| | Other Issues: previous | next | latest | archiveDatabase HIP2: An online database of human plasma proteins from healthy individuals Sudipto Saha, Scott H Harrison, Changyu Shen, Haixu Tang, Predrag Radivojac, Randy J Arnold, Xiang Zhang, and Jake Yue Chen PMCID: PMC2396660 New Jersey Center for Tourette Syndrome Sharing Repository: methods and sample description Gary A Heiman, Robert A King, and Jay A Tischfield PMCID: PMC2605751 Research Articles Biomarker expression patterns that correlate with high grade features in treatment naive, organ-confined prostate cancer Timothy J McDonnell, Nikhil S Chari, Jeong Hee Cho-Vega, Patricia Troncoso, Xuemei Wang, Carlos E Bueso-Ramos, Kevin Coombes, Shawn Brisbay, Remigio Lopez, George Prendergast, Christopher Logothetis, and Kim-Anh Do PMCID: PMC2227949 Microarray analysis in B cells among siblings with/without MS - role for transcription factor TCF2 Jagannadha R Avasarala, Sridar V Chittur, Ajish D George, and John A Tine PMCID: PMC2227948 Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors Markus Heidenblad, David Lindgren, Tord Jonson, Fredrik Liedberg, Srinivas Veerla, Gunilla Chebil, Sigurdur Gudjonsson, Åke Borg, Wiking Månsson, and Mattias Höglund PMCID: PMC2227947 Comparing the old and new generation SELDI-TOF MS: implications for serum protein profiling Marie-Christine W Gast, Judith YMN Engwegen, Jan HM Schellens, and Jos H Beijnen PMCID: PMC2263070 Robust SNP genotyping by multiplex PCR and arrayed primer extension Mohua Podder, Jian Ruan, Ben W Tripp, Zane E Chu, and Scott J Tebbutt PMCID: PMC2266772 Midkine is a NF-κB-inducible gene that supports prostate cancer cell survival Zongbing You, Ying Dong, Xiangtian Kong, Laurel A Beckett, Regina Gandour-Edwards, and Jonathan Melamed PMCID: PMC2254643 Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol Zhiqiang Pan, Ameeta K Agarwal, Tao Xu, Qin Feng, Scott R Baerson, Stephen O Duke, and Agnes M Rimando PMCID: PMC2330146 Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture Latha Satish, William A LaFramboise, David B O'Gorman, Sandra Johnson, Benjamin Janto, Bing Siang Gan, Mark E Baratz, Fen Z Hu, J Christopher Post, Garth D Ehrlich, and Sandeep Kathju PMCID: PMC2377253 Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists Jonathan D Mosley and Ruth A Keri PMCID: PMC2396170 The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis Adam I Riker, Steven A Enkemann, Oystein Fodstad, Suhu Liu, Suping Ren, Christopher Morris, Yaguang Xi, Paul Howell, Brandon Metge, Rajeev S Samant, Lalita A Shevde, Wenbin Li, Steven Eschrich, Adil Daud, Jingfang Ju, and Jaime Matta PMCID: PMC2408576 The role of the small intestine in the development of dietary fat-induced obesity and insulin resistance in C57BL/6J mice Nicole JW de Wit, Hanneke Bosch-Vermeulen, Philip J de Groot, Guido JEJ Hooiveld, Mechteld M Grootte Bromhaar, Jenny Jansen, Michael Müller, and Roelof van der Meer PMCID: PMC2396659 Classification of human cancers based on DNA copy number amplification modeling Samuel Myllykangas, Jarkko Tikka, Tom Böhling, Sakari Knuutila, and Jaakko Hollmén PMCID: PMC2397431 Investigating the complex genetic architecture of ankle-brachial index, a measure of peripheral arterial disease, in non-Hispanic whites Sharon LR Kardia, M Todd Greene, Eric Boerwinkle, Stephen T Turner, and Iftikhar J Kullo PMCID: PMC2412898 Pro-neural transcription factors as cancer markers Maria Vias, Charlie E Massie, Philip East, Helen Scott, Anne