Identification of novel stem cell markers using gap analysis of gene expression data

We describe a method for detecting marker genes in large heterogeneous collections of gene expression data. Markers are identified and characterized by the existence of demarcations in their expression values across the whole dataset, which suggest the presence of groupings of samples. We apply this method to DNA microarray data generated from 83 mouse stem cell related samples and describe 426 selected markers associated with differentiation to establish principles of stem cell evolution.

• Publication year

  2007

• Venue

  Genome Biology

• Publication date

  2007-09-17

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/gb-2007-8-9-r193PMID 17875203PMCID 2375031
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• R/parallel – speeding up bioinformatics analysis with R

  2008cited by this paper
• [''R"--project for statistical computing].

  2008cited by this paper
• Cytochrome P450 systems--biological variations of electron transport chains.

  2007cited by this paper
• Control of blood cell homeostasis in Drosophila larvae by the posterior signalling centre

  2007cited by this paper
• Gene function in early mouse embryonic stem cell differentiation

  2007cited by this paper
• Serpin-6 Expression Protects Embryonic Stem Cells from Lysis by Antigen-Specific CTL1

  2007cited by this paper
• Resident Endothelial Precursors in Muscle, Adipose, and Dermis Contribute to Postnatal Vasculogenesis

  2007cited by this paper
• Expression of the serine protease inhibitor neuroserpin in cells of the human myeloid lineage

  2007cited by this paper
• Generation of a functional mammary gland from a single stem cell

  2006cited by this paper
• Which cyclin E prevails as prognostic marker for breast cancer? Results from a retrospective study involving 635 lymph node-negative breast cancer patients.

  2006cited by this paper
• Activation of Canonical Wnt Pathway Promotes Proliferation of Retinal Stem Cells Derived from Adult Mouse Ciliary Margin

  2006cited by this paper
• Identification of a Novel Human Granzyme B Inhibitor Secreted by Cultured Sertoli Cells1

  2006cited by this paper
• Population-based case–control study of AhR (aryl hydrocarbon receptor) and CYP1A2 polymorphisms and breast cancer risk

  2006cited by this paper
• Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression

  2006cited by this paper
• A Common Regulatory Region Functions Bidirectionally in Transcriptional Activation of the Human CYP1A1 and CYP1A2 Genes

  2006cited by this paper
• Binary State Pattern Clustering: A Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer

  2006cited by this paper
• Metaphylogeny of 82 gene families sheds a new light on chordate evolution

  2006cited by this paper
• Critical Role for Ebf1 and Ebf2 in the Adipogenic Transcriptional Cascade

  2006cited by this paper
• Type I collagen in Hsp47-null cells is aggregated in endoplasmic reticulum and deficient in N-propeptide processing and fibrillogenesis.

  2006cited by this paper
• A high-resolution map of transcription in the yeast genome.

  2006cited by this paper
• Differential expression of the CD14/TLR4 complex and inflammatory signaling molecules following i.c.v. administration of LPS.

  2006cited by this paper
• An overview of the serpin superfamily

  2006cited by this paper
• Human breast epithelial stem cells and their regulation

  2006cited by this paper
• Cytochromes P450 as versatile biocatalysts.

  2006cited by this paper
• Stage specific gene expression of serpins and their cognate proteases during myeloid differentiation

  2006cited by this paper
• Sphere formation of ocular epithelial cells in the ciliary body is a reprogramming system for neural differentiation.

  2006cited by this paper
• Applications of DNA microarrays in biology.

  2005cited by this paper
• Suppression of Notch signalling by the COUP-TFII transcription factor regulates vein identity

  2005cited by this paper
• The Murine Cyp1a1 Gene Is Expressed in a Restricted Spatial and Temporal Pattern during Embryonic Development*

  2005cited by this paper
• Stem cell niche: structure and function.

  2005influential reference
• Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer.

  2005cited by this paper
• seven-up Controls switching of transcription factors that specify temporal identities of Drosophila neuroblasts.

  2005cited by this paper
• Characterization and Localization of Side Population Cells in Mouse Skin

  2005cited by this paper
• Multipotential differentiation of adipose tissue-derived stem cells.

  2005cited by this paper
• Isolation and Characterization of Multipotent Skin‐Derived Precursors from Human Skin

  2005cited by this paper
• Study of stem cell function using microarray experiments

  2005cited by this paper
• Inconsistencies over time in 5% of NetAffx probe-to-gene annotations

  2005cited by this paper
• Expression of cytochrome P4501b1 (Cyp1b1) during early murine development.

  2004cited by this paper
• Stem and Precursor Cells in the Nervous System

  2004cited by this paper
• NCBI GEO: mining millions of expression profiles—database and tools

  2004cited by this paper
• Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.

  2004cited by this paper
• Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer.

