Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.
Larsson Thomas P., Murray Christian G., Hill Tobias, Fredriksson Robert, Schiöth Helgi B., Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery, 10.1016/j.febslet.2004.12.046
Lander Eric S., Linton Lauren M., Birren Bruce, Nusbaum Chad, Zody Michael C., Baldwin Jennifer, Devon Keri, Dewar Ken, Doyle Michael, FitzHugh William, Funke Roel, Gage Diane, Harris Katrina, Heaford Andrew, Howland John, Kann Lisa, Lehoczky Jessica, LeVine Rosie, McEwan Paul, McKernan Kevin, Meldrim James, Mesirov Jill P., Miranda Cher, Morris William, Naylor Jerome, Raymond Christina, Rosetti Mark, Santos Ralph, Sheridan Andrew, Sougnez Carrie, Stange-Thomann Nicole, Stojanovic Nikola, Subramanian Aravind, Wyman Dudley, Rogers Jane, Sulston John, Ainscough Rachael, Beck Stephan, Bentley David, Burton John, Clee Christopher, Carter Nigel, Coulson Alan, Deadman Rebecca, Deloukas Panos, Dunham Andrew, Dunham Ian, Durbin Richard, French Lisa, Grafham Darren, Gregory Simon, Hubbard Tim, Humphray Sean, Hunt Adrienne, Jones Matthew, Lloyd Christine, McMurray Amanda, Matthews Lucy, Mercer Simon, Milne Sarah, Mullikin James C., Mungall Andrew, Plumb Robert, Ross Mark, Shownkeen Ratna, Sims Sarah, Waterston Robert H., Wilson Richard K., Hillier LaDeana W., McPherson John D., Marra Marco A., Mardis Elaine R., Fulton Lucinda A., Chinwalla Asif T., Pepin Kymberlie H., Gish Warren R., Chissoe Stephanie L., Wendl Michael C., Delehaunty Kim D., Miner Tracie L., Delehaunty Andrew, Kramer Jason B., Cook Lisa L., Fulton Robert S., Johnson Douglas L., Minx Patrick J., Clifton Sandra W., Hawkins Trevor, Branscomb Elbert, Predki Paul, Richardson Paul, Wenning Sarah, Slezak Tom, Doggett Norman, Cheng Jan-Fang, Olsen Anne, Lucas Susan, Elkin Christopher, Uberbacher Edward, Frazier Marvin, Gibbs Richard A., Muzny Donna M., Scherer Steven E., Bouck John B., Sodergren Erica J., Worley Kim C., Rives Catherine M., Gorrell James H., Metzker Michael L., Naylor Susan L., Kucherlapati Raju S., Nelson David L., Weinstock George M., Sakaki Yoshiyuki, Fujiyama Asao, Hattori Masahira, Yada Tetsushi, Toyoda Atsushi, Itoh Takehiko, Kawagoe Chiharu, Watanabe Hidemi, Totoki Yasushi, Taylor Todd, Weissenbach Jean, Heilig Roland, Saurin William, Artiguenave Francois, Brottier Philippe, Bruls Thomas, Pelletier Eric, Robert Catherine, Wincker Patrick, Rosenthal André, Platzer Matthias, Nyakatura Gerald, Taudien Stefan, Rump Andreas, Smith Douglas R., Doucette-Stamm Lynn, Rubenfield Marc, Weinstock Keith, Lee Hong Mei, Dubois JoAnn, Yang Huanming, Yu Jun, Wang Jian, Huang Guyang, Gu Jun, Hood Leroy, Rowen Lee, Madan Anup, Qin Shizen, Davis Ronald W., Federspiel Nancy A., Abola A. Pia, Proctor Michael J., Roe Bruce A., Chen Feng, Pan Huaqin, Ramser Juliane, Lehrach Hans, Reinhardt Richard, McCombie W. Richard, de la Bastide Melissa, Dedhia Neilay, Blöcker Helmut, Hornischer Klaus, Nordsiek Gabriele, Agarwala Richa, Aravind L., Bailey Jeffrey A., Bateman Alex, Batzoglou Serafim, Birney Ewan, Bork Peer, Brown Daniel G., Burge Christopher B., Cerutti Lorenzo, Chen Hsiu-Chuan, Church Deanna, Clamp Michele, Copley Richard R., Doerks Tobias, Eddy Sean R., Eichler Evan E., Furey Terrence S., Galagan James, Gilbert James G. R., Harmon Cyrus, Hayashizaki Yoshihide, Haussler David, Hermjakob Henning, Hokamp Karsten, Jang Wonhee, Johnson L. Steven, Jones Thomas A., Kasif Simon, Kaspryzk Arek, Kennedy Scot, Kent W. James, Kitts Paul, Koonin Eugene V., Korf Ian, Kulp David, Lancet Doron, Lowe Todd M., McLysaght Aoife, Mikkelsen Tarjei, Moran John V., Mulder Nicola, Pollara Victor J., Ponting Chris P., Schuler Greg, Schultz Jörg, Slater Guy, Smit Arian F. A., Stupka Elia, Szustakowki Joseph, Thierry-Mieg Danielle, Thierry-Mieg Jean, Wagner Lukas, Wallis John, Wheeler Raymond, Williams Alan, Wolf Yuri I., Wolfe Kenneth H., Yang Shiaw-Pyng, Yeh Ru-Fang, Collins Francis, Guyer Mark S., Peterson Jane, Felsenfeld Adam, Wetterstrand Kris A., Myers Richard M., Schmutz Jeremy, Dickson Mark, Grimwood Jane, Cox David R., Olson Maynard V., Kaul Rajinder, Raymond Christopher, Shimizu Nobuyoshi, Kawasaki Kazuhiko, Minoshima Shinsei, Evans Glen A., Athanasiou Maria, Schultz Roger, Patrinos Aristides, Morgan Michael J., Initial sequencing and analysis of the human genome, 10.1038/35057062
