My NCBISign In
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
Sami Kilpinen, Reija Autio, Kalle Ojala, Kristiina Iljin, Elmar Bucher, Henri Sara, Tommi Pisto, Matti Saarela, Rolf I Skotheim, Mari Björkman, John-Patrick Mpindi, Saija Haapa-Paananen, Paula Vainio, Henrik Edgren, Maija Wolf, Jaakko Astola, Matthias Nees, Sampsa Hautaniemi, Olli Kallioniemi
Genome Biol. 2008; 9(9): R139. Published online 2008 September 19. doi: 10.1186/gb-2008-9-9-r139
PMCID:
PMC2592717
Abstract Full Text PDF–2.2M Supplementary Material

Is Cited by the Following 45 Articles in this Archive:

Microsomal Glutathione Transferase 1 Protects Against Toxicity Induced by Silica Nanoparticles but Not by Zinc Oxide Nanoparticles
Jingwen Shi, Hanna L. Karlsson, Katarina Johansson, Vladimir Gogvadze, Lisong Xiao, Jiangtian Li, Terrance Burks, Alfonso Garcia-Bennett, Abdusalam Uheida, Mamoun Muhammed, Sanjay Mathur, Ralf Morgenstern, Valerian E. Kagan, Bengt Fadeel
ACS Nano. 2012 March 27; 6(3): 1925–1938. Published online 2012 February 5. doi: 10.1021/nn2021056
PMCID:
PMC3314313
Abstract Full Text PDF–1.8M Supplementary Material
Microsomal Glutathione Transferase 1 Protects Against Toxicity Induced by Silica Nanoparticles but Not by Zinc Oxide Nanoparticles
Jingwen Shi, Hanna L. Karlsson, Katarina Johansson, Vladimir Gogvadze, Lisong Xiao, Jiangtian Li, Terrance Burks, Alfonso Garcia-Bennett, Abdusalam Uheida, Mamoun Muhammed, Sanjay Mathur, Ralf Morgenstern, Valerian E. Kagan, Bengt Fadeel
ACS Nano. 2012 March 27; 6(3): 1925–1938. Published online 2012 February 5. doi: 10.1021/nn2021056
PMCID:
PMC3314313
Abstract Full Text PDF–1.8M Supplementary Material
Interaction with ErbB4 Promotes Hypoxia-inducible Factor-1α Signaling
Ilkka Paatero, Anne Jokilammi, Pekka T. Heikkinen, Kristiina Iljin, Olli-Pekka Kallioniemi, Frank E. Jones, Panu M. Jaakkola, Klaus Elenius
J Biol Chem. 2012 March 23; 287(13): 9659–9671. Published online 2012 February 3. doi: 10.1074/jbc.M111.299537
PMCID:
PMC3322979
Free in PMC on 2013/03/23
CD44 Expression in Oro-Pharyngeal Carcinoma Tissues and Cell Lines
Abirami Rajarajan, Angela Stokes, Balvinder K. Bloor, Rebecca Ceder, Hemini Desai, Roland C. Grafström, Edward W. Odell
PLoS One. 2012; 7(1): e28776. Published online 2012 January 5. doi: 10.1371/journal.pone.0028776
PMCID:
PMC3252301
Abstract Full Text PDF–1.6M
Maximizing biomarker discovery by minimizing gene signatures
Chang Chang, Junwei Wang, Chen Zhao, Jennifer Fostel, Weida Tong, Pierre R Bushel, Youping Deng, Lajos Pusztai, W Fraser Symmans, Tieliu Shi
BMC Genomics. 2011; 12(Suppl 5): S6. Published online 2011 December 23. doi: 10.1186/1471-2164-12-S5-S6
PMCID:
PMC3287502
Abstract Full Text PDF–811K Supplementary Material
Identification of proprotein convertase substrates using genome-wide expression correlation analysis
Hannu Turpeinen, Sampo Kukkurainen, Kati Pulkkinen, Timo Kauppila, Kalle Ojala, Vesa P Hytönen, Marko Pesu
BMC Genomics. 2011; 12: 618. Published online 2011 December 20. doi: 10.1186/1471-2164-12-618
PMCID:
PMC3258279
Abstract Full Text PDF–2.2M Supplementary Material