Warren, Zongxiang Zhou, Alexander Yu Nikitin, David E Neal, and Ian G Mills PMCID: PMC2413260 Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses Anat Zvi, Naomi Ariel, John Fulkerson, Jerald C Sadoff, and Avigdor Shafferman PMCID: PMC2442614 Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis Eleni M Tomazou, Vardhman K Rakyan, Gregory Lefebvre, Robert Andrews, Peter Ellis, David K Jackson, Cordelia Langford, Matthew D Francis, Liselotte Bäckdahl, Marcos Miretti, Penny Coggill, Diego Ottaviani, Denise Sheer, Adele Murrell, and Stephan Beck PMCID: PMC2430202 Generation of a non-small cell lung cancer transcriptome microarray Austin Tanney, Gavin R Oliver, Vadim Farztdinov, Richard D Kennedy, Jude M Mulligan, Ciaran E Fulton, Susan M Farragher, John K Field, Patrick G Johnston, D Paul Harkin, Vitali Proutski, and Karl A Mulligan PMCID: PMC2426710 Association of ABCB1 genetic variants with renal function in Africans and in Caucasians Murielle Bochud, Chin B Eap, Marc Maillard, Toby Johnson, Peter Vollenweider, Pascal Bovet, Robert C Elston, Sven Bergmann, Jacques S Beckmann, Dawn M Waterworth, Vincent Mooser, Anne Gabriel, and Michel Burnier PMCID: PMC2424071 Worldwide population differentiation at disease-associated SNPs Sean Myles, Dan Davison, Jeffrey Barrett, Mark Stoneking, and Nic Timpson PMCID: PMC2440747 A genome-wide search replicates evidence of a quantitative trait locus for circulating angiotensin I-converting enzyme (ACE) unlinked to the ACE gene Colin A McKenzie, Xiaofeng Zhu, Terrence E Forrester, Amy Luke, Adebowale A Adeyemo, Nourdine Bouzekri, and Richard S Cooper PMCID: PMC2442613 Genome wide SNP comparative analysis between EGFR and KRAS mutated NSCLC and characterization of two models of oncogenic cooperation in non-small cell lung carcinoma Hélène Blons, Karine Pallier, Delphine Le Corre, Claire Danel, Maxime Tremblay-Gravel, Claude Houdayer, Elizabeth Fabre-Guillevin, Marc Riquet, Philippe Dessen, and Pierre Laurent-Puig PMCID: PMC2527324 Whole genome assessment of the retinal response to diabetes reveals a progressive neurovascular inflammatory response Robert M Brucklacher, Kruti M Patel, Heather D VanGuilder, Georgina V Bixler, Alistair J Barber, David A Antonetti, Cheng-Mao Lin, Kathryn F LaNoue, Thomas W Gardner, Sarah K Bronson, and Willard M Freeman PMCID: PMC2442612 Molecular analysis of the vaginal response to estrogens in the ovariectomized rat and postmenopausal woman Scott A Jelinsky, Sung E Choe, Judy S Crabtree, Monette M Cotreau, Ewa Wilson, Kathryn Saraf, Andrew J Dorner, Eugene L Brown, Bryan J Peano, Xiaochun Zhang, Richard C Winneker, and Heather A Harris PMCID: PMC2453134 Pathway analysis reveals functional convergence of gene expression profiles in breast cancer Ronglai Shen, Arul M Chinnaiyan, and Debashis Ghosh PMCID: PMC2447843 Characterization of global transcription profile of normal and HPV-immortalized keratinocytes and their response to TNF treatment Lara Termini, Enrique Boccardo, Gustavo H Esteves, Roberto Hirata, Jr, Waleska K Martins, Anna Estela L Colo, E Jordão Neves, Luisa Lina Villa, and Luiz FL Reis PMCID: PMC2459201 Gene expression in periodontal tissues following treatment Thomas Beikler, Ulrike Peters, Karola Prior, Martin Eisenacher, and Thomas F Flemmig PMCID: PMC2491649 Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells Malene Herbsleb, Karin Birkenkamp-Demtroder, Thomas Thykjaer, Carsten Wiuf, Anne-Mette K Hein, Torben F Ørntoft, and Lars Dyrskjøt PMCID: PMC2492871 My sister's keeper?: genomic research and the identifiability of siblings Christopher A Cassa, Brian Schmidt, Isaac S Kohane, and Kenneth D Mandl PMCID: PMC2503988 Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines Neal AL Cody, Magdalena Zietarska, Ali Filali-Mouhim, Diane M Provencher, Anne-Marie Mes-Masson, and Patricia N Tonin PMCID: PMC2519080 Role of Caveolin 1, E-Cadherin, Enolase 2 and PKCalpha on resistance to methotrexate in human HT29 colon cancer cells Elisabet Selga, Cristina Morales, Véronique Noé, Miguel A Peinado, and Carlos J Ciudad PMCID: PMC2527490 Differential expression of genes mapping to recurrently abnormal chromosomal regions characterize neuroblastic tumours with distinct ploidy status Cinzia Lavarino, Idoia Garcia, Carlos Mackintosh, Nai-Kong V Cheung, Gema Domenech, José Ríos, Noelia Perez, Eva Rodríguez, Carmen de Torres, William L Gerald, Esperanza Tuset, Sandra Acosta, Helena Beleta, Enrique de Álava, and Jaume Mora PMCID: PMC2531130 An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma Domenica Ronchetti, Marta Lionetti, Laura Mosca, Luca Agnelli, Adrian Andronache, Sonia Fabris, Giorgio Lambertenghi Deliliers, and Antonino Neri PMCID: PMC2531129 Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males Peter C Charles, Brian D Alder, Eleanor G Hilliard, Jonathan C Schisler, Robert E Lineberger, Joel S Parker, Sabeen Mapara, Samuel S Wu, Andrea Portbury, Cam Patterson, and George A Stouffer PMCID: PMC2531187 Identification of a gene signature in cell cycle pathway for breast cancer prognosis using gene expression profiling data Jiangang Liu, Andrew Campen, Shuguang Huang, Sheng-Bin Peng, Xiang Ye, Mathew Palakal, A Keith Dunker, Yuni Xia, and Shuyu Li PMCID: PMC2551605 Transcriptomic signature of Bexarotene (Rexinoid LGD1069) on mammary gland from three transgenic mouse mammary cancer models Martin C Abba, Yuhui Hu, Carla C Levy, Sally Gaddis, Frances S Kittrell, Yun Zhang, Jamal Hill, Reid P Bissonnette, Daniel Medina, Powel H Brown, and C Marcelo Aldaz PMCID: PMC2563021 A high confidence, manually validated human blood plasma protein reference set Susann Schenk, Gary J Schoenhals, Gustavo de Souza, and Matthias Mann PMCID: PMC2563020 The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis Andrew H Sims, Graeme J Smethurst, Yvonne Hey, Michal J Okoniewski, Stuart D Pepper, Anthony Howell, Crispin J Miller, and Robert B Clarke PMCID: PMC2563019 Regulatory subunits of PKA define an axis of cellular proliferation/differentiation in ovarian cancer cells Chris Cheadle, Maria Nesterova, Tonya Watkins, Kathleen C Barnes, John C Hall, Antony Rosen, Kevin G Becker, and Yoon S Cho-Chung PMCID: PMC2577111 A genome-wide association study for late-onset Alzheimer's disease using DNA pooling Richard Abraham, Valentina Moskvina, Rebecca Sims, Paul Hollingworth, Angharad Morgan, Lyudmila Georgieva, Kimberley Dowzell, Sven Cichon, Axel M Hillmer, Michael C O'Donovan, Julie Williams, Michael J Owen, and George Kirov PMCID: PMC2570675 Gene expression in BMPR2 mutation carriers with and without evidence of Pulmonary Arterial Hypertension suggests pathways relevant to disease penetrance James West, Joy Cogan, Mark Geraci, Linda Robinson, John Newman, John A Phillips, Kirk Lane, Barbara Meyrick, and Jim Loyd PMCID: PMC2561034 A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining Bor-Sen Chen, Shih-Kuang Yang, Chung-Yu Lan, and Yung-Jen Chuang PMCID: PMC2567339 DNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage George S Watts, Bernard W Futscher, Nicholas Holtan, Koen DeGeest, Frederick E Domann, and Stephen L Rose PMCID: PMC2566571 The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study Allan P Davis, Cynthia G Murphy, Michael C Rosenstein, Thomas C Wiegers, and Carolyn J Mattingly PMCID: PMC2576347 The molecular basis of genistein-induced mitotic arrest and exit of self-renewal in embryonal carcinoma and primary cancer cell lines Christian RA Regenbrecht, Marc Jung, Hans Lehrach, and James Adjaye PMCID: PMC2577110 Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: Efficient identification of known microduplications and identification of a novel microduplication in ASMT Guiqing Cai, Lisa Edelmann, Juliet E Goldsmith, Ninette Cohen, Alisa Nakamine, Jennifer G Reichert, Ellen J Hoffman, Danielle M Zurawiecki, Jeremy M Silverman, Eric Hollander, Latha Soorya, Evdokia Anagnostou, Catalina Betancur, and Joseph D Buxbaum PMCID: PMC2588447 Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age Yohan Lee, Adrienne C Scheck, Timothy F Cloughesy, Albert Lai, Jun Dong, Haumith K Farooqi, Linda M Liau, Steve Horvath, Paul S Mischel, and Stanley F Nelson PMCID: PMC2596165 A global transcriptional view of apoptosis in human T-cell activation Min Wang, Dirk Windgassen, and Eleftherios T Papoutsakis PMCID: PMC2600644 The distinctive gastric fluid proteome in gastric cancer reveals a multi-biomarker diagnostic profile Oi Lian Kon, Tai-Tung Yip, Meng Fatt Ho, Weng Hoong Chan, Wai Keong Wong, Soo Yong Tan, Wai Har Ng, Siok Yuen Kam, Alvin KH Eng, Patrick Ho, Rosa Viner, Hock Soo Ong, and M Priyanthi Kumarasinghe PMCID: PMC2584050 Pathways affected by asbestos exposure in normal and tumour tissue of lung cancer patients Salla Ruosaari, Tuija Hienonen-Kempas, Anne Puustinen, Virinder K Sarhadi, Jaakko Hollmén, Sakari Knuutila, Juha Saharinen, Harriet Wikman, and Sisko Anttila PMCID: PMC2612681 Discovery of DNA methylation markers in cervical cancer using relaxation ranking Maté Ongenaert, G Bea A Wisman, Haukeline H Volders, Alice J Koning, Ate GJ van der Zee, Wim van Criekinge, and Ed Schuuring PMCID: PMC2605750 Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer Panagiotis A Konstantinopoulos, Elena Fountzilas, Kamana Pillay, Luiz F Zerbini, Towia A Libermann, Stephen A Cannistra, and Dimitrios Spentzos PMCID: PMC2613398 Global gene expression analyses of bystander and alpha particle irradiated normal human lung fibroblasts: Synchronous and differential responses Shanaz A Ghandhi, Benjamin Yaghoubian, and Sally A Amundson PMCID: PMC2627914 Technical Advances Predictive gene lists for breast cancer prognosis: A topographic visualisation study Mingmanas Sivaraksa and David Lowe PMCID: PMC2375896 Expression profiling with RNA from formalin-fixed, paraffin-embedded material Andrea Oberli, Vlad Popovici, Mauro Delorenzi, Anna Baltzer, Janine Antonov, Sybille Matthey, Stefan Aebi, Hans Jörg Altermatt, and Rolf Jaggi PMCID: PMC2359756 Genotyping panel for assessing response to cancer chemotherapy Zunyan Dai, Audrey C Papp, Danxin Wang, Heather Hampel, and Wolfgang Sadee PMCID: PMC2442111 An approach to analyse the specific impact of rapamycin on mRNA-ribosome association Raphael Genolet, Tanguy Araud, Laetitia Maillard, Pascale Jaquier-Gubler, and Joseph Curran PMCID: PMC2533349 Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease Jessica D Tenenbaum, Michael G Walker, Paul J Utz, and Atul J Butte PMCID: PMC2588448 |
