Atlas of gene expression in the developing kidney at microanatomic resolution.

A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84

Patterning a complex organ: branching morphogenesis and nephron segmentation in kidney development. Dev Cell (2010) 3.78

Advances in early kidney specification, development and patterning. Development (2009) 2.62

A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell (2010) 2.24

The GUDMAP database--an online resource for genitourinary research. Development (2011) 2.20

The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc (2010) 1.87

Mammalian kidney development: principles, progress, and projections. Cold Spring Harb Perspect Biol (2012) 1.80

Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor. PLoS Genet (2009) 1.77

The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epithelia. Am J Physiol Lung Cell Mol Physiol (2010) 1.61

Genes that confer the identity of the renin cell. J Am Soc Nephrol (2011) 1.52

BMP7 promotes proliferation of nephron progenitor cells via a JNK-dependent mechanism. Development (2009) 1.50

A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nat Genet (2017) 1.38

Temporal transcriptional profiling of somatic and germ cells reveals biased lineage priming of sexual fate in the fetal mouse gonad. PLoS Genet (2012) 1.38

Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell (2010) 1.34

Defining the molecular character of the developing and adult kidney podocyte. PLoS One (2011) 1.29

The pro-apoptotic protein Bim is a microRNA target in kidney progenitors. J Am Soc Nephrol (2011) 1.27

Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development. Development (2010) 1.21

Zebrafish nephrogenesis involves dynamic spatiotemporal expression changes in renal progenitors and essential signals from retinoic acid and irx3b. Dev Dyn (2011) 1.21

Spatial mapping of thymic stromal microenvironments reveals unique features influencing T lymphoid differentiation. Immunity (2009) 1.20

Clinically relevant subsets identified by gene expression patterns support a revised ontogenic model of Wilms tumor: a Children's Oncology Group Study. Neoplasia (2012) 1.19

Wt1 ablation and Igf2 upregulation in mice result in Wilms tumors with elevated ERK1/2 phosphorylation. J Clin Invest (2010) 1.17

FGF/EGF signaling regulates the renewal of early nephron progenitors during embryonic development. Development (2011) 1.16

Identification of a multipotent self-renewing stromal progenitor population during mammalian kidney organogenesis. Stem Cell Reports (2014) 1.14

Direct transcriptional reprogramming of adult cells to embryonic nephron progenitors. J Am Soc Nephrol (2013) 1.14

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development (2012) 1.13

Rhabdoid tumor: gene expression clues to pathogenesis and potential therapeutic targets. Lab Invest (2010) 1.11

Wilms tumor--a renal stem cell malignancy? Pediatr Nephrol (2011) 1.11

Notch pathway activation can replace the requirement for Wnt4 and Wnt9b in mesenchymal-to-epithelial transition of nephron stem cells. Development (2011) 1.10

Single cell dissection of early kidney development: multilineage priming. Development (2014) 1.09

Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways. PLoS One (2011) 1.07

The Renal Gene Ontology Annotation Initiative. Organogenesis (2010) 1.06

A high-resolution molecular atlas of the fetal mouse lower urogenital tract. Dev Dyn (2011) 1.06

Dynamics of salivary gland morphogenesis. J Dent Res (2011) 1.04

The number of fetal nephron progenitor cells limits ureteric branching and adult nephron endowment. Cell Rep (2014) 1.03

Subfractionation of differentiating human embryonic stem cell populations allows the isolation of a mesodermal population enriched for intermediate mesoderm and putative renal progenitors. Stem Cells Dev (2010) 1.02

Microarrays and RNA-Seq identify molecular mechanisms driving the end of nephron production. BMC Dev Biol (2011) 1.02

De novo lumen formation and elongation in the developing nephron: a central role for afadin in apical polarity. Development (2013) 0.98

RNA-Seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis: Hox supergenes. Dev Biol (2012) 0.98

Regenerative medicine for the kidney: stem cell prospects & challenges. Clin Transl Med (2013) 0.98

Mutations in SOX17 are associated with congenital anomalies of the kidney and the urinary tract. Hum Mutat (2010) 0.97

HNF1β is essential for nephron segmentation during nephrogenesis. J Am Soc Nephrol (2012) 0.97

