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The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
Da Wei Huang, Brad T Sherman, Qina Tan, Jack R Collins, W Gregory Alvord, Jean Roayaei, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki
Genome Biol. 2007; 8(9): R183. Published online 2007 September 4. doi: 10.1186/gb-2007-8-9-r183
PMCID:
PMC2375021
Abstract Full Text PDF–819K Supplementary Material

Is Cited by the Following 82 Articles in this Archive:

Ecological Genomics of Anopheles gambiae Along a Latitudinal Cline: A Population-Resequencing Approach
Changde Cheng, Bradley J. White, Colince Kamdem, Keithanne Mockaitis, Carlo Costantini, Matthew W. Hahn, Nora J. Besansky
Genetics. 2012 April; 190(4): 1417–1432. doi: 10.1534/genetics.111.137794
PMCID:
PMC3316653
Free in PMC on 2013/04/01
Mixing of Honeybees with Different Genotypes Affects Individual Worker Behavior and Transcription of Genes in the Neuronal Substrate
Tanja Gempe, Silke Stach, Kaspar Bienefeld, Martin Beye
PLoS One. 2012; 7(2): e31653. Published online 2012 February 14. doi: 10.1371/journal.pone.0031653
PMCID:
PMC3279409
Abstract Full Text PDF–478K Supplementary Material
Intrinsic gene expression subsets of diffuse cutaneous systemic sclerosis are stable in serial skin biopsies
Sarah A. Pendergrass, Raphael Lemaire, Ian Francis, J. Matthew Mahoney, Robert Lafyatis, Michael L. Whitfield
J Invest Dermatol. Author manuscript; available in PMC 2012 November 1.
Published in final edited form as: J Invest Dermatol. 2012 May; 132(5): 1363–1373. Published online 2012 February 9. doi: 10.1038/jid.2011.472
PMCID:
PMC3326181
Free in PMC on 2012/11/01
Intrinsic gene expression subsets of diffuse cutaneous systemic sclerosis are stable in serial skin biopsies
Sarah A. Pendergrass, Raphael Lemaire, Ian Francis, J. Matthew Mahoney, Robert Lafyatis, Michael L. Whitfield
J Invest Dermatol. Author manuscript; available in PMC 2012 November 1.
Published in final edited form as: J Invest Dermatol. 2012 May; 132(5): 1363–1373. Published online 2012 February 9. doi: 10.1038/jid.2011.472
PMCID:
PMC3326181
Free in PMC on 2012/11/01
Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jianrong Li, Tanguy Y. Seiwert, Ezra E. W. Cohen, H. Rosie Xing, Yves A. Lussier
PLoS Comput Biol. 2012 January; 8(1): e1002350. Published online 2012 January 26. doi: 10.1371/journal.pcbi.1002350
PMCID:
PMC3266878
Abstract Full Text PDF–2.2M Supplementary Material
Pooled shRNA screen for sensitizers to inhibition of the mitotic regulator polo-like kinase (PLK1)
Nancy Liu-Sullivan, Jianping Zhang, Amy Bakleh, John Marchica, Jinyu Li, Despina Siolas, Sylvie Laquerre, Yan Y. Degenhardt, Richard Wooster, Kenneth Chang, Gregory F. Hannon, Scott Powers
Oncotarget. 2011 December; 2(12): 1254–1264. Published online 2011 December 30.
PMCID:
PMC3282082
Abstract Full Text PDF–1.5M
Novel search method for the discovery of functional relationships
Fidel Ramírez, Glenn Lawyer, Mario Albrecht
Bioinformatics. 2012 January 15; 28(2): 269–276. Published online 2011 December 16. doi: 10.1093/bioinformatics/btr631
PMCID:
PMC3259435
Abstract Full Text PDF–674K Supplementary Material
Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model
Monica Llano-Diez, Ann-Marie Gustafson, Carl Olsson, Hanna Goransson , Lars Larsson
BMC Genomics. 2011; 12: 602. Published online 2011 December 13. doi: 10.1186/1471-2164-12-602
PMCID:
PMC3266306
Abstract Full Text PDF–566K Supplementary Material
AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations
Michael Defoin-Platel, Matthew M Hindle, Artem Lysenko, Stephen J Powers, Dimah Z Habash, Christopher J Rawlings, Mansoor Saqi
BMC Bioinformatics. 2011; 12: 431. Published online 2011 November 3. doi: 10.1186/1471-2105-12-431
PMCID:
PMC3237112
Abstract Full Text PDF–776K Supplementary Material
Hyperosmotic Stress Induces Aquaporin-dependent Cell Shrinkage, Polyphosphate Synthesis, Amino Acid Accumulation, and Global Gene Expression Changes in Trypanosoma cruzi
Zhu-Hong Li, Vanina E. Alvarez, Javier G. De Gaudenzi, Celso Sant'Anna, Alberto C. C. Frasch, Juan J. Cazzulo, Roberto Docampo
J Biol Chem. 2011 December 23; 286(51): 43959–43971. Published online 2011 October 28. doi: 10.1074/jbc.M111.311530
PMCID:
PMC3243512
Free in PMC on 2012/12/23
