References

Publications

Please cite this publication when you use Anduril.

• Kristian Ovaska, Marko Laakso et al. Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Medicine 2010, 2:65.\ Supplementary document, Genome Medicine commentary, TCGA commentary, original case study results, updated glioblastoma results.

• Alejandra Cervera, Ville Rantanen et al. Anduril 2: upgraded large-scale data integration framework, Bioinformatics, btz133, 2019

Learning material

• Marko Laakso, Kristian Ovaska, Sampsa Hautaniemi. Component-based workflow framework for data analysis.BREW2009. Workshop handout, slides
• Kristian Ovaska. Component-based workflow framework for gene expression microarray analysis. MSc Thesis, 2008. This provides a detailed description of Anduril architecture. Not fully up-to-date: refer to User Guide and Maintenance Guide for latest information.
• Kristian Ovaska, Marko Laakso, Sampsa Hautaniemi. Component-based framework for bioinformatics analysis. Poster at High Throughput Biology 2008.

Related publications

• Karinen S, Saarinen S, Lehtonen R, Rastas P, Vahteristo P, Aaltonen L A, Hautaniemi S. Rule-based induction method for haploptype comparison and identification of candidate disease loci. Genome Medicine, 2012, 4:2.
• Louhimo R, Lepikhova T, Monni O, Hautaniemi S. Comparative analysis of algorithms for integration of copy number and expression data.Nature Methods, 2012 Feb; 9(4):351-5.
• Anna-Maria Lahesmaa-Korpinen, Sari E. Jalkanen et al. FlowAnd: Comprehensive Computational Framework for Flow Cytometry Data Analysis. Journal of Proteomics & Bioinformatics, 2011, 4(197): 245-249, website
• Biswajyoti Sahu, Marko Laakso et al. Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signaling and prostate cancer. EMBO Journal, 2011, 30(19): 3962-3976
• Päivi Pihlajamaa, FP Zhang, et al. The phytoestrogen genistein is a tissue-specific androgen receptor modulator. Endocrinology, 2011
• Hans Blom, Daniel Rönnlund et al. Nearest neighbor analysis of dopamine D1 receptors and Na+-K+-ATPases in dendritic spines dissected by STED microscopy. Microscopy Research and Technique, 2011
• Pauliina I. Ehlers, Anne S. Kivimäki et al. High blood pressure-lowering and vasoprotective effects of milk products in experimental hypertension. British Journal of Nutrition, 2011, [in print]
• Pilvi Maliniemi and Emilia Carlsson et al. NAV3 copy number changes and target genes in basal and squamous cell cancers. Experimental Dermatology, 2011
• Ping Chen, Tatiana Lepikhova et al. Comprehensive Exon Array Data Processing Method for Quantitative Analysis of Alternative Spliced Variants. Nucleic Acids Research, 2011, 39(18): e123, website
• D.P. Mathiasen, C. Egebjerg et al. Identification of a c-Jun N-terminal kinase 2 dependent signal amplification cascade that regulates c-Myc levels in Ras transformation. Oncogene, 2011
• Sirkku Karinen, Tuomas Heikkinen et al. Data Integration Workflow for Search of Disease Driving Genes and Genetic Variants. PLoS ONE, 2011, 6(4), website
• Mira Heinonen, Annabrita Hemmes et al. Role of RNA binding protein HuR in ductal carcinoma in situ of the breast. The Journal of Pathology, 2011, 224(6): 529-539
• Riku Louhimo, Sampsa Hautaniemi, CNAmet: an R package for integrating copy number, methylation and expression data. Bioinformatics, 2011, 27(6): 887-888, website

• Marko Laakso, Sampsa Hautaniemi, Integrative Platform to Translate Gene Sets to Networks. Bioinformatics, 2010, 26(14):1802-1803, website

• Full list of publications.

Case study

Anduril scripts used in the case study (see Publications) for the glioblastoma multiforme dataset (source: Cancer Genome Atlas) are listed below.

Results can be browsed at Case Study Website (the search function requires JavaScript).

• Main analysis
• Settings
• Array CGH analysis
• Array CGH analysis function collection 1
• Array CGH analysis function collection 2
• Array CGH analysis function collection 3
• Array CGH integration to expression
• Gene expression analysis
• Transcript expression analysis based on median exon expression
• Methylation status analysis
• MicroRNA expression analysis
• Genotype specific survival analysis
• Transcript expression analysis
• Summary website generator

TCGA analysis results

We have analyzed four cancer data sets from the Cancer Genome Atlas. The following cancer result websites are currently available and more will be added.

• Breast invasive carcinoma (BRCA)
• Colorectal adenocarcinoma (COAD)
• Glioblastoma multiforme (GBM)
• Temozolomide treated subpopulation of GBM and
• Ovarian serous cystadenocarcinoma (OV).

With the exception of methylation data, we have used raw data (TCGA level 1, e.g., CEL-files) for all the different analysis platforms.