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This article is part of the supplement: Selected articles from the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2011

Open Access Research

Assessing the gain of biological data integration in gene networks inference

Fábio FR Vicente12*, Fabrício M Lopes1*, Ronaldo F Hashimoto2 and Roberto M Cesar23

Author Affiliations

1 Federal University of Technology - Paraná, Brazil

2 Institute of Mathematics and Statistics, University of São Paulo, Brazil

3 Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazil

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BMC Genomics 2012, 13(Suppl 6):S7  doi:10.1186/1471-2164-13-S6-S7

Published: 26 October 2012

Additional files

Additional file 1:

USP QC dataset. USP quality control dataset (leave out oligos with less than 25 samples)

Format: TXT Size: 2.8MB Download file

Open Data

Additional file 2:

USP QC dataset samples. File containing the normalized and quantized signal into three expression levels: -1,0 and 1 (down, null and up regulated). The value 3 means not observed.

Format: TXT Size: 612KB Download file

Open Data

Additional file 3:

Names of oligos. Name of each oligo in USP QC dataset samples.

Format: TXT Size: 105KB Download file

Open Data

Additional file 4:

PIP network. Protein-Protein Network obtained from LaCount et al, 2005.

Format: TXT Size: 37KB Download file

Open Data

Additional file 5:

PIP samples. Samples of the corresponding genes in PIP network.

Format: TXT Size: 102KB Download file

Open Data

Additional file 6:

Rosetta Stone network. Rosetta Stone proteins obtained from Date et al, 2006.

Format: TXT Size: 41KB Download file

Open Data

Additional file 7:

Rosetta Stone samples. Samples of the corresponding genes in Rosetta Stone network.

Format: TXT Size: 73KB Download file

Open Data

Additional file 8:

KEGG network. KEGG gold standard dataset obtained from Bozdech et al, 2003.

Format: TXT Size: 167KB Download file

Open Data

Additional file 9:

KEGG samples. Samples of the corresponding genes in KEGG network.

Format: TXT Size: 41KB Download file

Open Data

Additional file 10:

KEGG and GO network. KEGG and GO combined gold standard obtained from Date et al, 2006.

Format: TXT Size: 139KB Download file

Open Data

Additional file 11:

KEGG and GO samples. Samples of the corresponding genes in KEGG and GO network.

Format: TXT Size: 36KB Download file

Open Data

Additional file 12:

Intersection Gold Standard Datasets 1 (IGS1). Gold Standard network assembled from the intersection between KEGG and KEGG+GO.

Format: TXT Size: 1KB Download file

Open Data

Additional file 13:

IGS1 samples. Samples of the corresponding genes in IGS1.

Format: TXT Size: 3KB Download file

Open Data

Additional file 14:

Intersection Gold Standard Datasets 2 (IGS2). Gold Standard network assembled from the intersection between Rosetta Stone and KEGG.

Format: TXT Size: 1KB Download file

Open Data

Additional file 15:

Intersection Gold Standard Datasets 2 - samples. Samples of the corresponding genes in IGS2.

Format: TXT Size: 3KB Download file

Open Data

Additional file 16:

Intersection Gold Standard Datasets 3 (IGS3). Gold Standard network assembled from the intersection between Rosetta Stone and KEGG+GO.

Format: TXT Size: 1KB Download file

Open Data

Additional file 17:

Intersection Gold Standard Datasets 3 - samples. Samples of the corresponding genes in IGS3.

Format: TXT Size: 4KB Download file

Open Data

Additional file 18:

Intersection Gold Standard Datasets 4 (IGS4). Gold Standard assembled from the intersection between KEGG and KEGG+GO.

Format: TXT Size: 118KB Download file

Open Data

Additional file 19:

Intersection Gold Standard Datasets 5 - samples. Samples of the corresponding genes in IGS4.

Format: TXT Size: 32KB Download file

Open Data