Building the developmental oculome: systems biology in vertebrate eye development and disease. Wiley Interdiscip Rev Syst Biol Med (2010) 0.97

A Global Expression Switch Marks Pachytene Initiation during Mouse Male Meiosis. Genes (Basel) (2010) 0.96

Hs2st mediated kidney mesenchyme induction regulates early ureteric bud branching. Dev Biol (2010) 0.94

Orphan nuclear receptor Nur77 promotes acute kidney injury and renal epithelial apoptosis. J Am Soc Nephrol (2012) 0.92

Gene expression profiling at early organogenesis reveals both common and diverse mechanisms in foregut patterning. Dev Biol (2011) 0.91

Molecular anatomy of the kidney: what have we learned from gene expression and functional genomics? Pediatr Nephrol (2010) 0.91

Representing kidney development using the gene ontology. PLoS One (2014) 0.91

BMP signaling in the nephron progenitor niche. Pediatr Nephrol (2011) 0.91

A gene expression atlas of early craniofacial development. Dev Biol (2014) 0.90

Gene expression programs of mouse endothelial cells in kidney development and disease. PLoS One (2010) 0.90

Functional maturation of drug transporters in the developing, neonatal, and postnatal kidney. Mol Pharmacol (2011) 0.89

A protein kinase A and Wnt-dependent network regulating an intermediate stage in epithelial tubulogenesis during kidney development. Dev Biol (2012) 0.88

Comparative gene expression analysis of genital tubercle development reveals a putative appendicular Wnt7 network for the epidermal differentiation. Dev Biol (2010) 0.88

Subsets of very low risk Wilms tumor show distinctive gene expression, histologic, and clinical features. Clin Cancer Res (2009) 0.88

Changes in the gene expression programs of renal mesangial cells during diabetic nephropathy. BMC Nephrol (2012) 0.87

Development of the Mammalian Kidney. Curr Top Dev Biol (2016) 0.86

Induction and patterning of the metanephric nephron. Semin Cell Dev Biol (2014) 0.86

The nephrogenic potential of the transcription factors osr1, osr2, hnf1b, lhx1 and pax8 assessed in Xenopus animal caps. BMC Dev Biol (2011) 0.86

Comparison of the gene expression profiles from normal and Fgfrl1 deficient mouse kidneys reveals downstream targets of Fgfrl1 signaling. PLoS One (2012) 0.86

Hepatocyte nuclear factors 4α and 1α regulate kidney developmental expression of drug-metabolizing enzymes and drug transporters. Mol Pharmacol (2013) 0.85

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling. BMC Genomics (2011) 0.85

Concise review: can the intrinsic power of branching morphogenesis be used for engineering epithelial tissues and organs? Stem Cells Transl Med (2013) 0.85

Isolation and culture of cells from the nephrogenic zone of the embryonic mouse kidney. J Vis Exp (2011) 0.85

Renal organogenesis: what can it tell us about renal repair and regeneration? Organogenesis (2011) 0.84

Organic anion and cation SLC22 "drug" transporter (Oat1, Oat3, and Oct1) regulation during development and maturation of the kidney proximal tubule. PLoS One (2012) 0.84

Laser capture microdissection of embryonic cells and preparation of RNA for microarray assays. Methods Mol Biol (2014) 0.83

Genome-wide analysis of the p53 gene regulatory network in the developing mouse kidney. Physiol Genomics (2013) 0.83

Understanding the role of maternal diet on kidney development; an opportunity to improve cardiovascular and renal health for future generations. Nutrients (2015) 0.83

Intercellular transfer of GPRC5B via exosomes drives HGF-mediated outward growth. Curr Biol (2014) 0.83

SP8 regulates signaling centers during craniofacial development. Dev Biol (2013) 0.82

Sall1 balances self-renewal and differentiation of renal progenitor cells. Development (2014) 0.82

Molecular regulation of kidney development. Anat Cell Biol (2013) 0.81

The genetics and epigenetics of kidney development. Semin Nephrol (2013) 0.80

Microdissection of the gene expression codes driving nephrogenesis. Organogenesis (2011) 0.80

The proximal tubule is the primary target of injury and progression of kidney disease: role of the glomerulotubular junction. Am J Physiol Renal Physiol (2016) 0.80

