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Open Access Highly Accessed Research article

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency

Hsiang-Yuan Yeh1*, Shih-Wu Cheng2, Yu-Chun Lin2, Cheng-Yu Yeh2, Shih-Fang Lin2 and Von-Wun Soo13

Author Affiliations

1 Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan

2 Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan

3 Department of Computer Science and Information Engineering, National University of Kaohsiung, Kaohsiung 811, Taiwan

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BMC Medical Genomics 2009, 2:70  doi:10.1186/1755-8794-2-70

Published: 21 December 2009

Additional files

Additional file 1:

KNN imputed ratio. Table shows the maximal values can be imputed by KNN algorithm and the number of values is exactly imputed in each microarry data. The imputed ratio is the proportion of the real imputed genes to the maximal genes. The less the imputed ratio is, the more imputed data similar to real experiment data. The result shows that the imputed ratios of the microarray data are all less than 50%, it seems to be reasonable to assume the imputed dataset is good enough to analyze the gene regulatory network.

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Additional file 2:

All pair shortest path in cancer and normal network. We use all pairs shortest path Dijkstra's algorithm to detect the length of any one of gene link to other genes in cancer and normal network.

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Additional file 3:

Transcription regulator genes in cancer and normal network. It shows the transcription regulator genes in cancer and normal network.

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Additional file 4:

functional annotations and their p-values of dependent genes affected by transcription regulatory genes in cancer network. We filtered the functional annotations results at least 3 members in each functional category and P-value < 0.05 with Bonferroni correction and FDR<0.25 using DAVID online toolkit.

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Additional file 5:

the enrichment canonical pathways and their p-values in cancer network. We filtered the indeed functional enrichment canonical pathways of the overlap of the gene set in our networks with at least 3 members in each functional category and P value < 0.05 using GSEA online toolkit.

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Additional file 6:

The genes are belong to the enrichment canonical pathways in cancer network. The genes are belong to the functional enrichment pathways in cancer network.

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Additional file 7:

the p-value of pair of genes involved in the figure 12 and 13. It shows the p-value of pair of genes involved in the figure 12 and 13. The column "Co-expressed genes: denotes dependent genes (Dgs) of transcription regulator genes (Tgs). The column "TF" means transcription regulator genes (Tgs). The column "d-separated genes" denotes the minimum d-separated genes between Co-expressed genes and TF. The column "P-value" means the statistical p-value calculated by conditional independency testing in cancer and normal network.

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Additional file 8:

the conditional impendence testing results between without/with Bonferroni correction. It shows the conditional impendence testing results of two genes between without/with Bonferroni correction. The column "Co-expressed genes: denotes dependent genes (Dgs) of transcription regulator genes (Tgs). The column "TF" means transcription regulator genes (Tgs). The column "d-separated genes" denotes the minimum d-separated genes between Co-expressed genes and TF. The column "P-value" means the statistical p-value calculated by conditional independency testing. The column "with Bonferroni correction" and "without Bonferroni correction" show the multiple testing to verify the result dependent on d-separated genes and only with a significant value 0.05 to verify the results.

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Additional file 9:

Feedback loop network motifs in cancer and normal network. It shows the genes and their relations involved in the feedback loop network motifs in cancer and normal network. Tg denotes transcription regulatory gene and the sign (+, -) mean the activation or inhibition of pair of genes.

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Additional file 10:

Transcription regulator genes in DOR network motifs in cancer and normal networks. It shows only the transcription regulator genes involved in the dense overlapping regulons network motifs in cancer and normal network.

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Additional file 11:

Transcription regulator genes in FFL network motifs in cancer and normal networks. It shows only the transcription regulator genes in the feed forward loop network motifs in cancer and normal network. Tg denotes the first transcription regulatory gene and co-Tg means the second transcription regulatory gene which affects the dependent genes with the first Tg.

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Additional file 12:

Evaluated result of Transcription regulator genes with respect to prostate cancer. There are three labels which we used to evaluate each transcription regulator gene (Tg) implicated in cancer network: Match, Possible, and Not-related. "Match" means if Tg is published in the literature and reported an important role to affect the cancer. "Possible" means one of "Other genes possibly implicated in cancer" listed in Atlas of Genetics and Cytogenetics in Oncology and Haematology. If no information about the relationship of Tg and a cancer is labeled as "Not-related".

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Additional file 13:

Verifications based on literature reports of each Transcription regulator genes in cancer network. It shows the Verifications based on literature reports of each transcription regulator genes in cancer network and label the strength of those genes belong to the prostate cancer.

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