The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.
Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the "Functional Genomics in Embryonic Stem Cells" consortium (FunGenES) has...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-09-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2731164?pdf=render |
| _version_ | 1819110687513772032 |
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| author | Herbert Schulz Raivo Kolde Priit Adler Irène Aksoy Konstantinos Anastassiadis Michael Bader Nathalie Billon Hélène Boeuf Pierre-Yves Bourillot Frank Buchholz Christian Dani Michael Xavier Doss Lesley Forrester Murielle Gitton Domingos Henrique Jürgen Hescheler Heinz Himmelbauer Norbert Hübner Efthimia Karantzali Androniki Kretsovali Sandra Lubitz Laurent Pradier Meena Rai Jüri Reimand Alexandra Rolletschek Agapios Sachinidis Pierre Savatier Francis Stewart Mike P Storm Marina Trouillas Jaak Vilo Melanie J Welham Johannes Winkler Anna M Wobus Antonis K Hatzopoulos Functional Genomics in Embryonic Stem Cells Consortium |
| author_facet | Herbert Schulz Raivo Kolde Priit Adler Irène Aksoy Konstantinos Anastassiadis Michael Bader Nathalie Billon Hélène Boeuf Pierre-Yves Bourillot Frank Buchholz Christian Dani Michael Xavier Doss Lesley Forrester Murielle Gitton Domingos Henrique Jürgen Hescheler Heinz Himmelbauer Norbert Hübner Efthimia Karantzali Androniki Kretsovali Sandra Lubitz Laurent Pradier Meena Rai Jüri Reimand Alexandra Rolletschek Agapios Sachinidis Pierre Savatier Francis Stewart Mike P Storm Marina Trouillas Jaak Vilo Melanie J Welham Johannes Winkler Anna M Wobus Antonis K Hatzopoulos Functional Genomics in Embryonic Stem Cells Consortium |
| author_sort | Herbert Schulz |
| collection | DOAJ |
| description | Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the "Functional Genomics in Embryonic Stem Cells" consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in "Expression Waves" and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells. |
| first_indexed | 2024-12-22T03:45:41Z |
| format | Article |
| id | doaj.art-a15714b737874268aaa861978cda4038 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T03:45:41Z |
| publishDate | 2009-09-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a15714b737874268aaa861978cda40382022-12-21T18:40:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-09-0149e680410.1371/journal.pone.0006804The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.Herbert SchulzRaivo KoldePriit AdlerIrène AksoyKonstantinos AnastassiadisMichael BaderNathalie BillonHélène BoeufPierre-Yves BourillotFrank BuchholzChristian DaniMichael Xavier DossLesley ForresterMurielle GittonDomingos HenriqueJürgen HeschelerHeinz HimmelbauerNorbert HübnerEfthimia KarantzaliAndroniki KretsovaliSandra LubitzLaurent PradierMeena RaiJüri ReimandAlexandra RolletschekAgapios SachinidisPierre SavatierFrancis StewartMike P StormMarina TrouillasJaak ViloMelanie J WelhamJohannes WinklerAnna M WobusAntonis K HatzopoulosFunctional Genomics in Embryonic Stem Cells ConsortiumEmbryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the "Functional Genomics in Embryonic Stem Cells" consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in "Expression Waves" and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells.http://europepmc.org/articles/PMC2731164?pdf=render |
| spellingShingle | Herbert Schulz Raivo Kolde Priit Adler Irène Aksoy Konstantinos Anastassiadis Michael Bader Nathalie Billon Hélène Boeuf Pierre-Yves Bourillot Frank Buchholz Christian Dani Michael Xavier Doss Lesley Forrester Murielle Gitton Domingos Henrique Jürgen Hescheler Heinz Himmelbauer Norbert Hübner Efthimia Karantzali Androniki Kretsovali Sandra Lubitz Laurent Pradier Meena Rai Jüri Reimand Alexandra Rolletschek Agapios Sachinidis Pierre Savatier Francis Stewart Mike P Storm Marina Trouillas Jaak Vilo Melanie J Welham Johannes Winkler Anna M Wobus Antonis K Hatzopoulos Functional Genomics in Embryonic Stem Cells Consortium The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS ONE |
| title | The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. |
| title_full | The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. |
| title_fullStr | The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. |
| title_full_unstemmed | The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. |
| title_short | The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. |
| title_sort | fungenes database a genomics resource for mouse embryonic stem cell differentiation |
| url | http://europepmc.org/articles/PMC2731164?pdf=render |
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