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1. Supplementary Table S1 Legend from Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, primary, Liebel, Urban, primary, Schmidt, Christian, primary, Majety, Meher, primary, Sauermann, Mamatha, primary, Rosenfelder, Heiko, primary, Bechtel, Stephanie, primary, Mehrle, Alexander, primary, Bannasch, Detlev, primary, Schupp, Ingo, primary, Seiler, Markus, primary, Simpson, Jeremy C., primary, Hahne, Florian, primary, Moosmayer, Petra, primary, Ruschhaupt, Markus, primary, Guilleaume, Birgit, primary, Wellenreuther, Ruth, primary, Pepperkok, Rainer, primary, Sültmann, Holger, primary, Poustka, Annemarie, primary, and Wiemann, Stefan, primary

Published
2023
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2. Supplementary Figure S1B from Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, primary, Liebel, Urban, primary, Schmidt, Christian, primary, Majety, Meher, primary, Sauermann, Mamatha, primary, Rosenfelder, Heiko, primary, Bechtel, Stephanie, primary, Mehrle, Alexander, primary, Bannasch, Detlev, primary, Schupp, Ingo, primary, Seiler, Markus, primary, Simpson, Jeremy C., primary, Hahne, Florian, primary, Moosmayer, Petra, primary, Ruschhaupt, Markus, primary, Guilleaume, Birgit, primary, Wellenreuther, Ruth, primary, Pepperkok, Rainer, primary, Sültmann, Holger, primary, Poustka, Annemarie, primary, and Wiemann, Stefan, primary

Published
2023
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3. Supplementary Figure S1A-2 from Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, primary, Liebel, Urban, primary, Schmidt, Christian, primary, Majety, Meher, primary, Sauermann, Mamatha, primary, Rosenfelder, Heiko, primary, Bechtel, Stephanie, primary, Mehrle, Alexander, primary, Bannasch, Detlev, primary, Schupp, Ingo, primary, Seiler, Markus, primary, Simpson, Jeremy C., primary, Hahne, Florian, primary, Moosmayer, Petra, primary, Ruschhaupt, Markus, primary, Guilleaume, Birgit, primary, Wellenreuther, Ruth, primary, Pepperkok, Rainer, primary, Sültmann, Holger, primary, Poustka, Annemarie, primary, and Wiemann, Stefan, primary

Published
2023
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4. Supplementary Methods and Materials from Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, primary, Liebel, Urban, primary, Schmidt, Christian, primary, Majety, Meher, primary, Sauermann, Mamatha, primary, Rosenfelder, Heiko, primary, Bechtel, Stephanie, primary, Mehrle, Alexander, primary, Bannasch, Detlev, primary, Schupp, Ingo, primary, Seiler, Markus, primary, Simpson, Jeremy C., primary, Hahne, Florian, primary, Moosmayer, Petra, primary, Ruschhaupt, Markus, primary, Guilleaume, Birgit, primary, Wellenreuther, Ruth, primary, Pepperkok, Rainer, primary, Sültmann, Holger, primary, Poustka, Annemarie, primary, and Wiemann, Stefan, primary

Published
2023
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5. Data from Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, primary, Liebel, Urban, primary, Schmidt, Christian, primary, Majety, Meher, primary, Sauermann, Mamatha, primary, Rosenfelder, Heiko, primary, Bechtel, Stephanie, primary, Mehrle, Alexander, primary, Bannasch, Detlev, primary, Schupp, Ingo, primary, Seiler, Markus, primary, Simpson, Jeremy C., primary, Hahne, Florian, primary, Moosmayer, Petra, primary, Ruschhaupt, Markus, primary, Guilleaume, Birgit, primary, Wellenreuther, Ruth, primary, Pepperkok, Rainer, primary, Sültmann, Holger, primary, Poustka, Annemarie, primary, and Wiemann, Stefan, primary

Published
2023
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6. Supplementary Figures S1-S3 Legends from Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, primary, Liebel, Urban, primary, Schmidt, Christian, primary, Majety, Meher, primary, Sauermann, Mamatha, primary, Rosenfelder, Heiko, primary, Bechtel, Stephanie, primary, Mehrle, Alexander, primary, Bannasch, Detlev, primary, Schupp, Ingo, primary, Seiler, Markus, primary, Simpson, Jeremy C., primary, Hahne, Florian, primary, Moosmayer, Petra, primary, Ruschhaupt, Markus, primary, Guilleaume, Birgit, primary, Wellenreuther, Ruth, primary, Pepperkok, Rainer, primary, Sültmann, Holger, primary, Poustka, Annemarie, primary, and Wiemann, Stefan, primary

