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Identifying biological themes within lists of genes with EASE
Douglas A Hosack, Glynn Dennis, Jr, Brad T Sherman, H Clifford Lane, Richard A Lempicki
Genome Biol. 2003; 4(10): R70. Published online 2003 September 11.
PMCID:
PMC328459
Abstract Full Text PDF–221K

Is Cited by the Following 465 Articles in this Archive:

Protocadherin-18 Is a Novel Differentiation Marker and an Inhibitory Signaling Receptor for CD8+ Effector Memory T Cells
Edwin J. Vazquez-Cintron, Ngozi R. Monu, Jeremy C. Burns, Roy Blum, Gregory Chen, Peter Lopez, Jennifer Ma, Sasa Radoja, Alan B. Frey
PLoS One. 2012; 7(5): e36101. Published online 2012 May 2. doi: 10.1371/journal.pone.0036101
PMCID:
PMC3342238
Abstract Full Text PDF–1.8M Supplementary Material
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He
OMICS. 2012 May; 16(5): 284–287. doi: 10.1089/omi.2011.0118
PMCID:
PMC3339379
Free in PMC on 2013/05/01
Functional Annotation of Hierarchical Modularity
Kanchana Padmanabhan, Kuangyu Wang, Nagiza F. Samatova
PLoS One. 2012; 7(4): e33744. Published online 2012 April 4. doi: 10.1371/journal.pone.0033744
PMCID:
PMC3319548
Abstract Full Text PDF–664K Supplementary Material
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
Proteomic analysis of effluents from perfused human heart for transplantation: identification of potential biomarkers for ischemic heart damage
Hong Li, Jiyuan Li, Ying Wang, Tiande Yang
Proteome Sci. 2012; 10: 21. Published online 2012 March 23. doi: 10.1186/1477-5956-10-21
PMCID:
PMC3349588
Abstract Full Text PDF–1.2M Supplementary Material
Gene expression profiling of HCV genotype 3a initial liver fibrosis and cirrhosis patients using microarray
Waqar Ahmad, Bushra Ijaz, Sajida Hassan
J Transl Med. 2012; 10: 41. Published online 2012 March 7. doi: 10.1186/1479-5876-10-41
PMCID:
PMC3348056
Abstract Full Text PDF–854K
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
Comparison of Pathway Analysis Approaches Using Lung Cancer GWAS Data Sets
Gordon Fehringer, Geoffrey Liu, Laurent Briollais, Paul Brennan, Christopher I. Amos, Margaret R. Spitz, Heike Bickeböller, H. Erich Wichmann, Angela Risch, Rayjean J. Hung
PLoS One. 2012; 7(2): e31816. Published online 2012 February 21. doi: 10.1371/journal.pone.0031816
PMCID:
PMC3283683
Abstract Full Text PDF–190K
Annotator: Post-processing Software for generating function-based signatures from quantitative mass spectrometry
Juliesta E. Sylvester, Tyler S. Bray, Stephen J. Kron
J Proteome Res. Author manuscript; available in PMC 2013 March 2.
Published in final edited form as: J Proteome Res. 2012 March 2; 11(3): 1521–1536. Published online 2012 February 3. doi: 10.1021/pr200460s
PMCID:
PMC3292622
Free in PMC on 2013/03/02
CD34 marks angiogenic tip cells in human vascular endothelial cell cultures
Martin J. Siemerink, Ingeborg Klaassen, Ilse M. C. Vogels, Arjan W. Griffioen, Cornelis J. F. Van Noorden, Reinier O. Schlingemann
Angiogenesis. 2012 March; 15(1): 151–163. Published online 2012 January 17. doi: 10.1007/s10456-011-9251-z
PMCID:
PMC3274677
Abstract Full Text PDF–901K Supplementary Material
Protein Kinase C (PKC)ζ-mediated Gαq Stimulation of ERK5 Protein Pathway in Cardiomyocytes and Cardiac Fibroblasts
Carlota García-Hoz, Guzmán Sánchez-Fernández, Ramón García-Escudero, María Fernández-Velasco, Julia Palacios-García, Marisol Ruiz-Meana, Maria Teresa Díaz-Meco, Michael Leitges, Jorge Moscat, David García-Dorado, Lisardo Boscá, Federico Mayor, Jr., Catalina Ribas
