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1. Full Text What is principal component analysis?
by Ringnér, Markus and Onkologi och Patologi, MV and Lund University and Oncology and Pathology, MV and Lunds universitet
Nature Biotechnology, ISSN 1087-0156, 03/2008, Volume 26, Issue 3, pp. 303 - 304
Principal component analysis is often incorporated into genome-wide expression studies, but what is it and how can it be used to explore high-dimensional data? 
GENE-EXPRESSION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | TUMORS | Gene Expression Profiling - methods | Computational Biology - methods | Algorithms | Principal Component Analysis - methods | Biotechnology | Principal components analysis | Gene expression | Research methodology | Genomics | Index Medicus | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Cancer and Oncology | Medicin och hälsovetenskap | Cancer och onkologi
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2. Full Text Exosomes reflect the hypoxic status of glioma cells and mediate hypoxia-dependent activation of vascular cells during tumor development
by Paulina Kucharzewska and Helena C. Christianson and Johanna E. Welch and Katrin J. Svensson and Erik Fredlund and Markus Ringnér and Matthias Mörgelin and Erika Bourseau-Guilmain and Johan Bengzon and Mattias Belting and Onkologi och Patologi, MV and Lund University and Tumörmikromiljön and StemTherapy: National Initiative on Stem Cells for Regenerative Therapy and Oncology and Pathology, MV and Neurosurgery and Neurokirurgi and Tumor microenvironment and Infektionsmedicin and Lunds universitet and Division of Infection Medicine (BMC)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 4/2013, Volume 110, Issue 18, pp. 7312 - 7317
Hypoxia, or low oxygen tension, is a major regulator of tumor development and aggressiveness. However, how cancer cells adapt to hypoxia and communicate with... 
Angiogenesis | Messenger RNA | Glioma | Cell lines | Hypoxia | Exosomes | Brain hypoxia | Endothelial cells | Tumors | Cancer | Blood vessels | CNS | Biomarker | ANGIOGENESIS | MULTIDISCIPLINARY SCIENCES | blood vessels | MICROVESICLES | biomarker | CANCER | GLIOBLASTOMA | AUTOCRINE VEGF | MICROENVIRONMENT | ENDOTHELIAL-CELLS | GROWTH | GENE-EXPRESSION | CAVEOLIN-1 | Exosomes - metabolism | Blood Vessels - pathology | Humans | Brain Neoplasms - pathology | Gene Expression Regulation, Neoplastic | Brain Neoplasms - blood supply | Neoplasm Proteins - metabolism | Neovascularization, Pathologic - pathology | Glioma - genetics | Cell Transformation, Neoplastic - genetics | Pericytes - pathology | Glioma - pathology | Female | Autocrine Communication | Paracrine Communication | Endothelial Cells - metabolism | Pericytes - metabolism | Brain Neoplasms - genetics | Signal Transduction - genetics | Transcriptome - genetics | Mice, SCID | Glioma - blood supply | Xenograft Model Antitumor Assays | Animals | Cell Line, Tumor | Neovascularization, Pathologic - genetics | Mice | Tissue Donors | Cell Hypoxia - genetics | Cell Transformation, Neoplastic - pathology | Endothelial Cells - pathology | Proteome - metabolism | Physiological aspects | Metastasis | Research | Gliomas | Health aspects | Cancer cells | Signal transduction | Genotype & phenotype | RNA-protein interactions | Cellular biology | Index Medicus | Biological Sciences | Clinical Medicine | Basic Medicine | Neurologi | Neurology | Medical and Health Sciences | Medicin och hälsovetenskap | Medicinska och farmaceutiska grundvetenskaper | Cell and Molecular Biology | Klinisk medicin | Cancer and Oncology | Cell- och molekylärbiologi | Cancer och onkologi
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3. Full Text GOBO: Gene expression-based outcome for breast cancer online
by Ringnér, Markus and Fredlund, Erik and Häkkinen, Jari and Borg, Åke and Staaf, Johan and Create Health and Onkologi och Patologi, MV and Lund University and Oncology and Pathology, MV and Lunds universitet
PLoS ONE, ISSN 1932-6203, 2011, Volume 6, Issue 3, pp. e17911 - e17911
Microarray-based gene expression analysis holds promise of improving prognostication and treatment decisions for breast cancer patients. However, the... 
