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Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

Sami Kilpinen12, Reija Autio3, Kalle Ojala12, Kristiina Iljin1, Elmar Bucher1, Henri Sara1, Tommi Pisto1, Matti Saarela3, Rolf I Skotheim14, Mari Björkman1, John-Patrick Mpindi1, Saija Haapa-Paananen1, Paula Vainio1, Henrik Edgren12, Maija Wolf12, Jaakko Astola3, Matthias Nees1, Sampsa Hautaniemi5 and Olli Kallioniemi12*

Author Affiliations

1 Medical Biotechnology, VTT Technical Research Centre and University of Turku, Itäinen pitkäkatu 4C, Turku, Finland

2 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, Helsinki, Finland

3 Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 1, Tampere, Finland

4 Department of Cancer Prevention, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, NO-0310, Norway

5 Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Haartmaninkatu 8, Finland

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Genome Biology 2008, 9:R139  doi:10.1186/gb-2008-9-9-r139

Published: 19 September 2008

Additional files

Additional data file 1:

Distribution of preprocessed datapoints across the entire database (solid line) and normal distribution (N(8, 4)) estimated from it (dashed line).

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Additional data file 2:

(a) KLK3 (PSA) is a known prostate specific gene. This specificity is perfectly shown in its expression profile. (b) GFAP, a gene coding for glial fibrillary acidic protein, is known to be expressed in central nervous system. Its expression profile perfectly confirms this prior knowledge.

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Additional data file 3:

Sources for all the raw expression data files used in this study.

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Additional data file 4:

Various healthy tissues, cancers and non-cancer diseases represented by the samples in the database and the amounts of samples in each of these categories.

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Additional data file 5:

Rand indices for the different normalizations, and the distribution of array generations and tissues into clusters with Q and QAGC normalized data.

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Additional data file 6:

(a) Insulin (INS) has pancreas specific expression, as one expects it to have. (b) LDHC is a known testis-specific gene and it is expressed above background only in healthy testis.

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Additional data file 7:

Most interestingly this ETS-factor family member appears to have slightly elevated expression in prostate cancer when compared to healthy prostate.

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Additional data file 8:

Expression of the C1orf56 gene, also known as AF1Q or MLLT11, shows extreme expression in several cancers, especially in neuroblastoma.

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