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Open Access Methodology article

Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data

Tzu-Hsien Yang and Wei-Sheng Wu*

Author Affiliations

Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan

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BMC Systems Biology 2012, 6:102  doi:10.1186/1752-0509-6-102

Published: 16 August 2012

Additional files

Additional file 1:

Figure S1.Provides the detailed explanation of why we only reported the analyses results of 112 TFs.

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Additional file 2:

Table S1.Provides the numbers and the detailed gene lists of our refined (i.e., biologically interpretable) and the original TF knockout targets identified by Reimand et al. for the 112 TFs under study. Moreover, the identified path for each biologically interpretable TF knockout target can also be found in this table. The identified paths form experimentally testable hypotheses regarding the molecular mechanisms of how a TF may regulate its knockout targets.

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Additional file 3:

Table S2.Provides the detailed information about the functional enrichment test of the refined and the original datasets.

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Additional file 4:

Table S3.Provides the detailed information about the expression coherence test of the refined and the original datasets.

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Additional file 5:

Table S4.Provides the detailed information about the protein-protein interaction enrichment test of the refined and the original datasets.

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Additional file 6:

Table S5.Provides the detailed information about the 692 hypotheses (generated by our method) that have been experimentally validated in the literature [35].

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Additional file 7:

Table S6.Provides the detailed information about the tests of the functional enrichment, expression coherence, and the prevalence of protein-protein interactions of the signals and the noises.

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Additional file 8:

Table S7.Provides the detailed information about the tests of the functional enrichment, the expression coherence, and the prevalence of protein-protein interactions of our result and Hu et al.’s result.

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Additional file 9:

Table S8.Provides the detailed information about the tests of the functional enrichment, the expression coherence, and the prevalence of protein-protein interactions of our result and Jiang et al.’s result.

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Additional file 10:

Table S9.Provides the detailed information of those TF knockout targets that were predicted (by our method) as false positives but have independent TF regulation evidence in the literature [35] other than Reimand et al.’s study.

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