  2004cited by this paper
• Reinstatement of Rhodotorula colostri (Castelli) Lodder and Rhodotorula crocea Shifrine & Phaff, former synonyms of Rhodotorula aurantiaca (Saito) Lodder.

  2004cited by this paper
• Bioconductor: open software development for computational biology and bioinformatics

  2004cited by this paper
• Cancer stem cells in nervous system tumors

  2004cited by this paper
• Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays

  2004cited by this paper
• Insufficient folding of type IV collagen and formation of abnormal basement membrane-like structure in embryoid bodies derived from Hsp47-null embryonic stem cells.

  2004cited by this paper
• Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform.

  2004cited by this paper
• Cellular and molecular regulation of muscle regeneration.

  2004influential reference
• The Nuclear Orphan Receptor COUP-TFII Is Required for Limb and Skeletal Muscle Development

  2004cited by this paper
• A Complete Genetic Analysis of Neuronal Rab3 Function

  2004cited by this paper
• The functional landscape of mouse gene expression

  2004cited by this paper
• Global Identification of Human Transcribed Sequences with Genome Tiling Arrays

  2004cited by this paper
• Stem cells. 'Stemness' genes still elusive.

  2003cited by this paper
• CYP1B1 gene in endometrial cancer.

  2003cited by this paper
• The stem-cell menagerie.

  2003cited by this paper
• Selecting Differentially Expressed Genes from Microarray Experiments

  2003cited by this paper
• Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

  2003cited by this paper
• NetAffx: Affymetrix probesets and annotations

  2003cited by this paper
• The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells.

  2003cited by this paper
• 'Stemness' Genes Still Elusive

  2003cited by this paper
• Rab3D Is Not Required for Exocrine Exocytosis but for Maintenance of Normally Sized Secretory Granules

  2002cited by this paper
• Large-scale analysis of the human and mouse transcriptomes

  2002cited by this paper
• The utility of Ki-67 and BrdU as proliferative markers of adult neurogenesis.

  2002cited by this paper
• Cloning of a novel Olf-1/EBF-like gene, O/E-4, by degenerate oligo-based direct selection.

  2002cited by this paper
• Diagnosis of multiple cancer types by shrunken centroids of gene expression

  2002cited by this paper
• DNA microarray technology: devices, systems, and applications.

  2002cited by this paper
• Profiling alternative splicing on fiber-optic arrays

  2002cited by this paper
• Rab proteins as membrane organizers

  2001cited by this paper
• From hematopoiesis to neuropoiesis: Evidence of overlapping genetic programs

  2001cited by this paper
• A unique downstream estrogen responsive unit mediates estrogen induction of proteinase inhibitor-9, a cellular inhibitor of IL-1beta- converting enzyme (caspase 1).

  2001cited by this paper
• The Stanford Microarray Database

  2001cited by this paper
• Experimental annotation of the human genome using microarray technology

  2001cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• Direct isolation of human central nervous system stem cells.

  2000cited by this paper
• Retinal stem cells in the adult mammalian eye.

  2000cited by this paper
• The COE transcription factor Collier is a mediator of short-range Hedgehog-induced patterning of the Drosophila wing.

  1999cited by this paper
• The monomeric GTP binding protein, rab3a, is associated with the acrosome in mouse sperm

  1999cited by this paper
• Systematic determination of genetic network architecture

  1999cited by this paper
• Cluster analysis and display of genome-wide expression patterns.

  1998cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Cyp1a2(-/-) null mutant mice develop normally but show deficient drug metabolism.

  1996cited by this paper
• The nuclear receptor superfamily: the second decade.

  1995cited by this paper
• RT‐PCR cloning of Rab3 isoforms expressed in peritoneal mast cells

  1994cited by this paper
• Identification and characterization of Drosophila genes for synaptic vesicle proteins

  1993cited by this paper

• Longitudinal single-cell RNA-seq of hESCs-derived retinal organoids

  2021cites this paper
• DNA Methylation and miRNA Profiling of NSC Differentiation on Electrospun POMA Nanofibers

  2016cites this paper
• Therapeutic Implications of Newly Identified Stem Cell Populations from the Skin Dermis

  2015cites this paper
• Constitutive patterns of gene expression regulated by RNA-binding proteins

  2014cites this paper
• A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction

  2014cites this paper
• CellFinder: a cell data repository

  2013cites this paper
• MicroRNA-regulated gene networks during mammary cell differentiation are associated with breast cancer.

  2012cites this paper
• Deeply Dissecting Stemness: Making Sense to Non-Coding RNAs in Stem Cells

  2011cites this paper
• Preimplantation development regulatory pathway construction through a text-mining approach

  2011cites this paper
• Predicting molecular markers of development and regeneration through integrative analysis of high-throughput genomics data

  2010influential citation
• Recent developments in StemBase: a tool to study gene expression in human and murine stem cells

  2009cites this paper
• Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression

  2009influential citation