The Accuracy of Survival Time Prediction for Patients with Glioma Is Improved by Measuring Mitotic Spindle Checkpoint Gene Expression
Li Bie, Gang Zhao, Pui Cheng, Gaelle Rondeau, Steffen Porwollik, Yan Ju, Xiao-Qin Xia, Michael McClelland
PLoS One. 2011; 6(10): e25631. Published online 2011 October 12. doi: 10.1371/journal.pone.0025631
PMCID:
PMC3192043
Abstract Full Text PDF–340K Supplementary Material
Rational Design of Therapeutic siRNAs: Minimizing Off-targeting Potential to Improve the Safety of RNAi Therapy for Huntington's Disease
Ryan L Boudreau, Ryan M Spengler, Beverly L Davidson
Mol Ther. 2011 December; 19(12): 2169–2177. Published online 2011 September 27. doi: 10.1038/mt.2011.185
PMCID:
PMC3242660
Free in PMC on 2012/12/01
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells
Chao Cheng, Mark Gerstein
Nucleic Acids Res. 2012 January; 40(2): 553–568. Published online 2011 September 16. doi: 10.1093/nar/gkr752
PMCID:
PMC3258143
Abstract Full Text PDF–11M Supplementary Material
Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study
Keyur H. Desai, Chuen Seng Tan, Jeffrey T. Leek, Ronald V. Maier, Ronald G. Tompkins, John D. Storey, and the Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program
PLoS Med. 2011 September; 8(9): e1001093. Published online 2011 September 13. doi: 10.1371/journal.pmed.1001093
PMCID:
PMC3172280
Abstract Full Text PDF–767K Supplementary Material
SEAS: A System for SEED-Based Pathway Enrichment Analysis
Xizeng Mao, Yu Zhang, Ying Xu
PLoS One. 2011; 6(7): e22556. Published online 2011 July 22. doi: 10.1371/journal.pone.0022556
PMCID:
PMC3142180
Abstract Full Text PDF–348K Supplementary Material
Integrated Expression Profiling and Genome-Wide Analysis of ChREBP Targets Reveals the Dual Role for ChREBP in Glucose-Regulated Gene Expression
Yun-Seung Jeong, Deokhoon Kim, Yong Seok Lee, Ha-Jung Kim, Jung-Youn Han, Seung-Soon Im, Hansook Kim Chong, Je-Keun Kwon, Yun-Ho Cho, Woo Kyung Kim, Timothy F. Osborne, Jay D. Horton, Hee-Sook Jun, Yong-Ho Ahn, Sung-Min Ahn, Ji-Young Cha
PLoS One. 2011; 6(7): e22544. Published online 2011 July 21. doi: 10.1371/journal.pone.0022544
PMCID:
PMC3141076
Abstract Full Text PDF–1.6M Supplementary Material
Absolute quantification of microbial proteomes at different states by directed mass spectrometry
Alexander Schmidt, Martin Beck, Johan Malmström, Henry Lam, Manfred Claassen, David Campbell, Ruedi Aebersold
Mol Syst Biol. 2011; 7: 510. Published online 2011 July 19. doi: 10.1038/msb.2011.37
PMCID:
PMC3159967
Abstract Full Text PDF–1.9M Supplementary Material
Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments
Mikhail Jiline, Stan Matwin, Marcel Turcotte
Bioinformatics. 2011 September 1; 27(17): 2391–2398. Published online 2011 July 9. doi: 10.1093/bioinformatics/btr337
PMCID:
PMC3157920
Abstract Full Text PDF–483K
Comparison of Dorsocervical With Abdominal Subcutaneous Adipose Tissue in Patients With and Without Antiretroviral Therapy–Associated Lipodystrophy
Ksenia Sevastianova, Jussi Sutinen, Dario Greco, Meline Sievers, Kaisa Salmenkivi, Julia Perttilä, Vesa M. Olkkonen, Dick Wågsäter, Martin E. Lidell, Sven Enerbäck, Per Eriksson, Ulrich A. Walker, Petri Auvinen, Matti Ristola, Hannele Yki-Järvinen
Diabetes. 2011 July; 60(7): 1894–1900. Published online 2011 June 20. doi: 10.2337/db11-0075
PMCID:
PMC3121420
Free in PMC on 2012/07/01
Jejunal gene expression patterns correlate with severity of systemic infection in chicken
Dirkjan Schokker, Mari A Smits, Johanna MJ Rebel
BMC Proc. 2011; 5(Suppl 4): S4. Published online 2011 June 3. doi: 10.1186/1753-6561-5-S4-S4
PMCID:
PMC3108234
Abstract Full Text PDF–307K
Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila
Matthew Slattery, Lijia Ma, Nicolas Négre, Kevin P. White, Richard S. Mann
PLoS One. 2011; 6(4): e14686. Published online 2011 April 5. doi: 10.1371/journal.pone.0014686
PMCID:
PMC3071676
Abstract Full Text PDF–1.8M Supplementary Material
MicroRNA-26a Is a Novel Regulator of Vascular Smooth Muscle Cell Function
Nicholas J. Leeper, Azad Raiesdana, Yoko Kojima, Hyung J. Chun, Junya Azuma, Lars Maegdefessel, Ramendra K. Kundu, Thomas Quertermous, Philip S. Tsao, Joshua M. Spin
J Cell Physiol. Author manuscript; available in PMC 2011 June 6.
