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Evidence for large domains of similarly expressed genes in the Drosophila genome
Paul T Spellman, Gerald M Rubin
J Biol. 2002; 1(1): 5. Published online 2002 June 18.
PMCID:
PMC117248
Abstract Full Text PDF–578K Supplementary Material

Is Cited by the Following 128 Articles in this Archive:

A 3,000-Loci Transcription Map of Chromosome 3B Unravels the Structural and Functional Features of Gene Islands in Hexaploid Wheat
Camille Rustenholz, Frédéric Choulet, Christel Laugier, Jan Šafář, Hana Šimková, Jaroslav Doležel, Federica Magni, Simone Scalabrin, Federica Cattonaro, Sonia Vautrin, Arnaud Bellec, Hélène Bergès, Catherine Feuillet, Etienne Paux
Plant Physiol. 2011 December; 157(4): 1596–1608. Published online 2011 October 27. doi: 10.1104/pp.111.183921
PMCID:
PMC3327205
Free in PMC on 2012/12/01
Transcription factories in the context of the nuclear and genome organization
S. V. Razin, A. A. Gavrilov, A. Pichugin, M. Lipinski, O. V. Iarovaia, Yegor S. Vassetzky
Nucleic Acids Res. 2011 November; 39(21): 9085–9092. Published online 2011 August 30. doi: 10.1093/nar/gkr683
PMCID:
PMC3241665
Abstract Full Text PDF–136K
Regional Regulation of Transcription in the Bovine Genome
Arun Kommadath, Haisheng Nie, Martien A. M. Groenen, Marinus F. W. te Pas, Roel F. Veerkamp, Mari A. Smits
PLoS One. 2011; 6(6): e20413. Published online 2011 June 3. doi: 10.1371/journal.pone.0020413
PMCID:
PMC3108615
Abstract Full Text PDF–558K Supplementary Material
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos
Genome Biol. 2011; 12(5): R43. Published online 2011 May 11. doi: 10.1186/gb-2011-12-5-r43
PMCID:
PMC3219966
Abstract Full Text PDF–1.5M Supplementary Material
Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation
Claudia C Weber, Laurence D Hurst
Genome Biol. 2011; 12(3): R23. Published online 2011 March 17. doi: 10.1186/gb-2011-12-3-r23
PMCID:
PMC3129673
Abstract Full Text PDF–434K Supplementary Material
Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data
Guanghua Xiao, Xinlei Wang, Arkady B. Khodursky
J Am Stat Assoc. Author manuscript; available in PMC 2011 July 12.
Published in final edited form as: J Am Stat Assoc. 2011 March; 106(493): 61–72. doi: 10.1198/jasa.2010.ap0950
PMCID:
PMC3134274
Abstract Full Text PDF–6.1M
Gepoclu: a software tool for identifying and analyzing gene positional clusters in large-scale gene expression analysis
Tania Dottorini, Nicola Senin, Giorgio Mazzoleni, Kalle Magnusson, Andrea Crisanti
BMC Bioinformatics. 2011; 12: 34. Published online 2011 January 26. doi: 10.1186/1471-2105-12-34
PMCID:
PMC3040130
Abstract Full Text PDF–478K Supplementary Material
Genome-wide profiling of forum domains in Drosophila melanogaster
Nickolai A. Tchurikov, Olga V. Kretova, Dmitri V. Sosin, Ivan A. Zykov, Igor F. Zhimulev, Yuri V. Kravatsky
Nucleic Acids Res. 2011 May; 39(9): 3667–3685. Published online 2011 January 18. doi: 10.1093/nar/gkq1353
PMCID:
PMC3089479
Abstract Full Text PDF–17M Supplementary Material
Neighbourhood Continuity Is Not Required for Correct Testis Gene Expression in Drosophila
Lisa A. Meadows, Yuk Sang Chan, John Roote, Steven Russell
PLoS Biol. 2010 November; 8(11): e1000552. Published online 2010 November 30. doi: 10.1371/journal.pbio.1000552
PMCID:
PMC2994658
Abstract Full Text PDF–990K Supplementary Material
Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells
Lars-Oliver Tykocinski, Anna Sinemus, Esmail Rezavandy, Yanina Weiland, David Baddeley, Christoph Cremer, Stephan Sonntag, Klaus Willecke, Jens Derbinski, Bruno Kyewski
Proc Natl Acad Sci U S A. 2010 November 9; 107(45): 19426–19431. Published online 2010 October 21. doi: 10.1073/pnas.1009265107
PMCID:
PMC2984162
Abstract Full Text PDF–955K Supplementary Material
Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes
Fátima Al-Shahrour, Pablo Minguez, Tomás Marqués-Bonet, Elodie Gazave, Arcadi Navarro, Joaquín Dopazo
PLoS Comput Biol. 2010 October; 6(10): e1000953. Published online 2010 October 7. doi: 10.1371/journal.pcbi.1000953
PMCID:
PMC2951340
Abstract Full Text PDF–671K Supplementary Material
Global pattern of pairwise relationship in genetic network
Ao Yuan, Qingqi Yue, Victor Apprey, George E. Bonney
J Biomed Sci Eng. Author manuscript; available in PMC 2011 July 27.
