BMC Genomics Tutorials

1. Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR - how well do they correlate?

By Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR - how well do they correlate? Peter B Dallas , Nicholas G Gottardo , Martin J Firth , Alex H Beesley , Katrin Hoffmann , Philippa A Terry , Joseph R Freitas , Joanne M Boag , Aaron J Cummings and Ursula R Kees BMC Genomics 2005, 6:59     ... read more

2. Characterization of the GATC regulatory network in E. coli

By Characterization of the GATC regulatory network in E. coli Alessandra Riva1 , Marie-Odile Delorme1, 3 , Tony Chevalier2 , Nicolas Guilhot2 , Corinne Hénaut2 and Alain Hénaut1 1Laboratoire Génome et Informatique, UMR 8116, CNRS – Université d'Evry Val d'Essonne, ... read more

3. Inter-Platform comparability of microarrays in acute lymphoblastic leukemia

By Inter-Platform comparability of microarrays in acute lymphoblastic leukemia Stephanie A Mitchell1, 2 , Kevin M Brown3 , Michael M Henry1, 4 , Michelle Mintz1, 2 , Daniel Catchpoole5 , Bonnie LaFleur6 and Dietrich A Stephan7 1Research Center for Genetic Me... read more

4. Comparative analysis of somitogenesis related genes of the hairy/Enhancer of split class in Fugu and zebrafish

By Comparative analysis of somitogenesis related genes of the hairy/Enhancer of split class in Fugu and zebrafish Martin Gajewski and Chris Voolstra Universitaet zu Koeln, Institut fuer Genetik, Weyertal 121, 50931 Koeln, Germany BMC Genomics 2002, 3:21     doi:10.1186/1471-2164-3-21 The electronic version of this article is... read more

5. Identification, characterization and metagenome analysis of oocyte-specific genes organized in clusters in the mouse genome

By Background: Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the mouse, we have used an in silico subtraction methodology, and we have focused our attention on genes that are organized in genomic clusters. Results: In the present work, five... read more

6. Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes

By Background: The purpose of this work was to characterize the expression of drug and nutrient carriers along the anterior-posterior and crypt-villus axes of the intestinal epithelium and to study the validity of utilizing whole gut tissue rather than purified epithelial cells to examine regional variations in gene expression. Results: We have characterized the mRNA expression profiles of 76 % of... read more

7. Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: The Human GPCR-DB

By Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: The Human GPCR-DB Database Claes Wahlestedt1 , Anthony J Brookes2 and Salim Mottagui-Tabar1 1Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, 17177 Stockholm, Swe... read more

8. In vitroidentification and in silicoutilization of interspecies sequence similarities using GeneChip(R)technology

By In vitroidentification and in silicoutilization of interspecies sequence similarities using GeneChip(R)technology Dmitry N Grigoryev , Shwu-Fan Ma , Brett A Simon , Rafael A Irizarry , Shui Q Ye and Joe G.N Garcia BMC Genomics 2005, 6:62     doi:10.1186/1471-2164-6-62 Published   4 May 2005 read more

9. Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker discovery

By Gene expression profile of cervical tissue compared to exfoliated cells: Impact on biomarker discovery Martin Steinau , Daisy R Lee , Mangalathu S Rajeevan , Suzanne D Vernon , Mack T Ruffin and Elizabeth R Unger BMC Genomics 2005, 6:64     doi:10.1186/1471-2164-6-64 Published   5 May 2005 read more

10. Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data

By Background: Although the organisation of the bacterial chromosome is an area of active research, little is known yet on that subject. The difficulty lies in the fact that the system is dynamic and difficult to observe directly. The advent of massive hybridisation techniques opens the way to further studies of the chromosomal structure because the genes that are co-expressed, as identified by micr... read more

11. Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family

By Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family Einari A Niskanen1 , Vesa P Hytönen1 , Alessandro Grapputo1 , Henri R Nordlund1, 3 , Markku S Kulomaa1, 3 and Olli H Laitinen2 1NanoScience Center, Department of Biologic... read more

12. Identification and characterization of a novel mammalian Mg2+transporter with channel-like properties

By Identification and characterization of a novel mammalian Mg2+transporter with channel-like properties Angela Goytain and Gary A Quamme BMC Genomics 2005, 6:48     doi:10.1186/1471-2164-6-48 Published   1 April 2005 Abstract (provisional) read more