Published in final edited form as: J Cell Physiol. 2011 April; 226(4): 1035–1043. doi: 10.1002/jcp.22422
PMCID:
PMC3108574
Abstract Full Text PDF–2.8M Supplementary Material
Global Gene Expression Profiles of Subcutaneous Adipose and Muscle From Glucose-Tolerant, Insulin-Sensitive, and Insulin-Resistant Individuals Matched for BMI
Steven C. Elbein, Philip A. Kern, Neda Rasouli, Aiwei Yao-Borengasser, Neeraj K. Sharma, Swapan K. Das
Diabetes. 2011 March; 60(3): 1019–1029. Published online 2011 February 21. doi: 10.2337/db10-1270
PMCID:
PMC3046820
Abstract Full Text PDF–140K Supplementary Material
Hormone Depletion-Insensitivity of Prostate Cancer Cells Is Supported by the AR Without Binding to Classical Response Elements
Mesfin Gonit, Juan Zhang, Marcela d'Alincourt Salazar, Hongjuan Cui, Aymen Shatnawi, Robert Trumbly, Manohar Ratnam
Mol Endocrinol. 2011 April; 25(4): 621–634. Published online 2011 February 17. doi: 10.1210/me.2010-0409
PMCID:
PMC3063083
Abstract Full Text
Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue
Lorenza Mittempergher, Jorma J. de Ronde, Marja Nieuwland, Ron M. Kerkhoven, Iris Simon, Emiel J. Th. Rutgers, Lodewyk F. A. Wessels, Laura J. Van't Veer
PLoS One. 2011; 6(2): e17163. Published online 2011 February 11. doi: 10.1371/journal.pone.0017163
PMCID:
PMC3037966
Abstract Full Text PDF–2.2M Supplementary Material
In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development
Tiemo J. Klisch, Yuanxin Xi, Adriano Flora, Liguo Wang, Wei Li, Huda Y. Zoghbi
Proc Natl Acad Sci U S A. 2011 February 22; 108(8): 3288–3293. Published online 2011 February 7. doi: 10.1073/pnas.1100230108
PMCID:
PMC3044384
Abstract Full Text PDF–887K Supplementary Material
Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering
Shanaz A Ghandhi, Anshu Sinha, Marianthi Markatou, Sally A Amundson
BMC Genomics. 2011; 12: 2. Published online 2011 January 4. doi: 10.1186/1471-2164-12-2
PMCID:
PMC3022823
Abstract Full Text PDF–5.9M Supplementary Material
IntelliGO: a new vector-based semantic similarity measure including annotation origin
Sidahmed Benabderrahmane, Malika Smail-Tabbone, Olivier Poch, Amedeo Napoli, Marie-Dominique Devignes
BMC Bioinformatics. 2010; 11: 588. Published online 2010 December 1. doi: 10.1186/1471-2105-11-588
PMCID:
PMC3098105
Abstract Full Text PDF–936K
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Daniele Merico, Ruth Isserlin, Oliver Stueker, Andrew Emili, Gary D. Bader
PLoS One. 2010; 5(11): e13984. Published online 2010 November 15. doi: 10.1371/journal.pone.0013984
PMCID:
PMC2981572
Abstract Full Text PDF–1.9M Supplementary Material
Isolation of alveolar epithelial type II progenitor cells from adult human lungs
Naoya Fujino, Hiroshi Kubo, Takaya Suzuki, Chiharu Ota, Ahmed E Hegab, Mei He, Satoshi Suzuki, Takashi Suzuki, Mitsuhiro Yamada, Takashi Kondo, Hidemasa Kato, Mutsuo Yamaya
Lab Invest. 2011 March; 91(3): 363–378. Published online 2010 November 15. doi: 10.1038/labinvest.2010.187
PMCID:
PMC3125101
Abstract Full Text PDF–1.1M Supplementary Material
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