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions. mSystems (2016) 0.78

FAK-Src signalling is important to renal collecting duct morphogenesis: discovery using a hierarchical screening technique. Biol Open (2013) 0.78

Building an atlas of gene expression driving kidney development: pushing the limits of resolution. Pediatr Nephrol (2013) 0.78

Hnf1beta and nephron segmentation. Pediatr Nephrol (2013) 0.78

Does Renal Repair Recapitulate Kidney Development? J Am Soc Nephrol (2016) 0.78

Heat-shock mediated overexpression of HNF1β mutations has differential effects on gene expression in the Xenopus pronephric kidney. PLoS One (2012) 0.77

Defining the genetic blueprint of kidney development. Pediatr Nephrol (2011) 0.76

The contribution of branching morphogenesis to kidney development and disease. Nat Rev Nephrol (2016) 0.75

Establishment of a Conditionally Immortalized Wilms Tumor Cell Line with a Homozygous WT1 Deletion within a Heterozygous 11p13 Deletion and UPD Limited to 11p15. PLoS One (2016) 0.75

Deducing the stage of origin of Wilms' tumours from a developmental series of Wt1-mutant mice. Dis Model Mech (2015) 0.75

Pathogenic pathways are activated in each major cell type of the glomerulus in the Cd2ap mutant mouse model of focal segmental glomerulosclerosis. BMC Nephrol (2015) 0.75

Ablation of the epithelial-specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number. Dev Dyn (2016) 0.75

Uromodulin: from physiology to rare and complex kidney disorders. Nat Rev Nephrol (2017) 0.75

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46

Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60

Genome-wide atlas of gene expression in the adult mouse brain. Nature (2006) 28.02

Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics (2002) 12.88

Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A (2003) 9.03

Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2002) 8.89

Functional interaction between beta-catenin and FOXO in oxidative stress signaling. Science (2005) 4.61

The cellular basis of kidney development. Annu Rev Cell Dev Biol (2006) 4.57

The gene mutated in autosomal recessive polycystic kidney disease encodes a large, receptor-like protein. Nat Genet (2002) 4.54

Liver-enriched transcription factors and hepatocyte differentiation. FASEB J (1996) 3.18

Distinct and sequential tissue-specific activities of the LIM-class homeobox gene Lim1 for tubular morphogenesis during kidney development. Development (2005) 2.98

Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics (2007) 2.56

Fate mapping using Cited1-CreERT2 mice demonstrates that the cap mesenchyme contains self-renewing progenitor cells and gives rise exclusively to nephronic epithelia. Dev Biol (2007) 2.48

Oxidative stress antagonizes Wnt signaling in osteoblast precursors by diverting beta-catenin from T cell factor- to forkhead box O-mediated transcription. J Biol Chem (2007) 2.37

A transcriptional network in polycystic kidney disease. EMBO J (2004) 2.21

TCF transcription factors, mediators of Wnt-signaling in development and cancer. Dev Biol (2002) 1.93

Interaction of FOXO with beta-catenin inhibits beta-catenin/T cell factor activity. J Biol Chem (2008) 1.93

Tmem27: a cleaved and shed plasma membrane protein that stimulates pancreatic beta cell proliferation. Cell Metab (2005) 1.92

A catalogue of gene expression in the developing kidney. Kidney Int (2003) 1.83

A variant nuclear protein in dedifferentiated hepatoma cells binds to the same functional sequences in the beta fibrinogen gene promoter as HNF-1. EMBO J (1988) 1.79

A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expr Patterns (2007) 1.77

The HNF-1 target collectrin controls insulin exocytosis by SNARE complex formation. Cell Metab (2005) 1.72

Mutation of hepatocyte nuclear factor-1beta inhibits Pkhd1 gene expression and produces renal cysts in mice. J Clin Invest (2004) 1.67

Changes in global gene expression patterns during development and maturation of the rat kidney. Proc Natl Acad Sci U S A (2001) 1.48

LFB1 and LFB3 homeoproteins are sequentially expressed during kidney development. Development (1992) 1.33

Changes in gene expression patterns in the ureteric bud and metanephric mesenchyme in models of kidney development. Kidney Int (2003) 1.23

Temporal and spatial transcriptional programs in murine kidney development. Physiol Genomics (2005) 1.11

