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MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
Scott W Doniger, Nathan Salomonis, Kam D Dahlquist, Karen Vranizan, Steven C Lawlor, Bruce R Conklin
Genome Biol. 2003; 4(1): R7. Published online 2003 January 6.
PMCID:
PMC151291
Abstract Full Text PDF–139K Supplementary Material

Is Cited by the Following 215 Articles in this Archive:

Androgen regulation of gene expression in human meibomian gland and conjunctival epithelial cells
Payal Khandelwal, Shaohui Liu, David A. Sullivan
Mol Vis. 2012; 18: 1055–1067. Published online 2012 April 27.
PMCID:
PMC3351406
Abstract Full Text PDF–1.4M
Genome-Wide Gene Expression Analysis in Cancer Cells Reveals 3D Growth to Affect ECM and Processes Associated with Cell Adhesion but Not DNA Repair
Oliver Zschenker, Thomas Streichert, Stephanie Hehlgans, Nils Cordes
PLoS One. 2012; 7(4): e34279. Published online 2012 April 11. doi: 10.1371/journal.pone.0034279
PMCID:
PMC3324525
Abstract Full Text PDF–687K Supplementary Material
An update on the strategies in multicomponent activity monitoring within the phytopharmaceutical field
Johanna M Gostner, Oliver A Wrulich, Marcel Jenny, Dietmar Fuchs, Florian Ueberall
BMC Complement Altern Med. 2012; 12: 18. Published online 2012 March 14. doi: 10.1186/1472-6882-12-18
PMCID:
PMC3359261
Abstract Full Text PDF–7.5M
Quantitative Proteomic Analysis Revealed 4-(methylnitrosamino)-1-(3-pyridinyl)-1-butanone-induced Up-regulation of 20S Proteasome in Cultured Human Fibroblast Cells
John M. Prins, Yinsheng Wang
J Proteome Res. Author manuscript; available in PMC 2013 April 6.
Published in final edited form as: J Proteome Res. 2012 April 6; 11(4): 2347–2354. Published online 2012 March 9. doi: 10.1021/pr201088z
PMCID:
PMC3321129
Free in PMC on 2013/04/06
Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership
Ernesto Iacucci, Hans H. Zingg, Theodore J. Perkins
Front Genet. 2012; 3: 24. Prepublished online 2011 November 19. Published online 2012 February 23. doi: 10.3389/fgene.2012.00024
PMCID:
PMC3284693
Abstract Full Text PDF–1.8M
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
Purvesh Khatri, Marina Sirota, Atul J. Butte
PLoS Comput Biol. 2012 February; 8(2): e1002375. Published online 2012 February 23. doi: 10.1371/journal.pcbi.1002375
PMCID:
PMC3285573
Abstract Full Text PDF–663K Supplementary Material
Global gene expression profiling displays a network of dysregulated genes in non-atherosclerotic arterial tissue from patients with type 2 diabetes
Vibe Skov, Steen Knudsen, Malene Olesen, Maria L Hansen, Lars M Rasmussen
Cardiovasc Diabetol. 2012; 11: 15. Published online 2012 February 17. doi: 10.1186/1475-2840-11-15
PMCID:
PMC3348024
Abstract Full Text PDF–385K
Modeling of Molecular Interaction between Apoptin, BCR-Abl and CrkL - An Alternative Approach to Conventional Rational Drug Design
Soumya Panigrahi, Jörg Stetefeld, Jaganmohan R. Jangamreddy, Soma Mandal, Sanat K. Mandal, Marek Los
PLoS One. 2012; 7(1): e28395. Published online 2012 January 10. doi: 10.1371/journal.pone.0028395
PMCID:
PMC3254606
Abstract Full Text PDF–990K Supplementary Material
RP58 controls neuron and astrocyte differentiation by downregulating the expression of Id1–4 genes in the developing cortex
Shinobu Hirai, Akiko Miwa, Chiaki Ohtaka-Maruyama, Masataka Kasai, Shigeo Okabe, Yutaka Hata, Haruo Okado
EMBO J. 2012 March 7; 31(5): 1190–1202. Published online 2012 January 10. doi: 10.1038/emboj.2011.486
PMCID:
PMC3297993
Free in PMC on 2013/03/07
The Impact of Focused Gene Ontology Curation of Specific Mammalian Systems
Yasmin Alam-Faruque, Rachael P. Huntley, Varsha K. Khodiyar, Evelyn B. Camon, Emily C. Dimmer, Tony Sawford, Maria J. Martin, Claire O'Donovan, Philippa J. Talmud, Peter Scambler, Rolf Apweiler, Ruth C. Lovering