Membrane-Type-3 Matrix Metalloproteinase (MT3-MMP) Functions as a Matrix Composition-Dependent Effector of Melanoma Cell Invasion
Olga Tatti, Mariliina Arjama, Annamari Ranki, Stephen J. Weiss, Jorma Keski-Oja, Kaisa Lehti
PLoS One. 2011; 6(12): e28325. Published online 2011 December 2. doi: 10.1371/journal.pone.0028325
PMCID:
PMC3229567
Abstract Full Text PDF–819K Supplementary Material
Pancreatic Cancer Susceptibility Loci and Their Role in Survival
Cosmeri Rizzato, Daniele Campa, Nathalia Giese, Jens Werner, P. Sivaramakrishna Rachakonda, Rajiv Kumar, Michaela Schanné, William Greenhalf, Eithne Costello, Kay-tee Khaw, Tim J. Key, Afshan Siddiq, Justo Lorenzo-Bermejo, Barbara Burwinkel, John P. Neoptolemos, Markus W. Büchler, Jörg D. Hoheisel, Andrea Bauer, Federico Canzian
PLoS One. 2011; 6(11): e27921. Published online 2011 November 18. doi: 10.1371/journal.pone.0027921
PMCID:
PMC3220706
Abstract Full Text PDF–93K Supplementary Material
Characterization of Non-Specific Cytotoxic Cell Receptor Protein 1: A New Member of the Lectin-Type Subfamily of F-Box Proteins
Heini Kallio, Martti Tolvanen, Janne Jänis, Pei-wen Pan, Eeva Laurila, Anne Kallioniemi, Sami Kilpinen, Vilppu J. Tuominen, Jorma Isola, Jarkko Valjakka, Silvia Pastorekova, Jaromir Pastorek, Seppo Parkkila
PLoS One. 2011; 6(11): e27152. Published online 2011 November 7. doi: 10.1371/journal.pone.0027152
PMCID:
PMC3210139
Abstract Full Text PDF–2.0M Supplementary Material
Contribution of ARLTS1 Cys148Arg (T442C) Variant with Prostate Cancer Risk and ARLTS1 Function in Prostate Cancer Cells
Sanna Siltanen, Tiina Wahlfors, Martin Schindler, Outi R. Saramäki, John Patrick Mpindi, Leena Latonen, Robert L. Vessella, Teuvo L. J. Tammela, Olli Kallioniemi, Tapio Visakorpi, Johanna Schleutker
PLoS One. 2011; 6(10): e26595. Published online 2011 October 20. doi: 10.1371/journal.pone.0026595
PMCID:
PMC3197657
Abstract Full Text PDF–359K Supplementary Material
Genetic Examination of SETD7 and SUV39H1/H2 Methyltransferases and the Risk of Diabetes Complications in Patients With Type 1 Diabetes
Anna Syreeni, Assam El-Osta, Carol Forsblom, Niina Sandholm, Maikki Parkkonen, Lise Tarnow, Hans-Henrik Parving, Amy J. McKnight, Alexander P. Maxwell, Mark E. Cooper, Per-Henrik Groop, on behalf of the FinnDiane Study Group
Diabetes. 2011 November; 60(11): 3073–3080. Published online 2011 October 17. doi: 10.2337/db11-0073
PMCID:
PMC3198095
Free in PMC on 2012/11/01
Classification of unknown primary tumors with a data-driven method based on a large microarray reference database
Kalle A Ojala, Sami K Kilpinen, Olli P Kallioniemi
Genome Med. 2011; 3(9): 63. Published online 2011 October 17. doi: 10.1186/gm279
PMCID:
PMC3239238
Abstract Full Text PDF–575K Supplementary Material
SHARPIN is an endogenous inhibitor of beta1-integrin activation
Juha K. Rantala, Jeroen Pouwels, Teijo Pellinen, Stefan Veltel, Petra Laasola, Christopher S. Potter, Ted Duffy, John P. Sundberg, Olli Kallioniemi, Janet A. Askari, Martin Humphries, Maddy Parsons, Marko Salmi, Johanna Ivaska
Nat Cell Biol. Author manuscript; available in PMC 2012 January 13.
