Literature DB >> 17875203

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

Paul M Krzyzanowski1, Miguel A Andrade-Navarro.   

Abstract

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.

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Year:  2007        PMID： 17875203      PMCID： PMC2375031          DOI： 10.1186/gb-2007-8-9-r193

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  84 in total

1.  Generation of a functional mammary gland from a single stem cell.

Authors:  Mark Shackleton; François Vaillant; Kaylene J Simpson; John Stingl; Gordon K Smyth; Marie-Liesse Asselin-Labat; Li Wu; Geoffrey J Lindeman; Jane E Visvader
Journal:  Nature       Date:  2006-01-05       Impact factor: 49.962

2.  A common regulatory region functions bidirectionally in transcriptional activation of the human CYP1A1 and CYP1A2 genes.

Authors:  Rika Ueda; Hiromi Iketaki; Kiyoshi Nagata; Shioko Kimura; Frank J Gonzalez; Kazutomi Kusano; Tsutomu Yoshimura; Yasushi Yamazoe
Journal:  Mol Pharmacol       Date:  2006-02-27       Impact factor: 4.436

3.  A high-resolution map of transcription in the yeast genome.

Authors:  Lior David; Wolfgang Huber; Marina Granovskaia; Joern Toedling; Curtis J Palm; Lee Bofkin; Ted Jones; Ronald W Davis; Lars M Steinmetz
Journal:  Proc Natl Acad Sci U S A       Date:  2006-03-28       Impact factor: 11.205

4.  Which cyclin E prevails as prognostic marker for breast cancer? Results from a retrospective study involving 635 lymph node-negative breast cancer patients.

Authors:  Anieta M Sieuwerts; Maxime P Look; Marion E Meijer-van Gelder; Mieke Timmermans; Anita M A C Trapman; Roberto Rodriguez Garcia; Miranda Arnold; Anneke J W Goedheer; Vanja de Weerd; Henk Portengen; Jan G M Klijn; John A Foekens
Journal:  Clin Cancer Res       Date:  2006-06-01       Impact factor: 12.531

5.  Activation of canonical Wnt pathway promotes proliferation of retinal stem cells derived from adult mouse ciliary margin.

Authors:  Toshihiro Inoue; Tetsushi Kagawa; Mikiko Fukushima; Takeshi Shimizu; Yutaka Yoshinaga; Shinji Takada; Hidenobu Tanihara; Tetsuya Taga
Journal:  Stem Cells       Date:  2005-10-13       Impact factor: 6.277

6.  Population-based case-control study of AhR (aryl hydrocarbon receptor) and CYP1A2 polymorphisms and breast cancer risk.

Authors:  Ji-Rong Long; Kathleen M Egan; Lisa Dunning; Xiao-Ou Shu; Qiuyin Cai; Hui Cai; Qi Dai; Jordan Holtzman; Yu-Tang Gao; Wei Zheng
Journal:  Pharmacogenet Genomics       Date:  2006-04       Impact factor: 2.089

Review 7.  Cytochromes P450 as versatile biocatalysts.

Authors:  Rita Bernhardt
Journal:  J Biotechnol       Date:  2006-03-03       Impact factor: 3.307

8.  Type I collagen in Hsp47-null cells is aggregated in endoplasmic reticulum and deficient in N-propeptide processing and fibrillogenesis.

Authors:  Yoshihito Ishida; Hiroshi Kubota; Akitsugu Yamamoto; Akira Kitamura; Hans Peter Bächinger; Kazuhiro Nagata
Journal:  Mol Biol Cell       Date:  2006-03-08       Impact factor: 4.138

9.  Metaphylogeny of 82 gene families sheds a new light on chordate evolution.

Authors:  Alexandre Vienne; Pierre Pontarotti
Journal:  Int J Biol Sci       Date:  2006-04-10       Impact factor: 6.580

10.  Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression.

Authors:  Karin Richter; Valtteri Wirta; Lina Dahl; Sara Bruce; Joakim Lundeberg; Leif Carlsson; Cecilia Williams
Journal:  BMC Genomics       Date:  2006-04-06       Impact factor: 3.969
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  7 in total

Review 1.  Deeply dissecting stemness: making sense to non-coding RNAs in stem cells.

Authors:  Shizuka Uchida; Pascal Gellert; Thomas Braun
Journal:  Stem Cell Rev Rep       Date:  2012-03       Impact factor: 5.739

2.  Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression.

Authors:  Cecilia Williams; Luisa Helguero; Karin Edvardsson; Lars-Arne Haldosén; Jan-Ake Gustafsson
Journal:  Breast Cancer Res       Date:  2009-05-08       Impact factor: 6.466

3.  Longitudinal single-cell RNA-seq of hESCs-derived retinal organoids.

Authors:  Shaojun Wang; Sergio Poli; Xiaoliang Liang; Guang-Hua Peng
Journal:  Sci China Life Sci       Date:  2021-01-27       Impact factor: 6.038

4.  Preimplantation development regulatory pathway construction through a text-mining approach.

Authors:  Elisa Donnard; Adriano Barbosa-Silva; Rafael L M Guedes; Gabriel R Fernandes; Henrique Velloso; Matthew J Kohn; Miguel A Andrade-Navarro; J Miguel Ortega
Journal:  BMC Genomics       Date:  2011-12-22       Impact factor: 3.969

5.  Recent developments in StemBase: a tool to study gene expression in human and murine stem cells.

Authors:  Reatha Sandie; Gareth A Palidwor; Matthew R Huska; Christopher J Porter; Paul M Krzyzanowski; Enrique M Muro; Carolina Perez-Iratxeta; Miguel A Andrade-Navarro
Journal:  BMC Res Notes       Date:  2009-03-10

6.  CellFinder: a cell data repository.

Authors:  Harald Stachelscheid; Stefanie Seltmann; Fritz Lekschas; Jean-Fred Fontaine; Nancy Mah; Mariana Neves; Miguel A Andrade-Navarro; Ulf Leser; Andreas Kurtz
Journal:  Nucleic Acids Res       Date:  2013-12-03       Impact factor: 16.971

7.  A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction.

Authors:  Prashant K Srivastava; Taraka Ramji Moturu; Priyanka Pandey; Ian T Baldwin; Shree P Pandey
Journal:  BMC Genomics       Date:  2014-05-08       Impact factor: 3.969
  7 in total

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