Hammes Annette, Guo Jian-Kan, Lutsch Gudrun, Leheste Joerg-Robert, Landrock Danilo, Ziegler Ulrike, Gubler Marie-Claire, Schedl Andreas, Two Splice Variants of the Wilms' Tumor 1 Gene Have Distinct Functions during Sex Determination and Nephron Formation, 10.1016/s0092-8674(01)00453-6
Stark Kevin, Vainio Seppo, Vassileva Galya, McMahon Andrew P., Epithelial transformation of metanephric mesenchyme in the developing kidney regulated by Wnt-4, 10.1038/372679a0
Kreidberg Jordan A., Sariola Hannu, Loring Janet M., Maeda Masahiro, Pelletier Jerry, Housman David, Jaenisch Rudolf, WT-1 is required for early kidney development, 10.1016/0092-8674(93)90515-r
Saulnier Didier M.E., Ghanbari Hedyeh, Brändli André W., Essential Function of Wnt-4 for Tubulogenesis in the Xenopus Pronephric Kidney, 10.1006/dbio.2002.0712
Silva Ian V, Cebotaru Valeriu, Wang Hua, Wang Xi-Tao, Wang Sha Sha, Guo Gang, Devuyst Olivier, Thakker Rajesh V, Guggino William B, Guggino Sandra E, The ClC-5 Knockout Mouse Model of Dent's Disease Has Renal Hypercalciuria and Increased Bone Turnover, 10.1359/jbmr.2003.18.4.615
Wang S. S., Mice lacking renal chloride channel, CLC-5, are a model for Dent's disease, a nephrolithiasis disorder associated with defective receptor-mediated endocytosis, 10.1093/hmg/9.20.2937
Günther Willy, Piwon Nils, Jentsch Thomas J., The ClC-5 chloride channel knock-out mouse – an animal model for Dent's disease, 10.1007/s00424-002-0950-6
Piwon Nils, Günther Willy, Schwake Michael, Bösl Michael R., Jentsch Thomas J., ClC-5 Cl--channel disruption impairs endocytosis in a
mouse model for Dent's disease, 10.1038/35042597
Jentsch Thomas J, Neagoe Ioana, Scheel Olaf, CLC chloride channels and transporters, 10.1016/j.conb.2005.05.002
Waldegger Siegfried, Jentsch Thomas J., Functional and Structural Analysis of ClC-K Chloride Channels Involved in Renal Disease, 10.1074/jbc.m001987200
Christensen E. I., Devuyst O., Dom G., Nielsen R., Van Der Smissen P., Verroust P., Leruth M., Guggino W. B., Courtoy P. J., Loss of chloride channel ClC-5 impairs endocytosis by defective trafficking of megalin and cubilin in kidney proximal tubules, 10.1073/pnas.1432873100
Scheinman Steven J., Guay-Woodford Lisa M., Thakker Rajesh V., Warnock David G., Genetic Disorders of Renal Electrolyte Transport, 10.1056/nejm199904153401507
Lifton Richard P., Gharavi Ali G., Geller David S., Molecular Mechanisms of Human Hypertension, 10.1016/s0092-8674(01)00241-0
Vainio Seppo, Lin Yanfeng, Organogenesis: Coordinating early kidney development: lessons from gene targeting, 10.1038/nrg842
Simon D. B., Paracellin-1, a Renal Tight Junction Protein Required for Paracellular Mg2+ Resorption, 10.1126/science.285.5424.103
Müller Dominik, Kausalya P. Jaya, Claverie-Martin Felix, Meij Iwan C., Eggert Paul, Garcia-Nieto Victor, Hunziker Walter, A Novel Claudin 16 Mutation Associated with Childhood Hypercalciuria Abolishes Binding to ZO-1 and Results in Lysosomal Mistargeting, 10.1086/380418
Sharpe J., Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies, 10.1126/science.1068206
Kerwin Janet, Scott Mark, Sharpe James, Puelles Luis, Robson Stephen C, Martínez-de-la-Torre Margaret, Ferran Jose, Feng Guangjie, Baldock Richard, Strachan Tom, Davidson Duncan, Lindsay Susan, 10.1186/1471-2202-5-27
Moore Adrian W, Schedl Andreas, McInnes Lesley, Doyle Michael, Hecksher-Sorensen Jacob, D. Hastie Nicholas, YAC transgenic analysis reveals Wilms' Tumour 1 gene activity in the proliferating coelomic epithelium, developing diaphragm and limb, 10.1016/s0925-4773(98)00188-9
Bibliographic reference
Willnow, Te ; Antignac, C ; Brändli, Aw ; Christensen, Ei ; Cox, Rd ; et. al. The European renal genome project : an integrated approach towards understanding the genetics of kidney development and disease.. In: Organogenesis, Vol. 2, no. 2, p. 42-7 (2005)
