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GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists
Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Alberto Pascual-Montano
Genome Biol. 2007; 8(1): R3. Published online 2007 January 4. doi: 10.1186/gb-2007-8-1-r3
PMCID:
PMC1839127
Abstract Full Text PDF–1.4M Supplementary Material
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 Is Cited by the Following 54 Articles in this Archive:
Synergy Analysis Reveals Association between Insulin Signaling and Desmoplakin Expression in Palmitate Treated HepG2 Cells
Xuewei Wang, Aritro Nath, Xuerui Yang, Amanda Portis, S. Patrick Walton, Christina Chan
PLoS One. 2011; 6(11): e28138. Published online 2011 November 23. doi: 10.1371/journal.pone.0028138
PMCID:
PMC3223234
Abstract Full Text PDF–1.8M Supplementary Material
Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide
Sheila S. Teves, Steven Henikoff
Genes Dev. 2011 November 15; 25(22): 2387–2397. doi: 10.1101/gad.177675.111
PMCID:
PMC3222904
Abstract Full Text PDF–1.4M
Expression and Localization of microRNAs in Perinatal Rat Pancreas: Role of miR-21 in Regulation of Cholesterol Metabolism
Louise Larsen, Maiken W. Rosenstierne, Louise W. Gaarn, Annika Bagge, Lykke Pedersen, Christina M. Dahmcke, Jens H. Nielsen, Louise T. Dalgaard
PLoS One. 2011; 6(10): e25997. Published online 2011 October 11. doi: 10.1371/journal.pone.0025997
PMCID:
PMC3191174
Abstract Full Text PDF–875K Supplementary Material
Classification and Analysis of Regulatory Pathways Using Graph Property, Biochemical and Physicochemical Property, and Functional Property
Tao Huang, Lei Chen, Yu-Dong Cai, Kuo-Chen Chou
PLoS One. 2011; 6(9): e25297. Published online 2011 September 28. doi: 10.1371/journal.pone.0025297
PMCID:
PMC3182212
Abstract Full Text PDF–221K Supplementary Material
Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: Prediction and validation
Moumita Datta, Ananyo Choudhury, Ansuman Lahiri, Nitai P Bhattacharyya
BMC Genomics. 2011; 12: 463. Published online 2011 September 26. doi: 10.1186/1471-2164-12-463
PMCID:
PMC3228557
Abstract Full Text PDF–3.5M Supplementary Material
Functional Analysis beyond Enrichment: Non-Redundant Reciprocal Linkage of Genes and Biological Terms
Celia Fontanillo, Ruben Nogales-Cadenas, Alberto Pascual-Montano, Javier De Las Rivas
PLoS One. 2011; 6(9): e24289. Published online 2011 September 16. doi: 10.1371/journal.pone.0024289
PMCID:
PMC3174934
Abstract Full Text PDF–1.8M Supplementary Material
Improved haplotype-based detection of ongoing selective sweeps towards an application in Arabidopsis thaliana
Torsten Günther, Karl J Schmid
BMC Res Notes. 2011; 4: 232. Published online 2011 July 5. doi: 10.1186/1756-0500-4-232
PMCID:
PMC3148560
Abstract Full Text PDF–384K Supplementary Material
Zinc-finger transcription factors are associated with guanine quadruplex motifs in human, chimpanzee, mouse and rat promoters genome-wide
Pankaj Kumar, Vinod Kumar Yadav, Aradhita Baral, Parveen Kumar, Dhurjhoti Saha, Shantanu Chowdhury
Nucleic Acids Res. 2011 October; 39(18): 8005–8016. Published online 2011 July 4. doi: 10.1093/nar/gkr536
PMCID:
PMC3185432
Abstract Full Text PDF–7.0M Supplementary Material
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W316–W322. Published online 2011 June 27. doi: 10.1093/nar/gkr483
PMCID:
PMC3125809
Abstract Full Text PDF–1.9M
RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology
Aleksandra Gruca, Marek Sikora, Andrzej Polanski
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W293–W301. Published online 2011 June 27. doi: 10.1093/nar/gkr507
PMCID:
PMC3125813
Abstract Full Text PDF–2.4M
