Open Access Highly Accessed Research article

Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer

Wolfram Langer12*, Florian Sohler1, Gabriele Leder1, Georg Beckmann1, Henrik Seidel1, Jörn Gröne3, Michael Hummel4 and Anette Sommer1*

Author Affiliations

1 Bayer Schering Pharma AG, Global Drug Discovery (GDD) - Target Discovery, Müllerstrasse 178, 13342 Berlin, Germany

2 Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany

3 Dept. of General, Vascular and Thoracic Surgery, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany

4 Institute of Pathology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany

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BMC Genomics 2010, 11:676  doi:10.1186/1471-2164-11-676

Published: 30 November 2010

Additional files

Additional file 1:

Table S1: Tissue specimens. Clinical information for all paired tissue specimens.

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Additional file 2:

Data files S2: New probe set definition. ZIP-archive containing the new probe set definition provided as a probe group file (PGF), probe set and transcript cluster annotations in CSV format, and a meta probe set file defining the relationship between transcript cluster and probe sets. All file formats are in accordance with Affymetrix definitions.

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Additional file 3:

Table S3: Endpoint RT-PCR assays. Primer pairs for RT-PCR assays and amplicon lengths of the expected transcript variants.

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Additional file 4:

Table S4: Quantitative RT-PCR assays for detection with SYBR™. Primer pairs for transcript variant specific qRT-PCR assays together with the expected amplicon length.

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Additional file 5:

Text S5: Quality assurance of the NSCLC exon array data set. Quality assurance of the NSCLC exon array data set by principal component analysis and hierarchical clustering.

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Additional file 6:

Table S6: Analysis of the exon array NSCLC data set, primary result list.

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Additional file 7:

Table S7: Analysis of the exon array NSCLC data set, result sub-list A.

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Additional file 8:

Table S8: Analysis of the exon array NSCLC data set, result sub-list B.

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Additional file 9:

Table S9: Analysis of the exon array NSCLC data set, result sub-list C.

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Additional file 10:

Table S10: Analysis of the exon array NSCLC data set, final result list. The final result list is the union of sub-lists A, B, and C (additional file 7, 8, and 9, respectively).

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Additional file 11:

Table S11: Validation results of candidate genes.

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Additional file 12:

Text S12: Quantification of NCOR2 transcript variants in NSCLC.

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Additional file 13:

Figure S13: Expression of FOX1 in twelve different types of cancer and corresponding normal tissue as well as in 50 other healthy tissues. Geometric mean signal intensities of probe set 1553422_s_at (Affymetrix expression array HG-U133_Plus_2.0) which measures gene expression of A2BP1 (FOX1). The number of samples per group is shown (in total, 1015 samples). Error bars represent one standard deviation as calculated from the log-transformed intensities.

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Additional file 14:

Figure S14: Expression of FOX2 in twelve different types of cancer and corresponding normal tissue as well as in 50 other healthy tissues. Geometric mean signal intensities of probe set 212104_s_at (Affymetrix expression array HG-U133_Plus_2.0) which measures gene expression of RBM9 (FOX2). The number of samples per group is shown (in total, 1015 samples). Error bars represent one standard deviation as calculated from the log-transformed intensities.

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Additional file 15:

Table S15: Result list differential splicing in correlation to the NSCLC subtype.

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