MOLECULAR SUBTYPES | SURVIVAL | HISTOLOGIC GRADE | PREDICTOR | METASTASIS | INTEGRATIVE ANALYSIS | PROGNOSIS | CYCLIN B1 | BIOLOGY | STROMA | SIGNATURE | Cell Line, Tumor | Female | Gene Expression Profiling | Breast Neoplasms - genetics | Breast Neoplasms - pathology | Humans | Care and treatment | Analysis | Genes | Breast cancer | Genetic aspects | Gene expression | Cancer | Oncology | Identification | Metastasis | Subgroups | Datasets | Fibroblasts | Signatures | Immune system | Medical research | Wound healing | Principal components analysis | Assessments | Decision analysis | Patients | Studies | DNA microarrays | Medical prognosis | Cell lines | Breast | Internet | Tumors | Index Medicus | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Cancer and Oncology | Medicin och hälsovetenskap | Cancer och onkologi
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4. Full Text Landscape of somatic mutations in 560 breast cancer whole-genome sequences
by Nik-Zainal, Serena and Davies, Helen and Staaf, Johan and Ramakrishna, Manasa and Glodzik, Dominik and Zou, Xueqing and Martincorena, Inigo and Alexanov, Ludmil B and Martin, Sancha and Wedge, David C and van Loo, Peter and Ju, Young Seok and Smid, Marcel and Brinkman, Arie B and Morganella, Sano and Aure, Miriam R and Lingjærde, Ole Christian and Langerød, Anita and Ringnér, Markus and Ahn, Sung-Min and Boyault, Sanine and Brock, Jane E and Broeks, Annegien and Butler, Adam and Desmedt, Christine and Dirix, Luc and nov, Serge and Fatima, Aquila and Foekens, John A and Gerstung, Moritz and Hooijer, Gerrit K. J and Jang, Se Jin and Jones, David R and Kim, Hyung-Yong and King, Tari A and Krishnamurthy, Savitri and Lee, Hee Jin and Lee, Jeong-Yeon and Li, Yilong and McLaren, Stuart and Menzies, Anew and Mustonen, Ville and O'Meara, Sarah and Pauporté, Iris and Pivot, Xavier and Purdie, Colin A and Raine, Keiran and Ramakrishnan, Kamna and Roíguez-González, F. Germán and Romieu, Gilles and Sieuwerts, Anieta M and Simpson, Peter T and Shepherd, Rebecca and Stebbings, Lucy and Stefansson, Olafur A and Teague, Jon and Tommasi, Stefania and Treilleux, Isabelle and van den Eynden, Gert G and Vermeulen, Peter and Vincent-Salomon, Anne and Yates, Lucy and Caldas, Carlos and van't Veer, Laura and Tutt, Anew and Knappskog, Stian and Tan, Benita Kiat Tee and Jonkers, Jos and Borg, Åke and Ueno, Naoto T and Sotiriou, Christos and Viari, Alain and Futreal, P. Anew and Campbell, Peter J and Span, Paul N and van Laere, Steven and Lakhani, Sunil R and Eyfjord, Jorunn E and Thompson, Alastair M and Birney, Ewan and Stunnenberg, Henik G and van de Vijver, Marc J and Martens, John W. M and Børresen-Dale, Anne-Lise and Richardson, Anea L and Kong, Gu and Thomas, Gilles and Stratton, Michael R and Los Alamos National Lab. (LANL), Los Alamos, NM (United States) and Onkologi och Patologi, MV and Familial Breast Cancer and Lund University and MEMEG and Oncology and Pathology, MV and BioCARE: Biomarkers in Cancer Medicine improving Health Care, Education and Innovation and Lunds universitet and Familjär bröstcancer
Nature, ISSN 0028-0836, 2016, Volume 534, Issue 7605, pp. 47 - +
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational... 
