Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

PubWeight™: 68.44‹?› | Rank: Top 0.01% | All-Time Top 1000

🔗 View Article (PMC 14539)

Published in Proc Natl Acad Sci U S A on January 02, 2001

Authors

C Li1, W H Wong

Author Affiliations

1: Departments of Statistics and Human Genetics, University of California, Los Angeles, CA 90095.

Articles citing this

(truncated to the top 100)

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74

Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72

Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58

Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48

Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol (2001) 15.02

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46

MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci U S A (2006) 10.11

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol (2011) 9.60

Significance analysis of time course microarray experiments. Proc Natl Acad Sci U S A (2005) 8.65

PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics (2005) 8.41

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol (2005) 8.32

MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat Cell Biol (2011) 8.21

Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res (2003) 8.08

Pan-cancer patterns of somatic copy number alteration. Nat Genet (2013) 7.73

A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12

Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proc Natl Acad Sci U S A (2001) 6.68

Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nat Med (2007) 6.55

Cell intrinsic alterations underlie hematopoietic stem cell aging. Proc Natl Acad Sci U S A (2005) 6.32

Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci U S A (2005) 6.26

c-Myc is an important direct target of Notch1 in T-cell acute lymphoblastic leukemia/lymphoma. Genes Dev (2006) 6.19

Loss of stearoyl-CoA desaturase-1 function protects mice against adiposity. Proc Natl Acad Sci U S A (2002) 6.00

A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell (2007) 5.99

MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78

Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biol (2001) 5.61

Frozen robust multiarray analysis (fRMA). Biostatistics (2010) 5.57

Direct conversion of human fibroblasts to multilineage blood progenitors. Nature (2010) 5.35

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res (2003) 5.13

Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics (2005) 5.08

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol (2002) 5.04

Anti-diabetic drugs inhibit obesity-linked phosphorylation of PPARgamma by Cdk5. Nature (2010) 5.01

p53 and Pten control neural and glioma stem/progenitor cell renewal and differentiation. Nature (2008) 5.00

Initiation of myoblast to brown fat switch by a PRDM16-C/EBP-beta transcriptional complex. Nature (2009) 4.98

TGF-beta-dependent pathogenesis of mitral valve prolapse in a mouse model of Marfan syndrome. J Clin Invest (2004) 4.85

Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol (2004) 4.83

Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A (2003) 4.69

Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS Med (2006) 4.63

Peripheral CD103+ dendritic cells form a unified subset developmentally related to CD8alpha+ conventional dendritic cells. J Exp Med (2010) 4.56

Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell (2009) 4.43

Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res (2004) 4.43

REST and stress resistance in ageing and Alzheimer's disease. Nature (2014) 4.38

Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics (2009) 4.32

Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol (2006) 4.27

An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res (2006) 4.26

Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature (2009) 4.13

Activity-dependent regulation of inhibitory synapse development by Npas4. Nature (2008) 4.10

Genomic counter-stress changes induced by the relaxation response. PLoS One (2008) 3.86

Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res (2004) 3.83

Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell (2009) 3.75

Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis. J Clin Oncol (2008) 3.74

Cross-regulation between Notch and p63 in keratinocyte commitment to differentiation. Genes Dev (2006) 3.72

In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A (2004) 3.65

Revisiting global gene expression analysis. Cell (2012) 3.63

Contextual extracellular cues promote tumor cell EMT and metastasis by regulating miR-200 family expression. Genes Dev (2009) 3.58

Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics (2004) 3.56

Sequence polymorphisms cause many false cis eQTLs. PLoS One (2007) 3.54

A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. Plant Cell (2008) 3.54

An androgen-regulated miRNA suppresses Bak1 expression and induces androgen-independent growth of prostate cancer cells. Proc Natl Acad Sci U S A (2007) 3.54

Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol (2005) 3.49

Gene expression and viral prodution in latently infected, resting CD4+ T cells in viremic versus aviremic HIV-infected individuals. Proc Natl Acad Sci U S A (2003) 3.47

Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential. J Exp Med (2003) 3.46

