Transcriptome coexpression map of human embryonic stem cells

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Li, Huai ^a   Liu, Ying ^a   Shin, Soojung ^a   Sun, Yu ^a   Loring, Jeanne F ^b   Mattson, Mark P ^a   Rao, Mahendra S ^c,d   Zhan, Ming ^a  

^a NATIONAL INSTITUTE ON AGING   (United States)

^b BURNHAM INSTITUTE   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d INVITROGEN CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTOME;

ARTICLE; CELL DIFFERENTIATION; CHROMOSOME; CORRELATION COEFFICIENT; CYTOGENETICS; EMBRYO; EMBRYONIC STEM CELL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE MAPPING; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN CELL; MEDICAL RESEARCH; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ANIMALS; CELLS, CULTURED; CHROMOSOMES, HUMAN, PAIR 17; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; GENES; GENOME, HUMAN; HUMANS; MICE; TRANSCRIPTION, GENETIC;

EID: 33749317764     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-103     Document Type: Article

References (41)

1. Cohen BA Mitra RD Hughes JD Church GM A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression Nat Genet 2000 26 2 183-186 10.1038/79896 11017073
2. Caron H van Schaik B van der Mee M Baas F Riggins G van Sluis P Hermus MC van Asperen R Boon K Voute PA Heisterkamp S van Kampen A Versteeg R The human transcriptome map: Clustering of highly expressed genes in chromosomal domains Science 2001 291 5507 1289-1292 10.1126/ science.1056794 11181992
3. Fujii T Dracheva T Player A Chacko S Clifford R Strausberg RL Buetow K Azumi N Travis WD Jen J A preliminary transcriptome map of non-small cell lung cancer Cancer Res 2002 62 12 3340-3346 12067970
4. Zhou Y Luoh SM Zhang Y Watanabe C Wu TD Ostland M Wood WI Zhang Z Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis Cancer Res 2003 63 18 5781-5784 14522899
5. Lercher MJ Blumenthal T Hurst LD Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes Genome Res 2003 13 2 238-243 420373 12566401 10.1101/gr.553803
6. Boutanaev AM Kalmykova AI Shevelyov YY Nurminsky DI Large clusters of co-expressed genes in the Drosophila genome Nature 2002 420 6916 666-669 10.1038/nature01216 12478293
7. Spellman PT Rubin GM Evidence for large domains of similarly expressed genes in the Drosophila genome J Biol 2002 1 1 5 117248 12144710 10.1186/ 1475-4924-1-5
8. Lercher MJ Urrutia AO Hurst LD Clustering of housekeeping genes provides a unified model of gene order in the human genome Nat Genet 2002 31 2 180-183 10.1038/ng887 11992122
9. Qiu P Benbow L Liu S Greene JR Wang L Analysis of a human brain transcriptome map BMC Genomics 2002 3 1 10 103672 11955288 10.1186/ 1471-2164-3-10
10. Abeyta MJ Clark AT Rodriguez RT Bodnar MS Pera RA Firpo MT Unique gene expression signatures of independently-derived human embryonic stem cell lines Hum Mol Genet 2004 13 6 601-608 10.1093/hmg/ddh068 14749348
11. Skottman H Mikkola M Lundin K Olsson C Stromberg AM Tuuri T Otonkoski T Hovatta O Lahesmaa R Gene expression signatures of seven individual human embryonic stem cell lines Stem Cells 2005
12. Rao RR Calhoun JD Qin X Rekaya R Clark JK Stice SL Comparative transcriptional profiling of two human embryonic stem cell lines Biotechnol Bioeng 2004 88 3 273-286 10.1002/bit.20245 15493035
13. Sperger JM Chen X Draper JS Antosiewicz JE Chon CH Jones SB Brooks JD Andrews PW Brown PO Thomson JA Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors Proc Natl Acad Sci U S A 2003 100 23 13350-13355 263817 14595015 10.1073/ pnas.2235735100
14. Richards M Tan SP Tan JH Chan WK Bongso A The transcriptome profile of human embryonic stem cells as defined by SAGE Stem Cells 2004 22 1 51-64 10.1634/stemcells.22-1-51 14688391
15. Brandenberger R Wei H Zhang S Lei S Murage J Fisk GJ Li Y Xu C Fang R Guegler K Rao MS Mandalam R Lebkowski J Stanton LW Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation Nat Biotechnol 2004 22 6 707-716 10.1038/ nbt971 15146197
16. Miura T Luo Y Khrebtukova I Brandenberger R Zhou D Thies RS Vasicek T Young H Lebkowski J Carpenter MK Rao MS Monitoring early differentiation events in human embryonic stem cells by massively parallel signature sequencing and expressed sequence tag scan Stem Cells Dev 2004 13 6 694-715 10.1089/scd.2004.13.694 15684837
17. Oliphant A Barker DL Stuelpnagel JR Chee MS BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping Biotechniques 2002 Suppl 56-58 60-51 12083399
18. Oliver B Parisi M Clark D Gene expression neighborhoods J Biol 2002 1 1 4 117247 12144705 10.1186/1475-4924-1-4