13. Gene conversion homogenizes the CMT1A paralogous repeats

By Gene conversion homogenizes the CMT1A paralogous repeats Matthew E Hurles McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK BMC Genomics 2001, 2:11     doi:10.1186/1471-2164-2-11 The electronic version of this article is the complete one and can be found online at: http://www.biomedcent... read more

14. Three microarray platforms: an analysis of their concordance in profiling gene expression

By Three microarray platforms: an analysis of their concordance in profiling gene expression David Petersen , G.v.r Chandramouli , Joel Geoghegan , Joanne Hilburn , Jonathon Paarlberg , Chang Hee Kim , David Munroe , Lisa Gangi , Jing Han , Raj Puri , Lou Staudt , John Weinstein , J. Carl Barrett , Jeffrey Green and Ernest S Kawasaki BMC Genomics 2005, 6:63  ... read more

15. A study of inter-lab and inter-platform agreement of DNA microarray data

By As gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degree of agreement we can expect from different labs and different platforms. To add... read more

16. Outliers involving the Poly(A) effect among highly-expressed genes in microarrays

By Outliers involving the Poly(A) effect among highly-expressed genes in microarrays Shujia J Pan1 , David R Rigney2 and John L Ivy3 1Department of Kinesiology and Health Education, Bellmont Hall, Room 222, University of Texas at Austin, Austin TX 78712 U.S.A 2Department of Research and Development, GENETWORKS Inc., P.O... read more

17. Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in

By Background: Regional expression biases (REBs) are genetic intervals where gene expression is coordinately changed. For example, if a region of the genome is amplified, often the majority of genes that map within the amplified region show increased expression when compared to genes located in cytogenetically normal regions. As such, REBs have the potential to act as surrogates for cytogenetic data... read more

18. i-Genome: A database to summarize oligonucleotide data in genomes

By i-Genome: A database to summarize oligonucleotide data in genomes Feng-Mao Lin1 , Hsien-Da Huang2 , Yu-Chung Chang3 and Jorng-Tzong Horng1, 4 1Department of Computer Science and Information Engineering National Central University, Chung-Li 320, Taiwan 2Department of Biological Science and Techn... read more

19. The Retinome – Defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium

By The Retinome – Defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium Heidi L Schulz1 , Thomas Goetz1, 2 , Juergen Kaschkoetoe1 and Bernhard HF Weber1 1Institute of Human Genetics, Biocenter, University of Wuerzburg, D-97074 Wuerzburg, Germany 2German C... read more

20. The over-representation of binary DNA tracts in seven sequenced chromosomes

By The over-representation of binary DNA tracts in seven sequenced chromosomes Gad Yagil Dept. of Molecular Cell Biology, The Weizmann Institute of Biology, Rehovot, Israel 76100 BMC Genomics 2004, 5:19     doi:10.1186/1471-2164-5-19 The electronic version of this article is the complete one and can be found online at: http:/... read more

21. A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes

By A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes Frédérique Pitel1 , Behnam Abasht2 , Mireille Morisson1 , Richard PMA Crooijmans3 , Florence Vignoles1 , Sophie Leroux1 , Katia Feve1 , Suzanne Bardes1 , Denis Milan1 , Sandrine ... read more

22. Low-pass sequencing for microbial comparative genomics

By Low-pass sequencing for microbial comparative genomics Young Ah Goo1 , Jared Roach1 , Gustavo Glusman1 , Nitin S Baliga1 , Kerry Deutsch1 , Min Pan1 , Sean Kennedy2 , Shiladitya DasSarma2 , Wailap Victor Ng3 and Leroy Hood1 1Institute for Systems Biology,... read more

23. (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length

By Background: Creation of human gene families was facilitated significantly by gene duplication and diversification. The (TG/CA)n repeats exhibit length variability, display genome-wide distribution, and are abundant in the human genome. Accumulation of evidences for their multiple functional roles including regulation of transcription and stimulation of recombination and splicing elect them as fun... read more

24. Investigating hookworm genomes by comparative analysis of two Ancylostomaspecies

By Investigating hookworm genomes by comparative analysis of two Ancylostomaspecies Makedonka Mitreva , James P McCarter , Prema Arasu , John Hawdon , John Martin , Mike Dante , Todd Wylie , Jian Xu , Jason E Stajich , Wadim Kapulkin , Sandra W Clifton , Robert H Waterston and Richard K Wilson BMC Genomics 2005, 6:58     doi:10.1186/1471-2164-... read more