Identification of tumor-initiating cells in a p53-null mouse model of breast cancer. Cancer Res (2008) 3.45

Characterization and isolation of stem cell-enriched human hair follicle bulge cells. J Clin Invest (2006) 3.41

FoxOs cooperatively regulate diverse pathways governing neural stem cell homeostasis. Cell Stem Cell (2009) 3.37

Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res (2004) 3.37

Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant. J Med Genet (2008) 3.35

Human BAT possesses molecular signatures that resemble beige/brite cells. PLoS One (2012) 3.34

Transcriptional profiling of aging in human muscle reveals a common aging signature. PLoS Genet (2006) 3.34

ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res (2003) 3.31

Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication. Proc Natl Acad Sci U S A (2004) 3.30

A microRNA signature for a BMP2-induced osteoblast lineage commitment program. Proc Natl Acad Sci U S A (2008) 3.29

Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci U S A (2002) 3.29

Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney. Cancer Res (2009) 3.17

Identification of cellular genes targeted by KSHV-encoded microRNAs. PLoS Pathog (2007) 3.16

The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis. BMC Med Genomics (2008) 3.11

Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proc Natl Acad Sci U S A (2008) 3.10

PPARγ agonists induce a white-to-brown fat conversion through stabilization of PRDM16 protein. Cell Metab (2012) 3.09

The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc Natl Acad Sci U S A (2006) 3.07

Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Res (2003) 3.06

Dosage compensation is less effective in birds than in mammals. J Biol (2007) 3.04

LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci U S A (2005) 3.04

Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS One (2006) 3.03

Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A (2006) 3.03

Making sense of cancer genomic data. Genes Dev (2011) 3.01

MicroRNAs 221 and 222 bypass quiescence and compromise cell survival. Cancer Res (2008) 2.97

Modeling of DNA microarray data by using physical properties of hybridization. Proc Natl Acad Sci U S A (2003) 2.95

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics (2009) 2.90

Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One (2011) 2.89

Antibody responses to H-Y minor histocompatibility antigens correlate with chronic graft-versus-host disease and disease remission. Blood (2004) 2.89

Exon arrays provide accurate assessments of gene expression. Genome Biol (2007) 2.86

A HIF1alpha regulatory loop links hypoxia and mitochondrial signals in pheochromocytomas. PLoS Genet (2005) 2.85

Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell (2010) 2.84

TERT promotes epithelial proliferation through transcriptional control of a Myc- and Wnt-related developmental program. PLoS Genet (2007) 2.84

Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol (2005) 2.84

The MYCN oncogene is a direct target of miR-34a. Oncogene (2008) 2.80

Drosophila melanogaster MNK/Chk2 and p53 regulate multiple DNA repair and apoptotic pathways following DNA damage. Mol Cell Biol (2004) 2.75

Conditional mouse osteosarcoma, dependent on p53 loss and potentiated by loss of Rb, mimics the human disease. Genes Dev (2008) 2.74

Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages. J Exp Med (2012) 2.74

Using molecular classification to predict gains in maximal aerobic capacity following endurance exercise training in humans. J Appl Physiol (1985) (2010) 2.74

Articles by these authors

Analyzing high-density oligonucleotide gene expression array data. J Cell Biochem (2000) 16.73

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res (2001) 12.92

Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl (2001) 8.50

Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proc Natl Acad Sci U S A (2001) 6.68

Performance standards in positron emission tomography. J Nucl Med (1991) 1.78

Pain on injection of rocuronium: influence of two doses of lidocaine pretreatment. Br J Anaesth (2000) 1.37

Image improvement and design optimization of the time-of-flight PET. J Nucl Med (1983) 1.36

Cerebral ammonia metabolism in patients with severe liver disease and minimal hepatic encephalopathy. J Cereb Blood Flow Metab (1991) 1.35

Pten and p53 converge on c-Myc to control differentiation, self-renewal, and transformation of normal and neoplastic stem cells in glioblastoma. Cold Spring Harb Symp Quant Biol (2009) 1.29

Positron emission tomography with fluorine-18-deoxyglucose in the detection and staging of breast cancer. Cancer (1993) 1.20

