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This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology

Open Access Proceedings

Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs

Zhen Yang1, Dong Dong2, Zhaolei Zhang3, M James C Crabbe4, Li Wang5 and Yang Zhong16*

Author Affiliations

1 School of Life Sciences, Fudan University, Shanghai, 200433, China

2 Institute of Molecular Ecology and Evolution, iAIR, East China Normal University, Shanghai, 200062, China

3 Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 1A8, Canada

4 Institute of Biomedical and Environmental Science & Technology, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, Luton LU1 3JU, UK

5 Shanghai Center for Bioinformation Technology, Shanghai 200235, China

6 Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa, 850000, China

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BMC Genomics 2012, 13(Suppl 7):S14  doi:10.1186/1471-2164-13-S7-S14

Published: 13 December 2012

Additional files

Additional file 1:

Figure S1: GO term distribution of SE genes and FL genes (molecular function). The enriched GO terms were colored red for SE genes and green FL genes. A distinct GO term distribution of molecular function for the two sets of genes was observed. SE genes were mainly enriched in RNA binding, protein binding, NADH dehydrogenase activity and constituent of ribosome etc, whereas FL genes were mainly enriched in the receptor binding, cytokine activity, growth factor receptor binding, peptide hormone binding and dopamine binding etc.

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Additional file 2:

Figure S2: GO term distribution of SE genes and FL genes (biological process). The enriched GO terms were colored red for SE genes and green FL genes. A distinct GO term distribution of biological process for the two sets of genes was observed. SE genes were mainly enriched in translation, gene expression, macromolecule metabolic, biosynthetic etc, whereas FL genes were mainly enriched in signaling pathways, defense response, regulation of immune system process and mediated by a chemical signal etc.

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Additional file 3:

Figure S3: miRNA targets are not enriched in control group. This figure shows the number of miRNA targets and non-miRNA targets among control group predicted (A) by PicTar, (B) by TargetScan, (C) by both PicTar and TargetScan (intersections), (D) by PITA, (E) by miRanda and (F) by experimentally validated miRNA targets when 5% of the genes were randomly designated as SE genes and FL genes respectively.

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Additional file 4:

Figure S4: miRNA targets are enriched in SE genes (top 10%). This figure shows the number of miRNA targets and non-miRNA targets among SE genes and FL genes predicted (A) by PicTar, (B) by TargetScan, (C) by both PicTar and TargetScan (intersections) and (D) by PITA, (E) by miRanda and (F) by experimentally validated miRNA targets when top and bottom 10% of the gene designated as SE genes and FL genes respectively.

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Additional file 5:

Figure S5: miRNA targets are enriched in SE genes derived only from normal tissues. This figure shows the number of miRNA targets and non-miRNA targets among SE genes and FL genes predicted (A) by PicTar, (B) by TargetScan, (C) by both PicTar and TargetScan (intersections) and (D) by PITA, (E) by miRanda and (F) by experimentally validated miRNA targets when top and bottom 5% of the genes derived only from normal tissues designated as SE genes and FL genes respectively.

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Additional file 6:

Figure S6: correlation between gene expression fluctuation and number of regulatory miRNAs. No obvious correlation between expression fluctuation and number of regulatory miRNAs was observed. (A) average FL score and number of regulatory miRNAs from PicTar results, Pearson correlation coefficient, r = 0.16, p value: 0. 24. (B) average FL score and number of regulatory miRNAs from TargetScan results, Pearson correlation coefficient, r = 0.10, p value: 0.49. (C) average FL score and number of regulatory miRNAs from PITA results, Pearson correlation coefficient, r = 0.124, p value: 0.59.

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Additional file 7:

Table S1: retrieved SE-miRNAs and FL-miRNAs. This table lists the miRNA ID and number of targets in both SE genes and FL genes predicted by PicTar, TargetScan and PITA. The p value were inferred from Fisher exact test.

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Additional file 8:

Table S2: microarray data sets used for this analysis. This table lists the GEO ID, brief description, number of samples and sample type of 149 microarray data sets used for this analysis, which includes 69 data sets from normal tissue, 59 data sets from cancer tissue or cell line and 21 data sets from other disease.

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Additional file 9:

Table S2: retrieved SE genes and FL genes and their FL Scores. This table lists the SE genes and FL genes obtained from 149 microarray data sets and from 69 microarray data sets based on normal tissues respectively.

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