Published
2023
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7. Supplementary Table S1 from Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, primary, Liebel, Urban, primary, Schmidt, Christian, primary, Majety, Meher, primary, Sauermann, Mamatha, primary, Rosenfelder, Heiko, primary, Bechtel, Stephanie, primary, Mehrle, Alexander, primary, Bannasch, Detlev, primary, Schupp, Ingo, primary, Seiler, Markus, primary, Simpson, Jeremy C., primary, Hahne, Florian, primary, Moosmayer, Petra, primary, Ruschhaupt, Markus, primary, Guilleaume, Birgit, primary, Wellenreuther, Ruth, primary, Pepperkok, Rainer, primary, Sültmann, Holger, primary, Poustka, Annemarie, primary, and Wiemann, Stefan, primary

Published
2023
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9. The LIFEdb database in 2006

Author

Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, del Val, Coral, Arlt, Dorit, Hahne, Florian, Bechtel, Stephanie, Simpson, Jeremy, Hofmann, Oliver, Hide, Winston, Glatting, Karl-Heinz, Huber, Wolfgang, Pepperkok, Rainer, Poustka, Annemarie, and Wiemann, Stefan

Published
2006

10. The full-ORF clone resource of the German cDNA Consortium

Author

Michel Guenter, Hoerlein Andreas, Heubner Dagmar, Blöcker Helmut, Bahr Andre, Schuster Claudia, Mehrle Alexander, Wellenreuther Ruth, Ernst Ute, Schmidt Christian, Duda Anny, Rosenfelder Heiko, Bechtel Stephanie, Wedler Holger, Köhrer Karl, Ottenwälder Birgit, Poustka Annemarie, Wiemann Stefan, and Schupp Ingo

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. The lack of comprehensive ORFeome resources has thus far hampered systematic applications by protein gain-of-function analysis. Gene and ORF coverage with full-length ORF clones thus needs to be extended. In combination with a unique and versatile cloning system, these will provide the tools for genome-wide systematic functional analyses, to achieve a deeper insight into complex biological processes. Results Here we describe the generation of a full-ORF clone resource of human genes applying the Gateway cloning technology (Invitrogen). A pipeline for efficient cloning and sequencing was developed and a sample tracking database was implemented to streamline the clone production process targeting more than 2,200 different ORFs. In addition, a robust cloning strategy was established, permitting the simultaneous generation of two clone variants that contain a particular ORF with as well as without a stop codon by the implementation of only one additional working step into the cloning procedure. Up to 92 % of the targeted ORFs were successfully amplified by PCR and more than 93 % of the amplicons successfully cloned. Conclusion The German cDNA Consortium ORFeome resource currently consists of more than 3,800 sequence-verified entry clones representing ORFs, cloned with and without stop codon, for about 1,700 different gene loci. 177 splice variants were cloned representing 121 of these genes. The entry clones have been used to generate over 5,000 different expression constructs, providing the basis for functional profiling applications. As a member of the recently formed international ORFeome collaboration we substantially contribute to generating and providing a whole genome human ORFeome collection in a unique cloning system that is made freely available in the community.

Published
2007
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11. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Author

Taylor, Christopher, Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Ashburner, Michael, Bal, Catherine A., Binz, Pierre-Alain, Bogue, Molly, Booth, Tim, Brazma, Alvis, Brinkman, Ryan R., Clark, Adam Michael, Deutsch, Eric W., Fiehn, Oliver, Fostel, Jennifer, Ghazal, Peter, Gibson, Frank, Gray, Tanya, Grimes, Graeme, Hancock, John M., Hardy, Nigel W., Hermjakob, Henning, Julian, Randall K., Kane, Matthew, Kettner, Carsten, Kinsinger, Christopher, Kolker, Eugene, Kuiper, Martin, Le Novere, Nicholas, Leebens-mack, Jim, Lewis, Suzanna E., Lord, Phillip, Mallon, Anne-Marie, Marthandan, Nishanth, Masuya, Hiroshi, McNally, Ruth, Mehrle, Alexander, Morrison, Norman, Orchard, Sandra, Quackenbush, John, Reecy, James M., Robertson, Donald G., Rocca-Serra, Phillippe, Rodriguez, Henry, Rosenfelder, Heiko, Santoyo-lopez, Janvier, Scheuermann, Richard H., Schober, Daniel, Smith, Barry, Snape, Jason, Stoeckert, Christian J., Tipton, Keith, Sterk, Peter, Untergasser, Andreas, Vandesompele, Jo, Wiemann, Stefan, Taylor, Christopher, Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Ashburner, Michael, Bal, Catherine A., Binz, Pierre-Alain, Bogue, Molly, Booth, Tim, Brazma, Alvis, Brinkman, Ryan R., Clark, Adam Michael, Deutsch, Eric W., Fiehn, Oliver, Fostel, Jennifer, Ghazal, Peter, Gibson, Frank, Gray, Tanya, Grimes, Graeme, Hancock, John M., Hardy, Nigel W., Hermjakob, Henning, Julian, Randall K., Kane, Matthew, Kettner, Carsten, Kinsinger, Christopher, Kolker, Eugene, Kuiper, Martin, Le Novere, Nicholas, Leebens-mack, Jim, Lewis, Suzanna E., Lord, Phillip, Mallon, Anne-Marie, Marthandan, Nishanth, Masuya, Hiroshi, McNally, Ruth, Mehrle, Alexander, Morrison, Norman, Orchard, Sandra, Quackenbush, John, Reecy, James M., Robertson, Donald G., Rocca-Serra, Phillippe, Rodriguez, Henry, Rosenfelder, Heiko, Santoyo-lopez, Janvier, Scheuermann, Richard H., Schober, Daniel, Smith, Barry, Snape, Jason, Stoeckert, Christian J., Tipton, Keith, Sterk, Peter, Untergasser, Andreas, Vandesompele, Jo, and Wiemann, Stefan