Design and performance of POSICAM 6.5 BGO positron camera. J Nucl Med (1990) 1.18

Incorporation of correlated structural images in PET image reconstruction. IEEE Trans Med Imaging (1994) 1.14

Noninvasive assessment of coronary stenoses by myocardial perfusion imaging during pharmacologic coronary vasodilation. VIII. Clinical feasibility of positron cardiac imaging without a cyclotron using generator-produced rubidium-82. J Am Coll Cardiol (1986) 1.14

Temporal analysis of myocardial glucose metabolism by 2-[18F]fluoro-2-deoxy-D-glucose. Am J Physiol (1990) 0.99

Altered cerebral blood flow and glucose metabolism in patients with liver disease and minimal encephalopathy. J Cereb Blood Flow Metab (1991) 0.98

Evaluation of preoperative chemotherapy using PET with fluorine-18-fluorodeoxyglucose in breast cancer. J Nucl Med (1996) 0.94

Public awareness of hepatitis B infection: a population-based telephone survey in Hong Kong. Hong Kong Med J (2010) 0.94

Cutaneous vascular responses in diabetics. Microvasc Res (1975) 0.92

Detecting recurrent or residual lung cancer with FDG-PET. J Nucl Med (1995) 0.91

Extinction paradox and actual power scattered in light beam scattering: a two-dimensional study. J Opt Soc Am A Opt Image Sci Vis (2004) 0.91

Cervical and lumbar MRI in asymptomatic older male lifelong athletes: frequency of degenerative findings. J Comput Assist Tomogr (1996) 0.91

Comparison of fluorine-18-FDG PET and technetium-99m-MIBI SPECT in evaluation of musculoskeletal sarcomas. J Nucl Med (1996) 0.91

Protein folding simulation with genetic algorithm and supersecondary structure constraints. Proteins (1998) 0.91

Comparison of fluorine-18-fluorodeoxyglucose and carbon-11-methionine PET in detection of malignant tumors. J Nucl Med (1996) 0.89

Changes in blood flow in the skin and muscle with phototherapy. Pediatr Res (1974) 0.88

Evaluation of Streptomyces sp. strain g10 for suppression of Fusarium wilt and rhizosphere colonization in pot-grown banana plantlets. J Ind Microbiol Biotechnol (2005) 0.87

An organ-preserving selective arterial chemotherapy strategy for head and neck cancer. AJNR Am J Neuroradiol (1998) 0.85

Image restoration and reconstruction with a Bayesian approach. Med Phys (1998) 0.85

Changes in the capillary filtration coefficient of cutaneous vessels in women with premenstrual tension. Am J Obstet Gynecol (1972) 0.85

Low molecular weight dextran therapy for scleroderma. Effects of dextran 40 on blood flow and capillary filtration coefficient in scleroderma. Arch Dermatol (1974) 0.84

The coevolution of cell senescence and diploid sexual reproduction in unicellular organisms. Proc Natl Acad Sci U S A (2000) 0.83

Positron imaging of myocardial infarction with rubidium-82. J Nucl Med (1986) 0.83

En plaque meningioma of the basilar meninges and Meckel's cave: MR appearance. AJNR Am J Neuroradiol (1995) 0.81

Peripheral blood flow in the neonate; 1. Changes in total, skin, and muscle blood flow with gestational and postnatal age. Pediatr Res (1980) 0.80

Capillary filtration coefficient in the extremities of man in high environmental temperatures. Circ Res (1968) 0.80

Bayesian image processing in magnetic resonance imaging. Magn Reson Imaging (1991) 0.80

A comparison study of cerebral protection using Ginkgo biloba extract and Losartan on stroked rats. Neurosci Lett (2006) 0.79

Analysis of complex framing coil stability in a wide-necked aneurysm model. AJNR Am J Neuroradiol (2007) 0.79

Dynamic locomotor function in normals and patients with vertigo. Acta Otolaryngol (2001) 0.79

Extraspinal abnormalities detected on MR images of the spine. AJR Am J Roentgenol (1994) 0.78