GENE FUSIONS | TERT PROMOTER MUTATIONS | SIGNATURES | MULTIDISCIPLINARY SCIENCES | INVERTED REPEATS | COPY NUMBER | CARCINOMAS | DNA-REPAIR | TUMORS | HETEROZYGOSITY | DISCOVERY | Oncogenes - genetics | Recombinational DNA Repair - genetics | Genomics | Humans | Male | Mutation Rate | Mutation - genetics | Genome, Human - genetics | Breast Neoplasms - genetics | Mutagenesis | DNA Mutational Analysis | DNA Replication - genetics | Genes, BRCA2 | Female | DNA, Neoplasm - genetics | Genes, BRCA1 | Cohort Studies | Gene mutations | Oncology, Experimental | Cancer cells | Breast cancer | Genetic aspects | Research | Cancer | Nucleotide sequencing | Health aspects | Mutation (Biology) | DNA sequencing | DNA methylation | Genomes | Mutation | Genes | Deoxyribonucleic acid--DNA | Index Medicus | Life Sciences | BASIC BIOLOGICAL SCIENCES | Biological Science | Medical and Health Sciences | Medicin och hälsovetenskap | Breast Neoplasms | Klinisk medicin | Medicinsk genetik | Medical Genetics | DNA, Neoplasm | Oncogenes | Basic Medicine | Recombinational DNA Repair | Cell and Molecular Biology | DNA Replication | Clinical Medicine | Medicinska och farmaceutiska grundvetenskaper | Genome, Human | Cancer and Oncology | Cell- och molekylärbiologi | Cancer och onkologi
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5. Full Text Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
by Holm, Karolina and Hegardt, Cecilia and Staaf, Johan and Vallon-Christersson, Johan and Jönsson, Göran and Olsson, Håkan and Borg, Åke and Ringnér, Markus and Onkologi och Patologi, MV and EpiHealth: Epidemiology for Health and Lund University and Oncology and Pathology, MV and Lunds universitet
Breast Cancer Research, ISSN 1465-5411, 06/2010, Volume 12, Issue 3, pp. R36 - R36
Introduction: Five different molecular subtypes of breast cancer have been identified through gene expression profiling. Each subtype has a characteristic... 
HYPERMETHYLATION | MANAGEMENT | ONCOLOGY | B-CELL LYMPHOMAS | GENE-EXPRESSION | COMPARATIVE GENOMIC HYBRIDIZATION | IDENTIFICATION | POLYCOMB | SIGNATURE | TUMORS | SOMATIC MUTATIONS | Breast Neoplasms - classification | Prognosis | Oligonucleotide Array Sequence Analysis | Humans | Middle Aged | Survival Rate | Gene Dosage | Neoplasms, Basal Cell - pathology | Mutation - genetics | Breast - metabolism | Promoter Regions, Genetic - genetics | DNA Methylation | Neoplasms, Basal Cell - genetics | Breast Neoplasms - genetics | Breast Neoplasms - pathology | Polymerase Chain Reaction | CpG Islands | Genes, BRCA2 | Female | DNA, Neoplasm - genetics | Genes, BRCA1 | Neoplasms, Basal Cell - classification | Breast - pathology | Usage | DNA microarrays | DNA damage | Physiological aspects | Breast cancer | Genetic aspects | Research | Risk factors | Index Medicus | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Cancer and Oncology | Medicin och hälsovetenskap | Cancer och onkologi
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6. Full Text The CD44+/CD24- phenotype is enriched in basal-like breast tumors
by Honeth, Gabriella and Bendahl, Pär-Ola and Ringnér, Markus and Saal, Lao H and Gruvberger-Saal, Sofia K and Lövgren, Kristina and Grabau, Dorthe and Fernö, Mårten and Borg, Åke and Hegardt, Cecilia and Surgery (Lund) and Onkologi och Patologi, MV and Kirurgi, Lund and Lund University and Oncology and Pathology, MV and Lunds universitet
Breast Cancer Research, ISSN 1465-5411, 06/2008, Volume 10, Issue 3, pp. R53 - R53
Introduction Human breast tumors are heterogeneous and consist of phenotypically diverse cells. Breast cancer cells with a CD44(+)/CD24(-) phenotype have been... 