Published in final edited form as: J Biomed Sci Eng. 2010 October 1; 3(10): 977–985. doi: 10.4236/jbise.2010.310128
PMCID:
PMC3144784
Abstract Full Text PDF–1.2M
Coordinated Expression Domains in Mammalian Genomes
Yong H. Woo, Michael Walker, Gary A. Churchill
PLoS One. 2010; 5(8): e12158. Published online 2010 August 18. doi: 10.1371/journal.pone.0012158
PMCID:
PMC2923606
Abstract Full Text PDF–2.7M Supplementary Material
Whole-Genome Expression Plasticity across Tropical and Temperate Drosophila melanogaster Populations from Eastern Australia
Mia T. Levine, Melissa L. Eckert, David J. Begun
Mol Biol Evol. 2011 January; 28(1): 249–256. Published online 2010 July 29. doi: 10.1093/molbev/msq197
PMCID:
PMC3002243
Abstract Full Text PDF–372K Supplementary Material
Meta-analysis of cancer gene expression signatures reveals new cancer genes, SAGE tags and tumor associated regions of co-regulation
Erşen Kavak, Mustafa Ünlü, Monica Nistér, Ahmet Koman
Nucleic Acids Res. 2010 November; 38(20): 7008–7021. Published online 2010 July 9. doi: 10.1093/nar/gkq574
PMCID:
PMC2978353
Abstract Full Text PDF–1.1M Supplementary Material
Integrating one-dimensional and three-dimensional maps of genomes
Natalia Naumova, Job Dekker
J Cell Sci. 2010 June 15; 123(12): 1979–1988. Published online 2010 June 2. doi: 10.1242/jcs.051631
PMCID:
PMC2880011
Abstract Full Text Supplementary Material
Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning
Heather A Amthauer, Costas Tsatsoulis
BMC Genomics. 2010; 11: 340. Published online 2010 May 28. doi: 10.1186/1471-2164-11-340
PMCID:
PMC2890565
Abstract Full Text PDF–1.3M
Evolution and spermatogenesis
Helen White-Cooper, Nina Bausek
Philos Trans R Soc Lond B Biol Sci. 2010 May 27; 365(1546): 1465–1480. doi: 10.1098/rstb.2009.0323
PMCID:
PMC2871925
Abstract Full Text PDF–533K
Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture
Shuwei Li, Ching-Hua Shih, Michael H Kohn
BMC Genomics. 2010; 11: 322. Published online 2010 May 24. doi: 10.1186/1471-2164-11-322
PMCID:
PMC2891614
Abstract Full Text PDF–1.4M Supplementary Material
Drosophila SAF-B Links the Nuclear Matrix, Chromosomes, and Transcriptional Activity
Catalina Alfonso-Parra, Keith A. Maggert
PLoS One. 2010; 5(4): e10248. Published online 2010 April 20. doi: 10.1371/journal.pone.0010248
PMCID:
PMC2857882
Abstract Full Text PDF–6.6M
Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression
Oleg V Grinchuk, Efthimios Motakis, Vladimir A Kuznetsov
BMC Genomics. 2010; 11(Suppl 1): S9. Published online 2010 February 10. doi: 10.1186/1471-2164-11-S1-S9
PMCID:
PMC2822537
Abstract Full Text Supplementary Material
Regional regulation of transcription in the chicken genome
Haisheng Nie, Richard PMA Crooijmans, John WM Bastiaansen, Hendrik-Jan Megens, Martien AM Groenen
BMC Genomics. 2010; 11: 28. Published online 2010 January 14. doi: 10.1186/1471-2164-11-28
PMCID:
PMC2817690
Abstract Full Text PDF–913K Supplementary Material
Intraclonal Protein Expression Heterogeneity in Recombinant CHO Cells
Warren Pilbrough, Trent P. Munro, Peter Gray
PLoS One. 2009; 4(12): e8432. Published online 2009 December 23. doi: 10.1371/journal.pone.0008432
PMCID:
PMC2793030
Abstract Full Text PDF–660K Supplementary Material
Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
Itai Yanai, Craig P. Hunter
Genome Res. 2009 December; 19(12): 2214–2220. doi: 10.1101/gr.093815.109
PMCID:
PMC2792179
Abstract Full Text PDF–800K
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews
Genome Biol. 2009; 10(9): R97. Published online 2009 September 16. doi: 10.1186/gb-2009-10-9-r97
PMCID:
PMC2768986
Abstract Full Text PDF–2.6M Supplementary Material
Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome
Huai-Kuang Tsai, Pei-Ying Huang, Cheng-Yan Kao, Daryi Wang
Int J Mol Sci. 2009 August; 10(8): 3658–3670. Published online 2009 August 21. doi: 10.3390/ijms10083658
PMCID:
PMC2812831
Abstract Full Text PDF–130K
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster
Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar
Bioinformatics. 2009 October 1; 25(19): 2473–2477. Published online 2009 July 24. doi: 10.1093/bioinformatics/btp462
PMCID:
PMC2752616
Abstract Full Text PDF–216K
Microarray data mining using Bioconductor packages
Haisheng Nie, Pieter BT Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen, Martien AM Groenen
BMC Proc. 2009; 3(Suppl 4): S9. Published online 2009 July 16. doi: 10.1186/1753-6561-3-S4-S9
PMCID:
PMC2712752
Abstract Full Text PDF–258K Supplementary Material
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler
Genome Biol. 2009; 10(7): R73. Published online 2009 July 9. doi: 10.1186/gb-2009-10-7-r73
PMCID:
PMC2728527
Abstract Full Text PDF–1.6M Supplementary Material
Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pair
Chien-Chang Huang, Wun-Shaing Wayne Chang
BMC Mol Biol. 2009; 10: 67. Published online 2009 July 3. doi: 10.1186/1471-2199-10-67
PMCID:
PMC2713978
Abstract Full Text PDF–1.6M Supplementary Material
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