Concerning 1e- transfer in reduction by dihydronicotinamide: reaction of oxidized flavin and flavin radical with N-benzyl-1,5-dihydronicotinamide. Proc Natl Acad Sci U S A (1982) 0.78

Perceived skill and utilisation of information technology in medical education among final year medical students, Universiti Putra Malaysia. Med J Malaysia (2005) 0.77

Bayesian restoration of PET images using Gibbs priors. Prog Clin Biol Res (1991) 0.77

Successful carotid endarterectomy in a patient with an aberrant branch from the common carotid artery. Ann R Coll Surg Engl (2013) 0.76

Relationship between bispectral index and effect-site EC(50) for propofol. Br J Anaesth (2006) 0.75

Corticosteroid-induced vasoconstriction studied by xenon 133 clearance. J Invest Dermatol (1973) 0.75

Cutaneous ischemia from epinephrine ion transfer and counterpressure. J Appl Physiol (1969) 0.75

Reactive depression. Xianggang Hu Li Za Zhi (1980) 0.75

Effect of release of adrenergic vasoconstrictor tone on exchange function of circulation in skeletal muscle. Clin Sci (1968) 0.75

Conditional entropy coding of VQ indexes for image compression. IEEE Trans Image Process (1999) 0.75

Effect of an extract of Erioglossum edule on the central nervous system. J Ethnopharmacol (1989) 0.75

Application of stereoscopic viewing to maximum intensity projection images obtained in MR angiography. AJNR Am J Neuroradiol (1994) 0.75

Dose efficiency and the effects of resolution and noise on detail perceptibility in radiographic magnification. Med Phys (1981) 0.75

Resolution in radiographic magnification. Med Phys (1982) 0.75

Determination of domoic acid in phytoplankton by high-performance liquid chromatography of the 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate derivative. J Agric Food Chem (1999) 0.75

Anaesthesia for a patient with long QT syndrome undergoing renal transplantation. Med J Malaysia (2005) 0.75

Physiological studies of the peripheral circulation in a patient with Quincke's disease. J Invest Dermatol (1967) 0.75

Highly flexible near-infrared metamaterials. Opt Express (2012) 0.75

Design and fabrication of a polymeric flat focal field arrayed waveguide grating. Opt Express (2005) 0.75

Molecular dynamic simulation of chaperonin-mediated protein folding. J Protein Chem (1998) 0.75

Manual procedure for direct microassay of serum glucose by use of 0 -toluidine, and its adaptation to the SMA 12-60 AutoAnalyzer. Clin Chem (1971) 0.75

Splenic rupture: first case of successful conservation after caesarean delivery and anticoagulation. J Obstet Gynaecol (2013) 0.75

Effect of adrenaline iontophoresis on capillary filtration in the forearm of man. Cardiovasc Res (1968) 0.75

The differential clearance of sodium iodine and iodoantipyrene from the skin. J Invest Dermatol (1968) 0.75

Correction for photon attenuation in SPECT: analytical framework, average attenuation factors, and a new hybrid approach. Phys Med Biol (1993) 0.75

MR detection of white matter disease of the brain in patients with HIV infection: fast spin-echo vs conventional spin-echo pulse sequences. AJR Am J Roentgenol (1994) 0.75

Linkage analysis with adjustment for covariates: a method combining peeling with Gibbs sampling. Cytogenet Cell Genet (1992) 0.75

Positron emission tomography of glucose metabolism in breast cancer. Potential for tumor detection, staging, and evaluation of chemotherapy. Ann N Y Acad Sci (1993) 0.75

Nonspecular effects on reflection from absorbing media at and around Brewster's dip. J Opt Soc Am A Opt Image Sci Vis (2006) 0.75

Blood flow and venous distensibility in the upper and lower extremities of newborn infants. Acta Paediatr Scand (1976) 0.75

Determination of serum thyroxine after dissociation from thyroxine-binding globulin in alkaline solution and absorption on dextran-coated charcoal. Clin Chem (1975) 0.75

Localization of Ga-67 citrate in plasma cell granuloma of the lung. Clin Nucl Med (1979) 0.75