Published
2008

12. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Author

Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Ashburner, Michael, Ball, Catherine A., Binz, Pierre-Alain, Bogue, Molly, Booth, Tim, Brazma, Alvis, Brinkman, Ryan R., Clark, Adam Michael, Deutsch, Eric W., Fiehn, Oliver, Fostel, Jennifer, Ghazal, Peter, Gibson, Frank, Gray, Tanya, Grimes, Graeme, Hancock, John M., Hardy, Nigel W., Hermjakob, Henning, Julian, Randall K., Kane, Matthew, Kettner, Carsten, Kinsinger, Christopher, Kolker, Eugene, Kuiper, Martin, Le Novere, Nicolas, Leebens-Mack, Jim, Lewis, Suzanna E., Lord, Phillip, Mallon, Ann-Marie, Marthandan, Nishanth, Masuya, Hiroshi, McNally, Ruth, Mehrle, Alexander, Morrison, Norman, Orchard, Sandra, Quackenbush, John, Reecy, James M., Robertson, Donald G., Rocca-Serra, Philippe, Rodriguez, Henry, Rosenfelder, Heiko, Santoyo-Lopez, Javier, Scheuermann, Richard H., Schober, Daniel, Smith, Barry, Snape, Jason, Stoeckert, Christian J., Tipton, Keith, Sterk, Peter, Untergasser, Andreas, Vandesompele, Jo, Wiemann, Stefan, Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Ashburner, Michael, Ball, Catherine A., Binz, Pierre-Alain, Bogue, Molly, Booth, Tim, Brazma, Alvis, Brinkman, Ryan R., Clark, Adam Michael, Deutsch, Eric W., Fiehn, Oliver, Fostel, Jennifer, Ghazal, Peter, Gibson, Frank, Gray, Tanya, Grimes, Graeme, Hancock, John M., Hardy, Nigel W., Hermjakob, Henning, Julian, Randall K., Kane, Matthew, Kettner, Carsten, Kinsinger, Christopher, Kolker, Eugene, Kuiper, Martin, Le Novere, Nicolas, Leebens-Mack, Jim, Lewis, Suzanna E., Lord, Phillip, Mallon, Ann-Marie, Marthandan, Nishanth, Masuya, Hiroshi, McNally, Ruth, Mehrle, Alexander, Morrison, Norman, Orchard, Sandra, Quackenbush, John, Reecy, James M., Robertson, Donald G., Rocca-Serra, Philippe, Rodriguez, Henry, Rosenfelder, Heiko, Santoyo-Lopez, Javier, Scheuermann, Richard H., Schober, Daniel, Smith, Barry, Snape, Jason, Stoeckert, Christian J., Tipton, Keith, Sterk, Peter, Untergasser, Andreas, Vandesompele, Jo, and Wiemann, Stefan

Abstract

The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the range of extant checklists.

Published
2008

13. Modeling and Managing Experimental Data Using FuGE

Author

Jones, Andrew R., primary, Lister, Allyson L., additional, Hermida, Leandro, additional, Wilkinson, Peter, additional, Eisenacher, Martin, additional, Belhajjame, Khalid, additional, Gibson, Frank, additional, Lord, Phil, additional, Pocock, Matthew, additional, Rosenfelder, Heiko, additional, Santoyo-Lopez, Javier, additional, Wipat, Anil, additional, and Paton, Norman W., additional

Published
2009
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14. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Author

