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Open Access Highly Accessed Research article

Human transcriptional interactome of chromatin contribute to gene co-expression

Xiao Dong12, Chao Li123, Yunqin Chen4, Guohui Ding15* and Yixue Li15*

Author Affiliations

1 Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China

2 Graduate School of Chinese Academy of Sciences, Beijing, PR China

3 School of Life Science, University of Science and Technology of China, Hefei, PR China

4 School of Life Sciences and Technology, Tongji University, Shanghai, PR China

5 Shanghai Center for Bioinformation Technology, Shanghai, PR China

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BMC Genomics 2010, 11:704  doi:10.1186/1471-2164-11-704

Published: 14 December 2010

Additional files

Additional file 1:

Transcription control similarity (TCS) has a strong influence on gene co-expression as expected. For all gene pairs within a chromatin, transcription control similarity, as expected has a strong influence on the ranks of gene co-expression rates. Error bars represent standard error.

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Additional file 2:

Neighboring genes are more likely to be co-expressed. As being pointed out, neighboring genes are more likely to be co-expressed. Error bars represent standard error.

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Additional file 3:

For all gene pairs, association between TCS and Hi-C interactions exist. For all gene pairs, we plotted their Hi-C interactions against their TCS. And those with higher interactions, their TCS are more similar. Error bars represent standard error.

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Additional file 4:

Normalized distance has a significant effect on Hi-C interactions as expected. As expected, for all gene pairs the HI-C interactions of neighboring genes are significantly stronger than those distant ones. Error bars represent standard error.

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Additional file 5:

Correlation between Hi-C interaction and gene co-expression for gene pairs, which TCS are zero. For the pairs that TCS are zero, Hi-C interactions are plotted against the ranks of gene co-expression rates. Genes with more Hi-C interactions between them, would more likely to co-express. Error bars represent standard error. For all figure panels A, B, C & D, p values lower than 0.0125 are significant, under Bonferroni corrections.

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Additional file 6:

Correlation between Hi-C interaction and gene co-expression for gene pairs, which TCS are not zero. For the pairs that TCS are not zero, Hi-C interactions are plotted against the ranks of gene co-expression rates. Genes with more Hi-C interactions between them, would more likely to co-express. Error bars represent standard error. For all figure panels A, B, C & D, p values lower than 0.0125 are significant, under Bonferroni corrections.

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Additional file 7:

Co-expressed gene pairs have more Hi-C interactions than all pairs. T tests are used to test the difference between Hi-C interactions of co-expressed gene pairs and all pairs. In co-expressed gene pairs, the interactions are significantly higher. P values lower than 0.0125 are significant, under Bonferroni corrections.

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Additional file 8:

Correlations between co-expression and Hi-C interaction in co-expressed gene pairs. For co-expressed gene pairs (mutual ranks less than or equal to 50), we could also observed the correlation between Hi-C interaction and their mutual ranks of co-expression. For all figure panels A, B, C & D, p values lower than 0.0125 are significant, under Bonferroni corrections.

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Additional file 9:

Gene's GO similarities are related with their co-expression We plotted GO similarities between genes against their ranks of co-expression rates. Error bars represent standard error.

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