19. Cheung J Estivill X Khaja R MacDonald JR Lau K Tsui LC Scherer SW Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence Genome Biol 2003 4 4 R25 154576 12702206 10.1186/gb-2003-4-4-r25
20. Furey TS Haussler D Integration of the cytogenetic map with the draft human genome sequence Hum Mol Genet 2003 12 9 1037-1044 10.1093/hmg/ ddg113 12700172
21. Lee HK Hsu AK Sajdak J Qin J Pavlidis P Coexpression analysis of human genes across many microarray data sets Genome Res 2004 14 6 1085-1094 419787 15173114 10.1101/gr.1910904
22. Lord PW Stevens RD Brass A Goble CA Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation Bioinformatics 2003 19 10 1275-1283 10.1093/bioinformatics/ btg153 12835272
23. Reyal F Stransky N Bernard-Pierrot I Vincent-Salomon A de Rycke Y Elvin P Cassidy A Graham A Spraggon C Desille Y Fourquet A Nos C Pouillart P Magdelenat H Stoppa-Lyonnet D Couturier J Sigal-Zafrani B Asselain B Sastre-Garau X Delattre O Thiery JP Radvanyi F Visualizing chromosomes as transcriptome correlation maps: Evidence of chromosomal domains containing co-expressed genes - a study of 130 invasive ductal breast carcinomas Cancer Res 2005 65 4 1376-1383 10.1158/0008-5472.CAN-04-2706 15735024
24. Clark AT Rodriguez RT Bodnar MS Abeyta MJ Cedars MI Turek PJ Firpo MT Reijo Pera RA Human STELLAR, NANOG, and GDF3 genes are expressed in pluripotent cells and map to chromosome 12p13, a hotspot for teratocarcinoma Stem Cells 2004 22 2 169-179 10.1634/stemcells.22-2-169 14990856
25. Maitra A Arking DE Shivapurkar N Ikeda M Stastny V Kassauei K Sui G Cutler DJ Liu Y Brimble SN Noaksson K Hyllner J Schulz TC Zeng X Freed WJ Crook J Abraham S Colman A Sartipy P Matsui S Carpenter M Gazdar AF Rao M Chakravarti A Genomic alterations in cultured human embryonic stem cells Nat Genet 2005 37 10 1099-1103 10.1038/ng1631 16142235
26. Zeng X Chen J Liu Y Luo Y Schulz TC Robins AJ Rao MS Freed WJ BG01V: A variant human embryonic stem cell line which exhibits rapid growth after passaging and reliable dopaminergic differentiation Restor Neurol Neurosci 2004 22 6 421-428 15798361
27. Plaia TW Josephson R Liu Y Zeng X Ording C Toumadje A Brimble SN Sherrer ES Uhl EW Freed WJ Schulz TC Maitra A Rao MS Auerbach JM Characterization of a New NIH Registered Variant Human Embryonic Stem Cell Line BG01V: A Tool for Human Embryonic Stem Cell Research Stem Cells 2005 16293579
28. Bhattacharya B Miura T Brandenberger R Mejido J Luo Y Yang AX Joshi BH Ginis I Thies RS Amit M Lyons I Condie BG Itskovitz-Eldor J Rao MS Puri RK Gene expression in human embryonic stem cell lines: Unique molecular signature Blood 2004 103 8 2956-2964 10.1182/blood-2003-09-3314 15070671
29. Zhan M Miura T Xu X Rao MS Conservation and variation of gene regulation in embryonic stem cells assessed by comparative genomics Cell Biochem Biophys 2005 43 3 379-405 10.1385/CBB:43:3:379 16244364
30. Rao M Conserved and divergent paths that regulate self-renewal in mouse and human embryonic stem cells Dev Biol 2004 275 2 269-286 10.1016/ j.ydbio.2004.08.013 15501218
31. Moretti PA Davidson AJ Baker E Lilley B Zon LI D'Andrea RJ Molecular cloning of a human Vent-like homeobox gene Genomics 2001 76 (1-3) 21-29 10.1006/geno.2001.6574 11549314
32. Tanaka TS Kunath T Kimber WL Jaradat SA Stagg CA Usuda M Yokota T Niwa H Rossant J Ko MS Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity Genome Res 2002 12 12 1921-1928 187571 12466296 10.1101/ gr.670002
33. Zhan M Miura T Xu X Rao M Conservation and variation of gene regulation in embryonic stem cells assessed by comparative genomics Cell Biochem Biophy 2005
34. Niwa H Miyazaki J Smith AG Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells Nat Genet 2000 24 4 372-376 10.1038/74199 10742100
35. Maruyama M Ichisaka T Nakagawa M Yamanaka S Differential roles for Sox15 and Sox2 in transcriptional control in mouse embryonic stem cells J Biol Chem 2005 280 26 24371-24379 10.1074/jbc.M501423200 15863505
36. Brimble SN Zeng X Weiler DA Luo Y Liu Y Lyons IG Freed WJ Robins AJ Rao MS Schulz TC Karyotypic stability, genotyping, differentiation, feeder-free maintenance, and gene expression sampling in three human embryonic stem cell lines derived prior to August 9, 2001 Stem Cells Dev 2004 13 6 585-597 10.1089/scd.2004.13.585 15684826
37. NIH stem cell information home page http://stemcells.nih.gov/index.asp
38. NCBI reference sequence http://ncbi.nih.gov/RefSeq/
39. Home- Illumina, Inc http://www.illumina.com/
40. The gene ontology http://www.geneontology.org/
41. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci U S A 1998 95 25 14863-14868 24541 9843981 10.1073/pnas.95.25.14863