PLoS One. 2011; 6(12): e27541. Published online 2011 December 9. doi: 10.1371/journal.pone.0027541
PMCID:
PMC3235096
Abstract Full Text PDF–483K Supplementary Material
Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera
Maria de la Paz Celorio-Mancera, Seung-Joon Ahn, Heiko Vogel, David G Heckel
BMC Genomics. 2011; 12: 575. Published online 2011 November 23. doi: 10.1186/1471-2164-12-575
PMCID:
PMC3235194
Abstract Full Text PDF–689K Supplementary Material
Genome-Wide Screen for Differential DNA Methylation Associated with Neural Cell Differentiation in Mouse
Rene Cortese, Jörn Lewin, Liselotte Bäckdahl, Manuel Krispin, Reinhold Wasserkort, Florian Eckhardt, Stephan Beck
PLoS One. 2011; 6(10): e26002. Published online 2011 October 18. doi: 10.1371/journal.pone.0026002
PMCID:
PMC3196508
Abstract Full Text PDF–1.6M Supplementary Material
Early post-myocardial infarction survival in MRL mice is mediated by attenuated apoptosis and inflammation but depends on genetic background
Darlene L. Hunt, Patrick H. Campbell, Alexander C. Zambon, Karen Vranizan, Sylvia M. Evans, Hai-Chien Kuo, Ken D. Yamaguchi, Jeffrey H. Omens, Andrew D. McCulloch
Exp Physiol. Author manuscript; available in PMC 2013 January 1.
Published in final edited form as: Exp Physiol. 2012 January; 97(1): 102–114. Published online 2011 October 3. doi: 10.1113/expphysiol.2011.060269
PMCID:
PMC3253239
Free in PMC on 2013/01/01
Differential transcriptomic profiles effected by oil palm phenolics indicate novel health outcomes
Soon-Sen Leow, Shamala Devi Sekaran, Kalyana Sundram, YewAi Tan, Ravigadevi Sambanthamurthi
BMC Genomics. 2011; 12: 432. Published online 2011 August 25. doi: 10.1186/1471-2164-12-432
PMCID:
PMC3175228
Abstract Full Text PDF–2.4M Supplementary Material
Limited redundancy in genes regulated by Cyclin T2 and Cyclin T1
Rajesh Ramakrishnan, Wendong Yu, Andrew P Rice
BMC Res Notes. 2011; 4: 260. Published online 2011 July 26. doi: 10.1186/1756-0500-4-260
PMCID:
PMC3160394
Abstract Full Text PDF–2.1M
Identification of a neuronal gene expression signature: role of cell cycle arrest in murine neuronal differentiation in vitro
Hady Felfly, Jin Xue, Alexander C. Zambon, Alysson Muotri, Dan Zhou, Gabriel G. Haddad
Am J Physiol Regul Integr Comp Physiol. 2011 September; 301(3): R727–R745. Published online 2011 June 15. doi: 10.1152/ajpregu.00217.2011
PMCID:
PMC3174756
Free in PMC on 2012/09/01
g:Profiler—a web server for functional interpretation of gene lists (2011 update)
Jüri Reimand, Tambet Arak, Jaak Vilo
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W307–W315. Published online 2011 June 6. doi: 10.1093/nar/gkr378
PMCID:
PMC3125778
Abstract Full Text PDF–5.9M
Changes in Gene Expression in Human Meibomian Gland Dysfunction
Shaohui Liu, Stephen M. Richards, Kristine Lo, Mark Hatton, Aaron Fay, David A. Sullivan
Invest Ophthalmol Vis Sci. 2011 April; 52(5): 2727–2740. Published online 2011 April 25. doi: 10.1167/iovs.10-6482
PMCID:
PMC3088560
Abstract Full Text PDF–122K
Secretoglobin 3A2 Suppresses Bleomycin-induced Pulmonary Fibrosis by Transforming Growth Factor β Signaling Down-regulation
Reiko Kurotani, Satoshi Okumura, Tsutomu Matsubara, Utako Yokoyama, John R. Buckley, Takeshi Tomita, Kyohei Kezuka, Tomokazu Nagano, Dominic Esposito, Troy E. Taylor, William K. Gillette, Yoshihiro Ishikawa, Hiroyuki Abe, Jerrold M. Ward, Shioko Kimura
J Biol Chem. 2011 June 3; 286(22): 19682–19692. Published online 2011 April 10. doi: 10.1074/jbc.M111.239046
PMCID:
PMC3103347
Free in PMC on 2012/06/03
Identifying Causal Genes and Dysregulated Pathways in Complex Diseases
Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka
PLoS Comput Biol. 2011 March; 7(3): e1001095. Published online 2011 March 3. doi: 10.1371/journal.pcbi.1001095
PMCID:
PMC3048384
Abstract Full Text PDF–793K Supplementary Material
SOD2 Deficient Erythroid Cells Up-Regulate Transferrin Receptor and Down-Regulate Mitochondrial Biogenesis and Metabolism
Florent M. Martin, Xiuling Xu, Katharina von Löhneysen, Timothy J. Gilmartin, Jeffrey S. Friedman
PLoS One. 2011; 6(2): e16894. Published online 2011 February 4. doi: 10.1371/journal.pone.0016894
PMCID:
PMC3033911
Abstract Full Text PDF–1.1M Supplementary Material
Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling
Gordon R. O. Campbell, Ariane Baudhuin, Karen Vranizan, John Ngai
Mol Cell Neurosci. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: Mol Cell Neurosci. 2011 February; 46(2): 548–561. Published online 2010 December 29. doi: 10.1016/j.mcn.2010.12.012
PMCID:
PMC3040421
Abstract Full Text PDF–6.4M Supplementary Material
Toward a complete in silico, multi-layered embryonic stem cell regulatory network
Huilei Xu, Christoph Schaniel, Ihor R. Lemischka, Avi Ma’ayan
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2010 Nov–Dec; 2(6): 708–733. doi: 10.1002/wsbm.93
PMCID:
PMC2951283
Abstract Full Text PDF–1.9M
Evidence of aberrant lipid metabolism in hepatitis C and hepatocellular carcinoma
Jian-Min Wu, Nicholas J Skill, Mary A Maluccio
HPB (Oxford) 2010 November; 12(9): 625–636. doi: 10.1111/j.1477-2574.2010.00207.x
PMCID:
PMC2999790
Abstract Full Text PDF–513K
Dynamic interaction networks in a hierarchically organized tissue
Daniel C Kirouac, Caryn Ito, Elizabeth Csaszar, Aline Roch, Mei Yu, Edward A Sykes, Gary D Bader, Peter W Zandstra
Mol Syst Biol. 2010; 6: 417. Published online 2010 October 5. doi: 10.1038/msb.2010.71
PMCID:
PMC2990637
Abstract Full Text PDF–3.1M Supplementary Material
Arsenic- and Cadmium-Induced Toxicogenomic Response in Mouse Embryos Undergoing Neurulation
Joshua F. Robinson, Xiaozhong Yu, Estefania G. Moreira, Sungwoo Hong, Elaine M. Faustman
Toxicol Appl Pharmacol. Author manuscript; available in PMC 2012 January 15.
Published in final edited form as: Toxicol Appl Pharmacol. 2011 January 15; 250(2): 117–129. Published online 2010 September 29. doi: 10.1016/j.taap.2010.09.018
PMCID:
PMC3014392
Abstract Full Text PDF–2.3M Supplementary Material
Efficacy of the Multi-Kinase Inhibitor Enzastaurin is Dependent on Cellular Signaling Context
Wen-Liang Kuo, Jing Liu, Helena Mauceri, Everett E Vokes, Ralph Weichselbaum, Marsha Rich Rosner, Ezra Eddy Wyssam Cohen
Mol Cancer Ther. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: Mol Cancer Ther. 2010 October; 9(10): 2814–2824. Published online 2010 September 28. doi: 10.1158/1535-7163.MCT-10-0352
PMCID:
PMC2953602
Abstract Full Text PDF–1.6M Supplementary Material
Consistency, comprehensiveness, and compatibility of pathway databases
Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong
BMC Bioinformatics. 2010; 11: 449. Published online 2010 September 7. doi: 10.1186/1471-2105-11-449
PMCID:
PMC2944280
Abstract Full Text PDF–986K
Culture, Immortalization, and Characterization of Human Meibomian Gland Epithelial Cells
Shaohui Liu, Mark P. Hatton, Payal Khandelwal, David A. Sullivan
Invest Ophthalmol Vis Sci. 2010 August; 51(8): 3993–4005. doi: 10.1167/iovs.09-5108
PMCID:
PMC2910637
Abstract Full Text PDF–1.2M
Gene Expression Analysis of Forskolin Treated Basilar Papillae Identifies MicroRNA181a as a Mediator of Proliferation
Corey S. Frucht, Mohamed Uduman, Jamie L. Duke, Steven H. Kleinstein, Joseph Santos-Sacchi, Dhasakumar S. Navaratnam
PLoS One. 2010; 5(7): e11502. Published online 2010 July 9. doi: 10.1371/journal.pone.0011502
PMCID:
PMC2901389
Abstract Full Text PDF–755K Supplementary Material
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