Storage Analysis Both

Publications and schema

Applications: Cancer Yeast Arabidopsis Antirrhinum Drosophila Trypanosoma Neurospora Technique

Storage

• Simple scheme [jpg] [pdf]
  

• Detailed scheme [jpg] [pdf]
  

• Fellenberg K, Hauser, NC, Brors B, Hoheisel JD, Vingron M. Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis.
  Bioinformatics (2002) 18: 423-433 [abstract] [pdf] [supplemental material / data]

• Technical report: M-CHiPS storage concept. [html] [pdf]
  

• About ArrayExpress:
  Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel JD, Fellenberg K.
  Microarray data representation, annotation and storage.
  in: Advances in Biochemical Engineering/Biotechnology. 2002. Vol. 77 ("Chip Technology"): 113-139 [abstract] [pdf]

  
  

• Moghaddas Gholami A, Fellenberg K.
  Cross-species common regultory network inference without requirement for prior gene affiliation.
  Bioinformatics. 2010. (doi:10.1093/bioinformatics/btq096) [abstract] [pdf] [supplemental] [source code]

• Fellenberg K, Busold CH, Witt O, Bauer A, Beckmann B, Hauser NC, Frohme M, Winter S, Dippon J, Hoheisel JD.
  Systematic interpretation of microarray data using experiment annotations.
  BMC Genomics. 2006. 7:319 [abstract] [free full text] [pdf] [supplemental material / data].

• Busold CH, Winter S, Hauser N, Bauer A, Dippon J, Hoheisel J, Fellenberg K.
  Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data.
  Bioinformatics. 2005. 21(10): 2424-2429 [abstract] [pdf].

• Fellenberg K, Vingron M, Hauser NC, Hoheisel JD. Correspondence analysis with microarray data.
  in: Perspectives in Gene Expression (Appasani K, ed.), Eaton Publishing, Westborough, 307-343.

• Fellenberg K, Hauser, NC, Brors B, Neutzner A, Hoheisel JD, Vingron M. Correspondence anaylsis applied to microarray data.
  Proc Natl Acad Sci USA (2001) 98: 10781-10786 [abstract] [pdf] [data]
  

• Beißbarth T, Fellenberg K, Brors B, Arribas-Prat R, Boer JM, Hauser NC, Scheideler M, Hoheisel JD, Schuetz G, Poustka A, Vingron M.
  Processing and quality control of DNA array hybridization data.
  Bioinformatics. 2000. 16(11): 1014-1022 [abstract] [pdf].

• Poster #1

  
  

• Poster #2
  

• Fellenberg K. Storage and analysis of microarray data (2002) [abstract (scroll down page for english version)] [pdf (1.3 MB = 98 pages)]

• Fellenberg K. Correspondence Analysis and Data Warehousing with Microarray Data (postgrad. bioinformatics lecture at the "Akademie f. Weiterbildung" ) [lecture notes (1.4 MB = 63 pages) as screen-pdf] [as print-pdf]
  [practical]
  [`color-patch' incl. improved slides explaining the projection]

Applications

human cancer

• Microcystic tubulopapillary carcinoma of the pancreas: a new tumor entity?
  Esposito I, Bauer A, Hoheisel JD, Kleeff J, Friess H, Bergmann F, Rieker RJ, Otto HF, Kloppel G, Penzel R.
  Virchows Arch. 2004 444(5):447-53. [pdf]

• Use of complex DNA and antibody microarrays as tools in functional analyses.
  Bauer A, Beckmann B, Busold C, Brandt O, Kusnezow W, Pullat J, Aign V, Fellenberg K, Fleischer R, Jacob A, Frohme M, Hoheisel JD.
  Comp Funct Genom. 2003 4: 520-524.

• Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae.
  Lagorce A, Hauser NC, Labourdette D, Rodriguez C, Martin-Yken H, Arroyo J, Hoheisel JD, Francois, JM.
  J Biol Chem. 2003 278: 20345-20357.

• Glucose triggers different global responses in yeast, depending on the strenght of the signal, and transiently stablilizes ribosomal protein mRNAs.
  Yin Z, Wilson S, Hauser NC, Tournu H, Hoheisel JD, Brown AJP.
  Mol Microbiol. 2003. 48: 713-742.

• Genome-wide expression screens indicate a global role for protein kinase CK2 in chromatin remodeling.
  Barz T, Ackermann K, Dubois G, Eils R, Pyerin W.
  Journal of Cell Science. 2003. 116: 20345-20357. [abstract] [pdf].

• How to Discover Pathogenic Mechanisms - New Evaluation Tools Towards Drug Discovery.
  Hauser NC, Fellenberg K, Rupp S.
  Screening. 2002. 3: 28-31.

• Genome-wide analysis of yeast transcription upon calcium shortage.
  Lombardía LJ, Becerra M, Rodríguez-Belmonte E, Hauser NC, Cerdán, M.E.
  Cell Calcium. 2002. 32(2): 83-91. [abstract]

• The yeast transcriptome in aerobic and hypoxic conditions. Effects of HAP1 ROX1 ROX3 and SRB10 deletions.
  Becerra M, Lombardía-Ferreira LJ, Hauser NJ, Hoheisel JD, Tizon B, Cerdán, ME.
  Mol Microbiol. 2002. 43: 545-555. [abstract]

• Whole genome analysis of a wine yeast strain.
  Hauser NC, Fellenberg K, Gil R, Bastuck S, Hoheisel JD, Perez-Ortin JE.
  Comp Funct Genom. 2001. 2(4): 69-79 [abstract] [pdf].

• Monitoring the switch from housekeeping to pathogen defence metabolism in Arabidopsis thaliana using cDNA arrays.
  Scheideler M, Schlaich NL, Fellenberg K, Beißbarth T, Hauser NC, Vingron M, Slusarenko AJ, Hoheisel JD.
  J Biol Chem. 2002. 277(12): 10555-10561 [abstract] [pdf] [data].

• Characterization of Antirrhinum petal development and identification of target genes of the class B MADS-box Gene DEFICIENS.
  Bey M, Stüber K, Fellenberg K, Schwarz-Sommer Z, Sommer H, Saedler H, Zachgo S.
  Plant Cell. 2004. 16(12): 3197-3215 [abstract] [pdf] [data].
  

• An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.
  Hild M, Beckmann B, Haas SA, Koch B, Solovjev V, Busold C, Fellenberg K, Boutros M, Vingron M, Sauer F, Hoheisel JD, Paro R.
  Genome Biol. 2003. 5: R3 [abstract] [pdf]

• Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray.
  Diehl s, Diehl F, El-Sayed NM, Clayton C, Hoheisel JD.
  Mol Biochem Parasit. 2002. 123: 115-123.

• Analysis of nutrient-dependent transcript variations in Neurospora crassa.
  Aign V, Hoheisel JD.
  Fungal Genet Biol. 2003. 40(3): 225-33.

• Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform.
  Hauser NC, Martinez R, Jacob A, Rupp S, Hoheisel JD, Matysiak S.
  Nucleic Acids Res. 2006. 0: p. gkl671v1-11, doi:10.1093/nar/gkl671 [abstract] [pdf]