Identification of kidney mesenchymal genes by a combination of microarray analysis and Sall1-GFP knockin mice. Mech Dev (2004) 1.11

Regulation of the expression of human organic anion transporter 3 by hepatocyte nuclear factor 1alpha/beta and DNA methylation. Mol Pharmacol (2006) 1.04

Comprehensive microarray analysis of Hoxa11/Hoxd11 mutant kidney development. Dev Biol (2006) 1.02

Laser capture-microarray analysis of Lim1 mutant kidney development. Genesis (2007) 1.00

The role for HNF-1beta-targeted collectrin in maintenance of primary cilia and cell polarity in collecting duct cells. PLoS One (2007) 0.96

Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol (2002) 16.75

Efficient recombination in diverse tissues by a tamoxifen-inducible form of Cre: a tool for temporally regulated gene activation/inactivation in the mouse. Dev Biol (2002) 13.87

A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68

Rifaximin therapy for patients with irritable bowel syndrome without constipation. N Engl J Med (2011) 10.03

Derivation of embryonic stem-cell lines from human blastocysts. N Engl J Med (2004) 8.89

Canonical Wnt signaling in differentiated osteoblasts controls osteoclast differentiation. Dev Cell (2005) 7.64

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res (2009) 7.34

Fate tracing reveals the pericyte and not epithelial origin of myofibroblasts in kidney fibrosis. Am J Pathol (2009) 7.34

Distinct roles for Hedgehog and canonical Wnt signaling in specification, differentiation and maintenance of osteoblast progenitors. Development (2006) 7.08

Evidence for an expansion-based temporal Shh gradient in specifying vertebrate digit identities. Cell (2004) 7.01

Intrinsic epithelial cells repair the kidney after injury. Cell Stem Cell (2008) 6.54

An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24

Six2 defines and regulates a multipotent self-renewing nephron progenitor population throughout mammalian kidney development. Cell Stem Cell (2008) 5.76

Eotaxin-3 and a uniquely conserved gene-expression profile in eosinophilic esophagitis. J Clin Invest (2006) 5.48

Wnt9b plays a central role in the regulation of mesenchymal to epithelial transitions underlying organogenesis of the mammalian urogenital system. Dev Cell (2005) 4.91

Acquisition of granule neuron precursor identity is a critical determinant of progenitor cell competence to form Shh-induced medulloblastoma. Cancer Cell (2008) 4.68

Mouse brain organization revealed through direct genome-scale TF expression analysis. Science (2004) 4.55

Genetic manipulation of periostin expression reveals a role in cardiac hypertrophy and ventricular remodeling. Circ Res (2007) 4.53

An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Genome Biol (2003) 4.49

Cardiac-specific deletion of Gata4 reveals its requirement for hypertrophy, compensation, and myocyte viability. Circ Res (2006) 4.41

Inhibition of miR-33a/b in non-human primates raises plasma HDL and lowers VLDL triglycerides. Nature (2011) 4.34

ApoE and clusterin cooperatively suppress Abeta levels and deposition: evidence that ApoE regulates extracellular Abeta metabolism in vivo. Neuron (2004) 4.21

Sonic hedgehog regulates proliferation and differentiation of mesenchymal cells in the mouse metanephric kidney. Development (2002) 4.18

Blockade of chronic type I interferon signaling to control persistent LCMV infection. Science (2013) 4.14

A mitogen gradient of dorsal midline Wnts organizes growth in the CNS. Development (2002) 4.13

Pattern of sequence variation across 213 environmental response genes. Genome Res (2004) 3.93

The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell (2012) 3.91

Canonical Wnt signaling regulates organ-specific assembly and differentiation of CNS vasculature. Science (2008) 3.86

Hedgehog signaling in the neural crest cells regulates the patterning and growth of facial primordia. Genes Dev (2004) 3.83

Sonic hedgehog is required for progenitor cell maintenance in telencephalic stem cell niches. Neuron (2003) 3.76

Revised nomenclature for avian telencephalon and some related brainstem nuclei. J Comp Neurol (2004) 3.69

The morphogen sonic hedgehog is an axonal chemoattractant that collaborates with netrin-1 in midline axon guidance. Cell (2003) 3.66