J Biol Chem. 2012 March 2; 287(10): 7792–7802. Published online 2012 January 9. doi: 10.1074/jbc.M111.282210
PMCID:
PMC3293562
Free in PMC on 2013/03/02
Genome-Wide Analyses of Nkx2-1 Binding to Transcriptional Target Genes Uncover Novel Regulatory Patterns Conserved in Lung Development and Tumors
Jean-Bosco Tagne, Sumeet Gupta, Adam C. Gower, Steven S. Shen, Saaket Varma, Meenakshi Lakshminarayanan, Yuxia Cao, Avrum Spira, Thomas L. Volkert, Maria I. Ramirez
PLoS One. 2012; 7(1): e29907. Published online 2012 January 5. doi: 10.1371/journal.pone.0029907
PMCID:
PMC3252372
Abstract Full Text PDF–1.0M Supplementary Material
High Phosphorus Diet-Induced Changes in NaPi-IIb Phosphate Transporter Expression in the Rat Kidney: DNA Microarray Analysis
Tatsuya Suyama, Shinji Okada, Tomoko Ishijima, Kota Iida, Keiko Abe, Yuji Nakai
PLoS One. 2012; 7(1): e29483. Published online 2012 January 3. doi: 10.1371/journal.pone.0029483
PMCID:
PMC3250443
Abstract Full Text PDF–675K Supplementary Material
A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections
Stewart T Chang, Nicolas Tchitchek, Debashis Ghosh, Arndt Benecke, Michael G Katze
BMC Syst Biol. 2011; 5: 202. Published online 2011 December 22. doi: 10.1186/1752-0509-5-202
PMCID:
PMC3297540
Abstract Full Text PDF–994K Supplementary Material
Anti-phospholipid induced murine fetal loss: novel protective effect of a peptide targeting the β2glycoprotein I phospholipid-binding site. Implications for human fetal loss
Yeny Martinez de la Torre, Francesca Pregnolato, Fabio D’Amelio, Claudia Grossi, Nicoletta DiSimone, Fabio Pasqualini, Manuela Nebuloni, Pojen Chen, Silvia Pierangeli, Niccolò Bassani, Federico Ambrogi, Maria-Orietta Borghi, Annunciata Vecchi, Massimo Locati, Pier-Luigi Meroni
J Autoimmun. Author manuscript; available in PMC 2013 May 1.
Published in final edited form as: J Autoimmun. 2012 May; 38(2-3): J209–J215. Published online 2011 December 22. doi: 10.1016/j.jaut.2011.11.009
PMCID:
PMC3313005
Free in PMC on 2013/05/01
Metabolite profiling of antidepressant drug action reveals novel drug targets beyond monoamine elevation
C Webhofer, P Gormanns, V Tolstikov, W Zieglgänsberger, I Sillaber, F Holsboer, C W Turck
Transl Psychiatry. 2011 December; 1(12): e58. Published online 2011 December 13. doi: 10.1038/tp.2011.56
PMCID:
PMC3309495
Abstract Full Text PDF–478K Supplementary Material
Evidence for Widespread Genomic Methylation in the Migratory Locust, Locusta migratoria (Orthoptera: Acrididae)
Katie L. Robinson, Donya Tohidi-Esfahani, Nathan Lo, Stephen J. Simpson, Gregory A. Sword
PLoS One. 2011; 6(12): e28167. Published online 2011 December 5. doi: 10.1371/journal.pone.0028167
PMCID:
PMC3230617
Abstract Full Text PDF–674K Supplementary Material
Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer
Ana C Tahira, Márcia S Kubrusly, Michele F Faria, Bianca Dazzani, Rogério S Fonseca, Vinicius Maracaja-Coutinho, Sergio Verjovski-Almeida, Marcel CC Machado, Eduardo M Reis
Mol Cancer. 2011; 10: 141. Published online 2011 November 13. doi: 10.1186/1476-4598-10-141
PMCID:
PMC3225313
Abstract Full Text PDF–2.7M Supplementary Material
Modeling the Transcriptional Consequences of Epidermal Growth Factor Receptor Ablation in Ras-Initiated Squamous Cancer
Lisa Nolan Wright, Andrew Ryscavage, Glenn Merlino, Stuart H. Yuspa
Clin Cancer Res. Author manuscript; available in PMC 2013 January 1.