Metagenes Associated with Survival in Non-Small Cell Lung Cancer
Egon Urgard, Tõnu Vooder, Urmo Võsa, Kristjan Välk, Mingming Liu, Cheng Luo, Fabian Hoti, Retlav Roosipuu, Tarmo Annilo, Jukka Laine, Christopher M. Frenz, Liqing Zhang, Andres Metspalu
Cancer Inform. 2011; 10: 175–183. Published online 2011 June 2. doi: 10.4137/CIN.S7135
PMCID:
PMC3118451
Abstract Full Text PDF–897K Supplementary Material
ADGO 2.0: interpreting microarray data and list of genes using composite annotations
Sang-Mun Chi, Jin Kim, Seon-Young Kim, Dougu Nam
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W302–W306. Published online 2011 May 28. doi: 10.1093/nar/gkr392
PMCID:
PMC3125784
Abstract Full Text PDF–5.5M
TAFFEL: Independent Enrichment Analysis of gene sets
Mitja I Kurki, Jussi Paananen, Markus Storvik, Seppo Ylä-Herttuala, Juha E Jääskeläinen, Mikael von und zu Fraunberg, Garry Wong, Petri Pehkonen
BMC Bioinformatics. 2011; 12: 171. Published online 2011 May 19. doi: 10.1186/1471-2105-12-171
PMCID:
PMC3120704
Abstract Full Text PDF–1.2M Supplementary Material
RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity
Anja Nitzsche, Maciej Paszkowski-Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, Ingrid de Vries, Li Ding, Norbert Huebner, Matthias Mann, Hendrik G. Stunnenberg, Frank Buchholz
PLoS One. 2011; 6(5): e19470. Published online 2011 May 12. doi: 10.1371/journal.pone.0019470
PMCID:
PMC3093395
Abstract Full Text PDF–1.0M Supplementary Material
Consensus Pathways Implicated in Prognosis of Colorectal Cancer Identified Through Systematic Enrichment Analysis of Gene Expression Profiling Studies
Jesús Lascorz, Bowang Chen, Kari Hemminki, Asta Försti
PLoS One. 2011; 6(4): e18867. Published online 2011 April 25. doi: 10.1371/journal.pone.0018867
PMCID:
PMC3081819
Abstract Full Text PDF–173K Supplementary Material
Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development
Jesús Lascorz, Kari Hemminki, Asta Försti
J Carcinog. 2011; 10: 7. Published online 2011 March 24. doi: 10.4103/1477-3163.78268
PMCID:
PMC3072670
Abstract Full Text
LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data
Geert Geeven, Harold D. MacGillavry, Ruben Eggers, Marion M. Sassen, Joost Verhaagen, August B. Smit, Mathisca C. M. de Gunst, Ronald E. van Kesteren
Nucleic Acids Res. 2011 July; 39(13): 5313–5327. Published online 2011 March 21. doi: 10.1093/nar/gkr139
PMCID:
PMC3141251
Abstract Full Text PDF–5.4M Supplementary Material
Computational Analysis of HIV-1 Resistance Based on Gene Expression Profiles and the Virus-Host Interaction Network
Tao Huang, Zhongping Xu, Lei Chen, Yu-Dong Cai, Xiangyin Kong
PLoS One. 2011; 6(3): e17291. Published online 2011 March 4. doi: 10.1371/journal.pone.0017291
PMCID:
PMC3048858
Abstract Full Text PDF–233K Supplementary Material
A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes
Lee T. Sam, Doron Lipson, Tal Raz, Xuhong Cao, John Thompson, Patrice M. Milos, Dan Robinson, Arul M. Chinnaiyan, Chandan Kumar-Sinha, Christopher A. Maher
PLoS One. 2011; 6(3): e17305. Published online 2011 March 1. doi: 10.1371/journal.pone.0017305
PMCID:
PMC3046973
Abstract Full Text PDF–1.0M Supplementary Material
The Drosophila melanogaster transcriptome by paired-end RNA sequencing
Bryce Daines, Hui Wang, Liguo Wang, Yumei Li, Yi Han, David Emmert, William Gelbart, Xia Wang, Wei Li, Richard Gibbs, Rui Chen
Genome Res. 2011 February; 21(2): 315–324. doi: 10.1101/gr.107854.110
PMCID:
PMC3032934
Abstract Full Text PDF–770K
Analysis and Prediction of Translation Rate Based on Sequence and Functional Features of the mRNA
Tao Huang, Sibao Wan, Zhongping Xu, Yufang Zheng, Kai-Yan Feng, Hai-Peng Li, Xiangyin Kong, Yu-Dong Cai