CANCER-CELLS | STEM-CELLS | MOLECULAR PORTRAITS | GENE | ONCOLOGY | ADJUVANT TAMOXIFEN | PROGNOSTIC MARKER | CD24 EXPRESSION | PATIENT SURVIVAL | CARCINOMA | ESTROGEN-RECEPTOR | Immunohistochemistry | Prevalence | Oligonucleotide Array Sequence Analysis | CD24 Antigen - metabolism | Humans | Middle Aged | Gene Expression Regulation, Neoplastic | Gene Expression Profiling | Hyaluronan Receptors - genetics | Phenotype | Breast Neoplasms - pathology | Hyaluronan Receptors - metabolism | Aged, 80 and over | Breast Neoplasms - blood | CD24 Antigen - genetics | Adult | Aged | Cohort Studies | Genes | Estrogen | Stem cells | Breast cancer | Genetic aspects | Progesterone | Gene expression | Index Medicus | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Cancer and Oncology | Medicin och hälsovetenskap | Cancer och onkologi
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7. Full Text Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks
by Ringnér, Markus and Antonescu, Cristina R and Meltzer, Paul S and Ladanyi, Marc and Khan, Javed and Wei, Jun S and Peterson, Carsten and Saal, Lao H and Westermann, Frank and Berthold, Frank and Schwab, Manfred and Onkologi och Patologi, MV and Lund University and Oncology and Pathology, MV and Beräkningsbiologi och biologisk fysik and Computational Biology and Biological Physics and Lunds universitet
Nature Medicine, ISSN 1078-8956, 06/2001, Volume 7, Issue 6, pp. 673 - 679
The purpose of this study was to develop a method of classifying cancers to specific diagnostic categories based on their gene expression signatures using... 
MEDICINE, RESEARCH & EXPERIMENTAL | EWINGS-SARCOMA | DIFFERENTIAL-DIAGNOSIS | HUMAN BREAST | CELL TUMORS | BIOCHEMISTRY & MOLECULAR BIOLOGY | PATTERNS | CELL BIOLOGY | ROUND-CELL | MOLECULAR CLASSIFICATION | CDNA MICROARRAYS | NEUROECTODERMAL TUMOR | GROWTH | Data Interpretation, Statistical | Rhabdomyosarcoma - diagnosis | Burkitt Lymphoma - classification | Oligonucleotide Array Sequence Analysis | Humans | Neuroblastoma - genetics | Neoplasms - classification | Sarcoma, Ewing - classification | Sarcoma, Ewing - diagnosis | Burkitt Lymphoma - diagnosis | Gene Expression Profiling | Neoplasms - diagnosis | Neuroblastoma - diagnosis | Neoplasms - genetics | Models, Biological | Neuroblastoma - classification | Burkitt Lymphoma - genetics | Rhabdomyosarcoma - classification | Rhabdomyosarcoma - genetics | Tumor Cells, Cultured | Sarcoma, Ewing - genetics | Neural Networks (Computer) | Index Medicus | Biofysiks | Biological Sciences | Biologi | Naturvetenskap | Natural Sciences | Biophysics
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8. Full Text Poor Prognosis in Carcinoma Is Associated with a Gene Expression Signature of Aberrant PTEN Tumor Suppressor Pathway Activity
by Lao H. Saal and Peter Johansson and Karolina Holm and Sofia K. Gruvberger-Saal and Qing-Bai She and Matthew Maurer and Susan Koujak and Adolfo A. Ferrando and Per Malmström and Lorenzo Memeo and Jorma Isola and Pär-Ola Bendahl and Neal Rosen and Hanina Hibshoosh and Markus Ringnér and Åke Borg and Ramon Parsons and Onkologi och Patologi, MV and Lund University and Oncology and Pathology, MV and Beräkningsbiologi och biologisk fysik and Computational Biology and Biological Physics and Lunds universitet
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 5/2007, Volume 104, Issue 18, pp. 7564 - 7569
Pathway-specific therapy is the future of cancer management. The oncogenic phosphatidylinositol 3-kinase (PI3K) pathway is frequently activated in solid... 