Published in final edited form as: Clin Cancer Res. 2012 January 1; 18(1): 170–183. Published online 2011 November 8. doi: 10.1158/1078-0432.CCR-11-1349
PMCID:
PMC3251736
Free in PMC on 2013/01/01
Nuclear localization of γ-tubulin affects E2F transcriptional activity and S-phase progression
Greta Höög, Reihaneh Zarrizi, Kristoffer von Stedingk, Kristina Jonsson, Maria Alvarado-Kristensson
FASEB J. 2011 November; 25(11): 3815–3827. doi: 10.1096/fj.11-187484
PMCID:
PMC3205837
Abstract Full Text Supplementary Material
Integrating diverse genomic data using gene sets
Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani
Genome Biol. 2011; 12(10): R105. Published online 2011 October 21. doi: 10.1186/gb-2011-12-10-r105
PMCID:
PMC3333775
Abstract Full Text PDF–685K Supplementary Material
Cell-Type Independent MYC Target Genes Reveal a Primordial Signature Involved in Biomass Accumulation
Hongkai Ji, George Wu, Xiangcan Zhan, Alexandra Nolan, Cheryl Koh, Angelo De Marzo, Hoang Mai Doan, Jinshui Fan, Christopher Cheadle, Mohammad Fallahi, John L. Cleveland, Chi V. Dang, Karen I. Zeller
PLoS One. 2011; 6(10): e26057. Published online 2011 October 19. doi: 10.1371/journal.pone.0026057
PMCID:
PMC3198433
Abstract Full Text PDF–1.2M Supplementary Material
CAFET Algorithm Reveals Wnt/PCP Signature in Lung Squamous Cell Carcinoma
Yue Hu, Anna V. Galkin, Chunlei Wu, Venkateshwar Reddy, Andrew I. Su
PLoS One. 2011; 6(10): e25807. Published online 2011 October 10. doi: 10.1371/journal.pone.0025807
PMCID:
PMC3189939
Abstract Full Text PDF–658K Supplementary Material
Trachealess (Trh) regulates all tracheal genes during Drosophila embryogenesis
SeYeon Chung, Cy Chavez, Deborah J. Andrew
Dev Biol. Author manuscript; available in PMC 2012 December 1.
Published in final edited form as: Dev Biol. 2011 December 1; 360(1): 160–172. Published online 2011 September 22. doi: 10.1016/j.ydbio.2011.09.014
PMCID:
PMC3215829
Free in PMC on 2012/12/01
Comparison of genome-wide gene expression in suture- and alkali burn-induced murine corneal neovascularization
Changkai Jia, Wei Zhu, Shengwei Ren, Haijie Xi, Siyuan Li, Yiqiang Wang
Mol Vis. 2011; 17: 2386–2399. Published online 2011 September 2.
PMCID:
PMC3171500
Abstract Full Text PDF–1.8M
Significant Effects of Antiretroviral Therapy on Global Gene Expression in Brain Tissues of Patients with HIV-1-Associated Neurocognitive Disorders
Alejandra Borjabad, Susan Morgello, Wei Chao, Seon-Young Kim, Andrew I. Brooks, Jacinta Murray, Mary Jane Potash, David J. Volsky
PLoS Pathog. 2011 September; 7(9): e1002213. Published online 2011 September 1. doi: 10.1371/journal.ppat.1002213
PMCID:
PMC3164642
Abstract Full Text PDF–4.5M Supplementary Material
Genome wide expression profiling and mutagenesis studies reveal that LPS responsiveness appears to be absolutely dependent on TLR4 and MD-2 expression and is dependent upon intermolecular ionic interactions
Jianmin Meng, Mei Gong, Harry Björkbacka, Douglas T. Golenbock
J Immunol. Author manuscript; available in PMC 2012 October 1.
Published in final edited form as: J Immunol. 2011 October 1; 187(7): 3683–3693. Published online 2011 August 24. doi: 10.4049/jimmunol.1101397
PMCID:
PMC3178671
Free in PMC on 2012/10/01
Expression Profiling Reveals Differential Gene Induction Underlying Specific and Non-Specific Memory for Pheromones in Mice
Sudarshan C. Upadhya, Thuy K. Smith, Peter A. Brennan, Josyf C. Mychaleckyj, Ashok N. Hegde
Neurochem Int. Author manuscript; available in PMC 2012 November 1.
Published in final edited form as: Neurochem Int. 2011 November; 59(6): 787–803. Published online 2011 August 23. doi: 10.1016/j.neuint.2011.08.009
PMCID:
PMC3206202
Free in PMC on 2012/11/01
Exploring the genomic basis of pharmacoresistance in epilepsy: an integrative analysis of large-scale gene expression profiling studies on brain tissue from epilepsy surgery
Nasir Mirza, Olga Vasieva, Anthony Guy Marson, Munir Pirmohamed
Hum Mol Genet. 2011 November 15; 20(22): 4381–4394. Published online 2011 August 18. doi: 10.1093/hmg/ddr365
PMCID:
PMC3196887
Free in PMC on 2012/11/15
The Proteomic Signature of Aspergillus fumigatus During Early Development
Steven E. Cagas, Mohit Raja Jain, Hong Li, David S. Perlin
Mol Cell Proteomics. 2011 November; 10(11): M111.010108. Published online 2011 August 8. doi: 10.1074/mcp.M111.010108
PMCID:
PMC3226407
Free in PMC on 2012/11/01
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