PLoS One. 2011; 6(1): e16036. Published online 2011 January 6. doi: 10.1371/journal.pone.0016036
PMCID:
PMC3017080
Abstract Full Text PDF–247K Supplementary Material
A Widespread Distribution of Genomic CeMyoD Binding Sites Revealed and Cross Validated by ChIP-Chip and ChIP-Seq Techniques
Haiyan Lei, Tetsunari Fukushige, Wei Niu, Mihail Sarov, Valerie Reinke, Michael Krause
PLoS One. 2010; 5(12): e15898. Published online 2010 December 29. doi: 10.1371/journal.pone.0015898
PMCID:
PMC3012110
Abstract Full Text PDF–747K Supplementary Material
Yeast Biological Networks Unfold the Interplay of Antioxidants, Genome and Phenotype, and Reveal a Novel Regulator of the Oxidative Stress Response
Jose M. Otero, Manos A. Papadakis, D. B. R. K. Gupta Udatha, Jens Nielsen, Gianni Panagiotou
PLoS One. 2010; 5(10): e13606. Published online 2010 October 25. doi: 10.1371/journal.pone.0013606
PMCID:
PMC2963615
Abstract Full Text PDF–1.5M Supplementary Material
Prediction of the Clinical Outcome in Invasive Candidiasis Patients Based on Molecular Fingerprints of Five Anti-Candida Antibodies in Serum
Aida Pitarch, César Nombela, Concha Gil
Mol Cell Proteomics. 2011 January; 10(1): M110.004010. Published online 2010 September 21. doi: 10.1074/mcp.M110.004010
PMCID:
PMC3013459
Abstract Full Text
Cooperative and individualistic functions of the microRNAs in the miR-23a~27a~24-2 cluster and its implication in human diseases
Ravindresh Chhabra, Richa Dubey, Neeru Saini
Mol Cancer. 2010; 9: 232. Published online 2010 September 3. doi: 10.1186/1476-4598-9-232
PMCID:
PMC2940846
Abstract Full Text PDF–1.0M Supplementary Material
A simple method for gene expression and chromatin profiling of individual cell types within a tissue
Roger B. Deal, Steven Henikoff
Dev Cell. Author manuscript; available in PMC 2010 December 1.
Published in final edited form as: Dev Cell. 2010 June 15; 18(6): 1030–1040. doi: 10.1016/j.devcel.2010.05.013
PMCID:
PMC2905389
Abstract Full Text PDF–3.1M Supplementary Material
The E1A-Associated p400 Protein Modulates Cell Fate Decisions by the Regulation of ROS Homeostasis
Lise Mattera, Céline Courilleau, Gaëlle Legube, Takeshi Ueda, Rikiro Fukunaga, Martine Chevillard-Briet, Yvan Canitrot, Fabrice Escaffit, Didier Trouche
PLoS Genet. 2010 June; 6(6): e1000983. Published online 2010 June 10. doi: 10.1371/journal.pgen.1000983
Correction in:
PLoS Genet. 2010 July; 6(7): 10.1371/annotation/cc3111d5-d475-43ea-8d7f-f8b477b27164.
PMCID:
PMC2883595
Abstract Full Text PDF–1.0M Supplementary Material Correction
Association Rule Based Similarity Measures for the Clustering of Gene Expression Data
Prerna Sethi, Sathya Alagiriswamy
Open Med Inform J. 2010; 4: 63–73. Published online 2010 May 28. doi: 10.2174/1874431101004010063
PMCID:
PMC3096052
Abstract Full Text PDF–3.2M
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
Ignacio Medina, José Carbonell, Luis Pulido, Sara C. Madeira, Stefan Goetz, Ana Conesa, Joaquín Tárraga, Alberto Pascual-Montano, Ruben Nogales-Cadenas, Javier Santoyo, Francisco García, Martina Marbà, David Montaner, Joaquín Dopazo
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W210–W213. Published online 2010 May 15. doi: 10.1093/nar/gkq388
PMCID:
PMC2896184
Abstract Full Text PDF–80K Supplementary Material
Pro-tumorigenic Effects of miR-31 Loss in Mesothelioma
Sergey V. Ivanov, Chandra M. V. Goparaju, Peter Lopez, Jiri Zavadil, Ginat Toren-Haritan, Shai Rosenwald, Moshe Hoshen, Ayelet Chajut, Dalia Cohen, Harvey I. Pass
J Biol Chem. 2010 July 23; 285(30): 22809–22817. Published online 2010 May 12. doi: 10.1074/jbc.M110.100354
PMCID:
PMC2906272
Abstract Full Text Supplementary Material
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