Datasets | Messenger RNA | Prognosis | Carcinoma | Genes | Signatures | Gene expression | Lesions | Tumors | Cancer | Stathmin | Breast cancer | Metastasis | Microarray | SURVIVAL | PROFILES | INSTABILITY | MULTIDISCIPLINARY SCIENCES | breast cancer | CLASSIFICATION | AKT | HUMAN BREAST-CANCER | stathmin | CELL LUNG-CANCER | OVEREXPRESSION | microarray | INHIBITION | metastasis | PTEN Phosphohydrolase - genetics | Signal Transduction | Humans | Gene Expression Regulation, Neoplastic | PTEN Phosphohydrolase - metabolism | Survival Rate | Treatment Outcome | Gene Expression Profiling | Phosphatidylinositol 3-Kinases - metabolism | Biomarkers, Tumor | Phosphatidylinositol 3-Kinases - genetics | Carcinoma - genetics | Carcinoma - metabolism | Carcinoma - pathology | Genetic aspects | Research | Oncology | Kinases | Medical prognosis | Index Medicus | Biological Sciences | Clinical Medicine | Medical and Health Sciences | Medicin och hälsovetenskap | Klinisk medicin | Cancer and Oncology | Cancer och onkologi
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9. Full Text CD44 isoforms are heterogeneously expressed in breast cancer and correlate with tumor subtypes and cancer stem cell markers
by Olsson, Eleonor and Honeth, Gabriella and Bendahl, Pär-Ola and Saal, Lao H and Gruvberger-Saal, Sofia and Ringnér, Markus and Vallon-Christersson, Johan and Jönsson, Göran and Holm, Karolina and Lövgren, Kristina and Fernö, Mårten and Grabau, Dorthe and Borg, Åke and Hegardt, Cecilia and Surgery (Lund) and Onkologi och Patologi, MV and Kirurgi, Lund and Lund University and Oncology and Pathology, MV and Lunds universitet
BMC Cancer, ISSN 1471-2407, 09/2011, Volume 11, Issue 1, pp. 418 - 418
Background: The CD44 cell adhesion molecule is aberrantly expressed in many breast tumors and has been implicated in the metastatic process as well as in the... 
SURVIVAL | MOLECULAR PORTRAITS | METASTASIS | ONCOLOGY | PHENOTYPE | ADJUVANT TAMOXIFEN | RECEPTOR | CARCINOMA | SIGNATURE | SOFTWARE | Breast Neoplasms - classification | Alternative Splicing | Humans | Gene Expression Regulation, Neoplastic | Kaplan-Meier Estimate | Gene Expression Profiling | RNA, Messenger - metabolism | Hyaluronan Receptors - genetics | Breast Neoplasms - genetics | Neoplastic Stem Cells - metabolism | Hyaluronan Receptors - metabolism | Biomarkers, Tumor - metabolism | Cell Line, Tumor | Breast Neoplasms - mortality | Female | Cluster Analysis | Protein Isoforms - genetics | Index Medicus | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Cancer and Oncology | Medicin och hälsovetenskap | Cancer och onkologi
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10. Full Text High Myc Pathway Activity and Low Stage of Neuronal Differentiation Associate with Poor Outcome in Neuroblastoma
by Erik Fredlund and Markus Ringnér and John M. Maris and Sven Påhlman and Onkologi och Patologi, MV and Lund University and Oncology and Pathology, MV and Lunds universitet and Institutionen för translationell medicin and Department of Translational Medicine
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 9/2008, Volume 105, Issue 37, pp. 14094 - 14099
The childhood cancer neuroblastoma arises in the developing sympathetic nervous system and is a genotypically and phenotypically heterogeneous disease.... 
Datasets | Health outcomes | Correlations | Genes | Cogs | Neuroblastoma | Signatures | Gene expression | Tumors | Cancer | Pathway analysis | MYCN | Differentiation | Myc | HIGH-RISK NEUROBLASTOMAS | differentiation | MULTIDISCIPLINARY SCIENCES | neuroblastoma | C-MYC | PHENOTYPE | CLASSIFICATION | SPECIFICATION | pathway analysis | IDENTIFICATION | TUMORS | N-MYC | LINEAGE | GENE-EXPRESSION SIGNATURES | Up-Regulation | Follow-Up Studies | Signal Transduction | Humans | Neuroblastoma - genetics | Risk Factors | Treatment Outcome | Gene Expression Profiling | Neuroblastoma - therapy | Proto-Oncogene Proteins c-myc - metabolism | Gene Amplification | Cell Differentiation | Neuroblastoma - metabolism | Proto-Oncogene Proteins c-myc - genetics | Neoplasm Staging | Neuroblastoma - pathology | Evaluation | Development and progression | Cell differentiation | Properties | Neurons | Index Medicus | Biological Sciences | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Cancer and Oncology | Medicin och hälsovetenskap | Cancer och onkologi
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11. Full Text Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
by Staaf, Johan and Vallon-Christersson, Johan and Lindgren, David and Juliusson, Gunnar and Rosenquist, Richard and Höglund, Mattias and Borg, Åke and Ringnér, Markus and Medicinska fakulteten and Medicinska och farmaceutiska vetenskapsområdet and Institutionen för genetik och patologi and Uppsala universitet
BMC Bioinformatics, ISSN 1471-2105, 10/2008, Volume 9, Issue 1, pp. 409 - 409
Background: Illumina Infinium whole genome genotyping (WGG)