References
Academic Papers
Ortholog Finder Tool is using data from the following academic publications
For S. cerevisiae
Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast
Paul Jorgensen, Joy L. Nishikawa, Bobby-Joe Breitkreutz, Mike Tyers
Published in Science doi:10.1126/science.1070850
Published on 19 July, 2002
Paul Jorgensen, Joy L. Nishikawa, Bobby-Joe Breitkreutz, Mike Tyers
Published in Science doi:10.1126/science.1070850
Published on 19 July, 2002
A pharmaco-epistasis strategy reveals a new cell size controlling pathway in yeast
Fabien Moretto, Isabelle Sagot, Bertrand Daignan-Fornier, and Benoit Pinson
Published in Molecular Systems Biology doi:10.1038/msb.2013.60
Published on 27 September, 2013
Fabien Moretto, Isabelle Sagot, Bertrand Daignan-Fornier, and Benoit Pinson
Published in Molecular Systems Biology doi:10.1038/msb.2013.60
Published on 27 September, 2013
For S. pombe
A genome-wide resource of cell cycle and cell shape genes of fission yeast
Jacqueline Hayles, Valerie Wood, Linda Jeffery, Kwang-Lae Hoe, Dong-Uk Kim, Han-Oh Park, Silvia Salas-Pino, Christian Heichinger and Paul Nurse
Published in Open biology 10.1098/rsob.130053
Published on 22 May, 2013
Jacqueline Hayles, Valerie Wood, Linda Jeffery, Kwang-Lae Hoe, Dong-Uk Kim, Han-Oh Park, Silvia Salas-Pino, Christian Heichinger and Paul Nurse
Published in Open biology 10.1098/rsob.130053
Published on 22 May, 2013
A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression.
Veronika Graml, Xenia Studera, Jonathan L.D. Lawson, Anatole Chessel, Marco Geymonat, Miriam Bortfeld-Miller, Thomas Walter, Laura Wagstaff, Eugenia Piddini and Rafael E. Carazo-Salas,
Published in Developemental cell 10.1016/j.devcel.2014.09.005
Published on 27 October, 2014
Veronika Graml, Xenia Studera, Jonathan L.D. Lawson, Anatole Chessel, Marco Geymonat, Miriam Bortfeld-Miller, Thomas Walter, Laura Wagstaff, Eugenia Piddini and Rafael E. Carazo-Salas,
Published in Developemental cell 10.1016/j.devcel.2014.09.005
Published on 27 October, 2014
For D. melanogaster
Identification of pathways regulating cell size and cell-cycle progression by RNAi
Mikael Björklund, Minna Taipale, Markku Varjosalo, Juha Saharinen, Juhani Lahdenperä and Jussi Taipale
Published in Nature 10.1038/nature04469
Published on 23 February, 2006
Mikael Björklund, Minna Taipale, Markku Varjosalo, Juha Saharinen, Juhani Lahdenperä and Jussi Taipale
Published in Nature 10.1038/nature04469
Published on 23 February, 2006
For H. sapiens
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
Beate Neumann, Thomas Walter, Jean-Karim Hériché, Jutta Bulkescher, Holger Erfle, Christian Conrad, Phill Rogers, Ina Poser, Michael Held, Urban Liebel, Cihan Cetin, Frank Sieckmann, Gregoire Pau, Rolf Kabbe, Annelie Wünsche, Venkata Satagopam, Michael H. A. Schmitz, Catherine Chapuis, Daniel W. Gerlich, Reinhard Schneider, Roland Eils, Wolfgang Huber, Jan-Michael Peters, Anthony A. Hyman, Richard Durbin, Rainer Pepperkok & Jan Ellenberg
Published in Nature 10.1038/nature08869
Published on 22 January, 2010
Beate Neumann, Thomas Walter, Jean-Karim Hériché, Jutta Bulkescher, Holger Erfle, Christian Conrad, Phill Rogers, Ina Poser, Michael Held, Urban Liebel, Cihan Cetin, Frank Sieckmann, Gregoire Pau, Rolf Kabbe, Annelie Wünsche, Venkata Satagopam, Michael H. A. Schmitz, Catherine Chapuis, Daniel W. Gerlich, Reinhard Schneider, Roland Eils, Wolfgang Huber, Jan-Michael Peters, Anthony A. Hyman, Richard Durbin, Rainer Pepperkok & Jan Ellenberg
Published in Nature 10.1038/nature08869
Published on 22 January, 2010
For A. thaliana
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Michael Ashburner, Catherine A. Ball, Judith A. Blake, David Botstein, Heather Butler, J. Michael Cherry, Allan P. Davis, Kara Dolinski, Selina S. Dwight, Janan T. Eppig, Midori A. Harris, David P. Hill, Laurie Issel-Tarver, Andrew Kasarskis, Suzanna Lewis, John C. Matese, Joel E. Richardson, Martin Ringwald, Gerald M. Rubin & Gavin Sherlock
Published in Nature genetics doi.org/10.1038/75556
Published on 01 May, 2000
Michael Ashburner, Catherine A. Ball, Judith A. Blake, David Botstein, Heather Butler, J. Michael Cherry, Allan P. Davis, Kara Dolinski, Selina S. Dwight, Janan T. Eppig, Midori A. Harris, David P. Hill, Laurie Issel-Tarver, Andrew Kasarskis, Suzanna Lewis, John C. Matese, Joel E. Richardson, Martin Ringwald, Gerald M. Rubin & Gavin Sherlock
Published in Nature genetics doi.org/10.1038/75556
Published on 01 May, 2000
Databases
Ortholog Finder Tool is using the following databases with the versions indicated
| Database name | Used Version | Last updated on | Reference | Database URL |
| BioGRID | 3.2.112 | 25 April, 2014 | Chatr-Aryamontri A et al., 2012 |
http://thebiogrid.org/  |
| eggNOG | 4.0 | 12 December, 2013 | Powell S et al., 2014 |
http://eggnogdb.embl.de/ |
| inParanoid | 8.0 | 12 December, 2013 | Ostlung G et al., 2010 |
http://inparanoid.sbc.su.se/cgi-bin/ |
| intAct | 2013-11-20 | 12 December, 2013 | Hermjakob H et al., 2014 |
https://www.ebi.ac.uk/intact/ |
| MitoCheck | ens73 | 12 December, 2013 | Neumann B et al., 2010 |
http://www.mitocheck.org/ |
| PomBase Manually Curated Pombe<>Human and Pombe<>Cerevisiae Ortholog Lists |
Pombe<>Human: 5 May, 2014 Pombe<>Cerevisiae: V2.19 |
5 May, 2014 | Wood V et al., 2011 |
http://www.pombase.org/ |
| Universal Protein Resource (UniProt) for ID Mapping & ID check |
2014_04 | 16 April, 2014 | Uniprot Consortium, 2014 |
http://www.uniprot.org/ |
This tool is a part of my PhD Thesis
A system-level approach to identify novel cell size regulators
Zoltán Dul PhD thesis, King's College London, 2019
Download from KCL Pure
Zoltán Dul PhD thesis, King's College London, 2019
Download from KCL Pure
Source code of the Tool
All source files such as codes and files are publicly available in my GitHub repository on the following address:
https://github.com/ZoliQua/Ortholog-Finder-Tool