Published in final edited form as: Nat Cell Biol. 2011 September 25; 13(11): 1315–1324. doi: 10.1038/ncb2340
PMCID:
PMC3257806
Abstract Full Text PDF–3.4M Supplementary Material
The tumour antigen PRAME is a subunit of a Cul2 ubiquitin ligase and associates with active NFY promoters
Adalberto Costessi, Nawel Mahrour, Esther Tijchon, Rieka Stunnenberg, Marieke A Stoel, Pascal W Jansen, Dotan Sela, Skylar Martin-Brown, Michael P Washburn, Laurence Florens, Joan W Conaway, Ronald C Conaway, Hendrik G Stunnenberg
EMBO J. 2011 September 14; 30(18): 3786–3798. Published online 2011 August 5. doi: 10.1038/emboj.2011.262
PMCID:
PMC3173790
Free in PMC on 2012/09/14
LGI2 Truncation Causes a Remitting Focal Epilepsy in Dogs
Eija H. Seppälä, Tarja S. Jokinen, Masaki Fukata, Yuko Fukata, Matthew T. Webster, Elinor K. Karlsson, Sami K. Kilpinen, Frank Steffen, Elisabeth Dietschi, Tosso Leeb, Ranja Eklund, Xiaochu Zhao, Jennifer J. Rilstone, Kerstin Lindblad-Toh, Berge A. Minassian, Hannes Lohi
PLoS Genet. 2011 July; 7(7): e1002194. Published online 2011 July 28. doi: 10.1371/journal.pgen.1002194
PMCID:
PMC3145619
Abstract Full Text PDF–1.1M Supplementary Material
Expression cartography of human tissues using self organizing maps
Henry Wirth, Markus Löffler, Martin von Bergen, Hans Binder
BMC Bioinformatics. 2011; 12: 306. Published online 2011 July 27. doi: 10.1186/1471-2105-12-306
PMCID:
PMC3161046
Abstract Full Text PDF–7.9M Supplementary Material
Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas
Guro E Lind, Stine A Danielsen, Terje Ahlquist, Marianne A Merok, Kim Andresen, Rolf I Skotheim, Merete Hektoen, Torleiv O Rognum, Gunn I Meling, Geir Hoff, Michael Bretthauer, Espen Thiis-Evensen, Arild Nesbakken, Ragnhild A Lothe
Mol Cancer. 2011; 10: 85. Published online 2011 July 21. doi: 10.1186/1476-4598-10-85
PMCID:
PMC3166273
Abstract Full Text PDF–994K Supplementary Material
A Compendium of Canine Normal Tissue Gene Expression
Joseph Briggs, Melissa Paoloni, Qing-Rong Chen, Xinyu Wen, Javed Khan, Chand Khanna
PLoS One. 2011; 6(5): e17107. Published online 2011 May 31. doi: 10.1371/journal.pone.0017107
PMCID:
PMC3104984
Abstract Full Text PDF–3.3M Supplementary Material
GENT: Gene Expression Database of Normal and Tumor Tissues
Gwangsik Shin, Tae-Wook Kang, Sungjin Yang, Su-Jin Baek, Yong-Su Jeong, Seon-Young Kim
Cancer Inform. 2011; 10: 149–157. Published online 2011 May 9. doi: 10.4137/CIN.S7226
PMCID:
PMC3118449
Abstract Full Text PDF–2.1M Supplementary Material
Large Scale RNAi Screen Reveals That the Inhibitor of DNA Binding 2 (ID2) Protein Is Repressed by p53 Family Member p63 and Functions in Human Keratinocyte Differentiation
Ning Wu, David Castel, Marie-Anne Debily, Maria Alessandra Vigano, Olivier Alibert, Roberto Mantovani, Kristina Iljin, Paul-Henri Romeo, Xavier Gidrol
J Biol Chem. 2011 June 10; 286(23): 20870–20879. Published online 2011 April 10. doi: 10.1074/jbc.M110.169433
PMCID:
PMC3121489
Free in PMC on 2012/06/10
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data
Sami K Kilpinen, Kalle A Ojala, Olli P Kallioniemi
BioData Min. 2011; 4: 5. Published online 2011 March 31. doi: 10.1186/1756-0381-4-5
PMCID:
PMC3080808
Abstract Full Text PDF–3.5M Supplementary Material
A cell spot microarray method for production of high density siRNA transfection microarrays
Juha K Rantala, Rami Mäkelä, Anna-Riina Aaltola, Petra Laasola, John-Patrick Mpindi, Matthias Nees, Petri Saviranta, Olli Kallioniemi
BMC Genomics. 2011; 12: 162. Published online 2011 March 28. doi: 10.1186/1471-2164-12-162
PMCID:
PMC3073923
Abstract Full Text PDF–3.8M Supplementary Material
GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets
John Patrick Mpindi, Henri Sara, Saija Haapa-Paananen, Sami Kilpinen, Tommi Pisto, Elmar Bucher, Kalle Ojala, Kristiina Iljin, Paula Vainio, Mari Björkman, Santosh Gupta, Pekka Kohonen, Matthias Nees, Olli Kallioniemi
PLoS One. 2011; 6(2): e17259. Published online 2011 February 18. doi: 10.1371/journal.pone.0017259
Correction in:
PLoS One. 2011; 6(4): 10.1371/annotation/7d571883-faf0-4f66-86a2-806c36c4741c.