Taylor, Chris F, primary, Field, Dawn, additional, Sansone, Susanna-Assunta, additional, Aerts, Jan, additional, Apweiler, Rolf, additional, Ashburner, Michael, additional, Ball, Catherine A, additional, Binz, Pierre-Alain, additional, Bogue, Molly, additional, Booth, Tim, additional, Brazma, Alvis, additional, Brinkman, Ryan R, additional, Michael Clark, Adam, additional, Deutsch, Eric W, additional, Fiehn, Oliver, additional, Fostel, Jennifer, additional, Ghazal, Peter, additional, Gibson, Frank, additional, Gray, Tanya, additional, Grimes, Graeme, additional, Hancock, John M, additional, Hardy, Nigel W, additional, Hermjakob, Henning, additional, Julian, Randall K, additional, Kane, Matthew, additional, Kettner, Carsten, additional, Kinsinger, Christopher, additional, Kolker, Eugene, additional, Kuiper, Martin, additional, Novère, Nicolas Le, additional, Leebens-Mack, Jim, additional, Lewis, Suzanna E, additional, Lord, Phillip, additional, Mallon, Ann-Marie, additional, Marthandan, Nishanth, additional, Masuya, Hiroshi, additional, McNally, Ruth, additional, Mehrle, Alexander, additional, Morrison, Norman, additional, Orchard, Sandra, additional, Quackenbush, John, additional, Reecy, James M, additional, Robertson, Donald G, additional, Rocca-Serra, Philippe, additional, Rodriguez, Henry, additional, Rosenfelder, Heiko, additional, Santoyo-Lopez, Javier, additional, Scheuermann, Richard H, additional, Schober, Daniel, additional, Smith, Barry, additional, Snape, Jason, additional, Stoeckert, Christian J, additional, Tipton, Keith, additional, Sterk, Peter, additional, Untergasser, Andreas, additional, Vandesompele, Jo, additional, and Wiemann, Stefan, additional

Published
2008
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15. The full-ORF clone resource of the German cDNA Consortium

Author

Bechtel, Stephanie, primary, Rosenfelder, Heiko, additional, Duda, Anny, additional, Schmidt, Christian, additional, Ernst, Ute, additional, Wellenreuther, Ruth, additional, Mehrle, Alexander, additional, Schuster, Claudia, additional, Bahr, Andre, additional, Blöcker, Helmut, additional, Heubner, Dagmar, additional, Hoerlein, Andreas, additional, Michel, Guenter, additional, Wedler, Holger, additional, Köhrer, Karl, additional, Ottenwälder, Birgit, additional, Poustka, Annemarie, additional, Wiemann, Stefan, additional, and Schupp, Ingo, additional

Published
2007
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16. Functional Profiling: From Microarrays via Cell-Based Assays to Novel Tumor Relevant Modulators of the Cell Cycle

Author

Arlt, Dorit, primary, Huber, Wolfgang, additional, Liebel, Urban, additional, Schmidt, Christian, additional, Majety, Meher, additional, Sauermann, Mamatha, additional, Rosenfelder, Heiko, additional, Bechtel, Stephanie, additional, Mehrle, Alexander, additional, Bannasch, Detlev, additional, Schupp, Ingo, additional, Seiler, Markus, additional, Simpson, Jeremy C., additional, Hahne, Florian, additional, Moosmayer, Petra, additional, Ruschhaupt, Markus, additional, Guilleaume, Birgit, additional, Wellenreuther, Ruth, additional, Pepperkok, Rainer, additional, Sültmann, Holger, additional, Poustka, Annemarie, additional, and Wiemann, Stefan, additional

Published
2005
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17. Modeling and managing experimental data using FuGE.

Author

Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M, Belhajjame K, Gibson F, Lord P, Pocock M, Rosenfelder H, Santoyo-Lopez J, Wipat A, and Paton NW

Subjects
Computer Simulation, Flow Cytometry instrumentation, Flow Cytometry methods, Reproducibility of Results, Software, User-Computer Interface, Computational Biology methods, Genomics methods, Models, Theoretical
Abstract

The Functional Genomics Experiment data model (FuGE) has been developed to increase the consistency and efficiency of experimental data modeling in the life sciences, and it has been adopted by a number of high-profile standardization organizations. FuGE can be used: (1) directly, whereby generic modeling constructs are used to represent concepts from specific experimental activities; or (2) as a framework within which method-specific models can be developed. FuGE is both rich and flexible, providing a considerable number of modeling constructs, which can be used in a range of different ways. However, such richness and flexibility also mean that modelers and application developers have choices to make when applying FuGE in a given context. This paper captures emerging best practice in the use of FuGE in the light of the experience of several groups by: (1) proposing guidelines for the use and extension of the FuGE data model; (2) presenting design patterns that reflect recurring requirements in experimental data modeling; and (3) describing a community software tool kit (STK) that supports application development using FuGE. We anticipate that these guidelines will encourage consistent usage of FuGE, and as such, will contribute to the development of convergent data standards in omics research.

Published
2009
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