Efficient gene modulation in mouse epiblast using a Sox2Cre transgenic mouse strain. Mech Dev (2002) 3.49

WNT7b mediates macrophage-induced programmed cell death in patterning of the vasculature. Nature (2005) 3.44

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43

Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome. Physiol Genomics (2007) 3.37

Activation of IKKalpha target genes depends on recognition of specific kappaB binding sites by RelB:p52 dimers. EMBO J (2004) 3.32

Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network. Development (2008) 3.30

Avian brains and a new understanding of vertebrate brain evolution. Nat Rev Neurosci (2005) 3.29

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

Wnt11 and Ret/Gdnf pathways cooperate in regulating ureteric branching during metanephric kidney development. Development (2003) 3.08

A novel somatic mouse model to survey tumorigenic potential applied to the Hedgehog pathway. Cancer Res (2006) 3.06

Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics (2009) 3.03

Chronic epithelial kidney injury molecule-1 expression causes murine kidney fibrosis. J Clin Invest (2013) 3.03

Distinct and sequential tissue-specific activities of the LIM-class homeobox gene Lim1 for tubular morphogenesis during kidney development. Development (2005) 2.98

Sprouty1 is a critical regulator of GDNF/RET-mediated kidney induction. Dev Cell (2005) 2.95

Wnt/beta-catenin signaling regulates nephron induction during mouse kidney development. Development (2007) 2.92

Macrophage Wnt7b is critical for kidney repair and regeneration. Proc Natl Acad Sci U S A (2010) 2.87

The cdx genes and retinoic acid control the positioning and segmentation of the zebrafish pronephros. PLoS Genet (2007) 2.85

Sonic hedgehog signaling is required for expansion of granule neuron precursors and patterning of the mouse cerebellum. Dev Biol (2004) 2.77

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

A side order of stem cells: the SP phenotype. Stem Cells (2006) 2.73

Disruption of Fgf10/Fgfr2b-coordinated epithelial-mesenchymal interactions causes cleft palate. J Clin Invest (2004) 2.72

Notch2, but not Notch1, is required for proximal fate acquisition in the mammalian nephron. Development (2007) 2.70

Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol (2007) 2.70

Mouse proteome analysis. Genome Res (2003) 2.69

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb. Genes Dev (2008) 2.66

The cell surface membrane proteins Cdo and Boc are components and targets of the Hedgehog signaling pathway and feedback network in mice. Dev Cell (2006) 2.62

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res (2002) 2.60

Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development (2007) 2.60

Clusterin promotes amyloid plaque formation and is critical for neuritic toxicity in a mouse model of Alzheimer's disease. Proc Natl Acad Sci U S A (2002) 2.58

Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock. Mol Med (2007) 2.58

Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics (2007) 2.56

A Wnt7b-dependent pathway regulates the orientation of epithelial cell division and establishes the cortico-medullary axis of the mammalian kidney. Development (2009) 2.55

Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes Dev (2010) 2.50

GUDMAP: the genitourinary developmental molecular anatomy project. J Am Soc Nephrol (2008) 2.45

Genetic induction of proinflammatory immunity in children with biliary atresia. Lancet (2002) 2.44

Noncanonical Wnt signaling through G protein-linked PKCdelta activation promotes bone formation. Dev Cell (2007) 2.41

Ihh signaling is directly required for the osteoblast lineage in the endochondral skeleton. Development (2004) 2.39

Ectodermal Wnt3/beta-catenin signaling is required for the establishment and maintenance of the apical ectodermal ridge. Genes Dev (2003) 2.34

Neural crest origins of the neck and shoulder. Nature (2005) 2.31

A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nat Genet (2005) 2.26

A global role for EKLF in definitive and primitive erythropoiesis. Blood (2005) 2.24

Gene expression signature for biliary atresia and a role for interleukin-8 in pathogenesis of experimental disease. Hepatology (2014) 2.20

MicroRNA-21 promotes fibrosis of the kidney by silencing metabolic pathways. Sci Transl Med (2012) 2.20

The GUDMAP database--an online resource for genitourinary research. Development (2011) 2.20

Evaluation of myc E-box phylogenetic footprints in glycolytic genes by chromatin immunoprecipitation assays. Mol Cell Biol (2004) 2.19