PMCID:
PMC3041823
Abstract Full Text PDF–1.5M Supplementary Material Correction
Arachidonic Acid Pathway Members PLA2G7, HPGD, EPHX2, and CYP4F8 Identified as Putative Novel Therapeutic Targets in Prostate Cancer
Paula Vainio, Santosh Gupta, Kirsi Ketola, Tuomas Mirtti, John-Patrick Mpindi, Pekka Kohonen, Vidal Fey, Merja Perälä, Frank Smit, Gerald Verhaegh, Jack Schalken, Kalle A. Alanen, Olli Kallioniemi, Kristiina Iljin
Am J Pathol. 2011 February; 178(2): 525–536. doi: 10.1016/j.ajpath.2010.10.002
PMCID:
PMC3128506
Abstract Full Text PDF–2.7M Supplementary Material
Identification of fusion genes in breast cancer by paired-end RNA-sequencing
Henrik Edgren, Astrid Murumagi, Sara Kangaspeska, Daniel Nicorici, Vesa Hongisto, Kristine Kleivi, Inga H Rye, Sandra Nyberg, Maija Wolf, Anne-Lise Borresen-Dale, Olli Kallioniemi
Genome Biol. 2011; 12(1): R6. Published online 2011 January 19. doi: 10.1186/gb-2011-12-1-r6
PMCID:
PMC3091304
Abstract Full Text PDF–1.9M Supplementary Material
SKP2 Oncogene Is a Direct MYC Target Gene and MYC Down-regulates p27KIP1 through SKP2 in Human Leukemia Cells
Gabriel Bretones, Juan C. Acosta, Juan M. Caraballo, Nuria Ferrándiz, M. Teresa Gómez-Casares, Marta Albajar, Rosa Blanco, Paula Ruiz, Wen-Chun Hung, M. Pilar Albero, Ignacio Perez-Roger, Javier León
J Biol Chem. 2011 March 18; 286(11): 9815–9825. Published online 2011 January 18. doi: 10.1074/jbc.M110.165977
PMCID:
PMC3059036
Abstract Full Text Supplementary Material
The essential role of evasion from cell death in cancer
Gemma Kelly, Andreas Strasser
Adv Cancer Res. Author manuscript; available in PMC 2011 July 1.
Published in final edited form as: Adv Cancer Res. 2011; 111: 39–96. doi: 10.1016/B978-0-12-385524-4.00002-7
PMCID:
PMC3128425
Abstract Full Text PDF–1.3M
Analysis of Kinase Gene Expression Patterns across 5681 Human Tissue Samples Reveals Functional Genomic Taxonomy of the Kinome
Sami Kilpinen, Kalle Ojala, Olli Kallioniemi
PLoS One. 2010; 5(12): e15068. Published online 2010 December 3. doi: 10.1371/journal.pone.0015068
PMCID:
PMC2997066
Abstract Full Text PDF–1.5M Supplementary Material
Integrative Functional Genomics Analysis of Sustained Polyploidy Phenotypes in Breast Cancer Cells Identifies an Oncogenic Profile for GINS2
Juha K Rantala, Henrik Edgren, Laura Lehtinen, Maija Wolf, Kristine Kleivi, Hans Kristian Moen Vollan, Anna-Riina Aaltola, Petra Laasola, Sami Kilpinen, Petri Saviranta, Kristiina Iljin, Olli Kallioniemi
Neoplasia. 2010 November; 12(11): 877–888.
PMCID:
PMC2981730
Abstract Full Text PDF–4.1M Supplementary Material
The vent-like homeobox gene VENTX promotes human myeloid differentiation and is highly expressed in acute myeloid leukemia
Vijay P. S. Rawat, Natalia Arseni, Farid Ahmed, Medhanie A. Mulaw, Silvia Thoene, Bernhard Heilmeier, Tim Sadlon, Richard J. D'Andrea, Wolfgang Hiddemann, Stefan K. Bohlander, Christian Buske, Michaela Feuring-Buske
Proc Natl Acad Sci U S A. 2010 September 28; 107(39): 16946–16951. Published online 2010 September 10. doi: 10.1073/pnas.1001878107
PMCID:
PMC2947867
Abstract Full Text PDF–841K Supplementary Material
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