pollet, Nicolas</creatorcontrib><creatorcontrib>Delius, Hajo</creatorcontrib><creatorcontrib>Vingron, Martin</creatorcontrib><creatorcontrib>Pfister, Ralf</creatorcontrib><creatorcontrib>Nitsch, Rebecca</creatorcontrib><creatorcontrib>Blumenstock, Claudia</creatorcontrib><creatorcontrib>Niehrs, Christof</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Mechanisms of development</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gawantka, Volker</au><au>Pollet, Nicolas</au><au>Delius, Hajo</au><au>Vingron, Martin</au><au>Pfister, Ralf</au><au>Nitsch, Rebecca</au><au>Blumenstock, Claudia</au><au>Niehrs, Christof</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning</atitle><jtitle>Mechanisms of development</jtitle><addtitle>Mech Dev</addtitle><date>1998-10-01</date><risdate>1998</risdate><volume>77</volume><issue>2</issue><spage>95</spage><epage>141</epage><pages>95-141</pages><issn>0925-4773</issn><eissn>1872-6356</eissn><abstract>In a large-scale gene expression screen 1765 randomly picked cDNAs were analyzed by whole-mount in situ hybridization in
Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 204 of which are novel in
Xenopus. Partial DNA sequences and expression patterns were documented and assembled into a database, `AXelDB'. Approximately 30% of cDNAs analyzed represent differentially expressed genes and about 5% show highly regionalized expression. Novel marker genes and potential developmental regulators were found. Differential expression of mitochondrial genes was observed. Marker genes were used to study regionalization of the entire gastrula as well as the tail forming region and the epidermis of the tailbud embryo. Four `synexpression' groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation were identified. According to their probable functional significance these groups are designated as Delta1, Bmp4, ER-import and Chromatin group. Within synexpression groups, a likely function of genes without sequence similarity can be predicted. The results indicate that synexpression groups have strong prognostic value. A cluster analysis was made by comparing gene expression patterns to derive a novel parameter, `tissue relatedness'. In conclusion, this study describes a semi-functional approach to investigate genes expressed during early development and provides global insight into embryonic patterning.</abstract><cop>Ireland</cop><pub>Elsevier Ireland Ltd</pub><pmid>9831640</pmid><doi>10.1016/S0925-4773(98)00115-4</doi><tpages>47</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0925-4773 |
| ispartof | Mechanisms of development, 1998-10, Vol.77 (2), p.95-141 |
| issn | 0925-4773 1872-6356 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_70082150 |
| source | MEDLINE; Elsevier ScienceDirect Journals Complete; EZB Electronic Journals Library |
| subjects | Amphibian Animals Bmp4 Body Patterning - genetics cDNA sequencing Chromatin Databases, Factual Delta Developmental biology Differentiation Early development Ectoderm Embryo, Nonmammalian Embryology Embryonic Induction - genetics Endoderm Endoplasmic reticulum Epidermis Epidermis - embryology Expressed sequence tags Expression profiles Functional genomics Gastrula Gastrulation Gene expression Gene Expression Regulation, Developmental Genetic Techniques Genome In situ hybridization In Situ Hybridization - methods Mesoderm Mitochondria Neurula Partial cDNA sequencing Pattern formation Regionalization Screening Synexpression Tail - embryology Tailbud Tissue relatedness Transcriptional regulation Xenopus - embryology Xenopus - genetics Xenopus laevis |
| title | Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-17T18%3A08%3A50IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Gene%20expression%20screening%20in%20Xenopus%20identifies%20molecular%20pathways,%20predicts%20gene%20function%20and%20provides%20a%20global%20view%20of%20embryonic%20patterning&rft.jtitle=Mechanisms%20of%20development&rft.au=Gawantka,%20Volker&rft.date=1998-10-01&rft.volume=77&rft.issue=2&rft.spage=95&rft.epage=141&rft.pages=95-141&rft.issn=0925-4773&rft.eissn=1872-6356&rft_id=info:doi/10.1016/S0925-4773(98)00115-4&rft_dat=%3Cproquest_cross%3E70082150%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=70082150&rft_id=info:pmid/9831640&rft_els_id=S0925477398001154&rfr_iscdi=true |